Did you uninstall first? If not, try dragging the FEniCS icon from Applications to the trash. Then reinstall using the new package. Also run instant-clean before running your program.
Johannes On Jan 21, 2015 4:24 PM, "Adrian Butscher" <[email protected]> wrote: > Hi, > > Similar problem, unfortunately. Output from the python interpreter and > from the logfile appended below. Thanks for looking into this. > > Adrian > > --- > > >>> import dolfin > > >>> f = dolfin.Expression('0') > > Calling DOLFIN just-in-time (JIT) compiler, this may take some time. > > In instant.recompile: The module did not compile with command 'make > VERBOSE=1', see > '/Users/butscher/.instant/error/dolfin_compile_code_b757fe2d4b67080e62c39305d8769e84590cb779/compile.log' > > Traceback (most recent call last): > > File "<stdin>", line 1, in <module> > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/functions/expression.py", > line 602, in __new__ > > mpi_comm=mpi_comm) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", > line 217, in compile_expressions > > mpi_comm=mpi_comm) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", > line 145, in compile_expression_code > > mpi_comm=mpi_comm) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", > line 64, in mpi_jit > > return local_jit(*args, **kwargs) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", > line 458, in compile_extension_module > > **instant_kwargs) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/build.py", > line 563, in build_module > > recompile(modulename, module_path, new_compilation_checksum, > build_system) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/build.py", > line 165, in recompile > > instant_error(msg % (cmd, compile_log_filename_dest)) > > File > "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/output.py", > line 85, in instant_error > > raise RuntimeError(text) > > RuntimeError: In instant.recompile: The module did not compile with > command 'make VERBOSE=1', see > '/Users/butscher/.instant/error/dolfin_compile_code_b757fe2d4b67080e62c39305d8769e84590cb779/compile.log' > > --- > > -- The C compiler identification is Clang 6.0.0 > -- The CXX compiler identification is Clang 6.0.0 > -- Check for working C compiler: /usr/bin/gcc > -- Check for working C compiler: /usr/bin/gcc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Check for working CXX compiler: /usr/bin/g++ > -- Check for working CXX compiler: /usr/bin/g++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- Found SWIG: /Applications/FEniCS.app/Contents/Resources/bin/swig (found > version "2.0.8") > -- Configuring done > -- Generating done > CMake Warning: > Manually-specified variables were not used by the project: > > DEBUG > > > -- Build files have been written to: > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /Applications/FEniCS.app/Contents/Resources/bin/cmake > -H/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > -B/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > --check-build-system CMakeFiles/Makefile.cmake 0 > /Applications/FEniCS.app/Contents/Resources/bin/cmake -E > cmake_progress_start > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/progress.marks > /Applications/Xcode.app/Contents/Developer/usr/bin/make -f > CMakeFiles/Makefile2 all > /Applications/Xcode.app/Contents/Developer/usr/bin/make -f > CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/build.make > CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/depend > /Applications/FEniCS.app/Contents/Resources/bin/cmake -E > cmake_progress_report > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles > 1 > [ 50%] Swig source > /Applications/FEniCS.app/Contents/Resources/bin/cmake -E make_directory > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /Applications/FEniCS.app/Contents/Resources/bin/swig -python -module > dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 -shadow > -modern -modernargs -fastdispatch -fvirtual -nosafecstrings -noproxydel > -fastproxy -fastinit -fastunpack -fastquery -nobuildnone > -DDOLFIN_VERSION="1.5.0" -DBOOST_UBLAS_NDEBUG -DDOLFIN_SIZE_T=8 > -DDOLFIN_LA_INDEX_SIZE=4 -DHAS_HDF5 -DHAS_TRILINOS -DHAS_SLEPC -DHAS_PETSC > -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_ZLIB -DHAS_MPI -DHAS_VTK > -DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MINOR=6 -DNUMPY_VERSION_MICRO=2 > -c++ -fcompact -O -I. -small -outdir > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > -c++ -I/Applications/FEniCS.app/Contents/Resources/include > -I/usr/include/libxml2 > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources/include/suitesparse > -I/Applications/FEniCS.app/Contents/Resources/include/suitesparse > -I/Applications/FEniCS.app/Contents/Resources/include -I/usr/include > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources/include/eigen3 > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources/lib/cmake/Trilinos/../../../include/trilinos > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources/include/trilinos > -I/Applications/FEniCS.app/Contents/Resources/include/suitesparse > -I/Applications/FEniCS.app/Contents/Resources/include > -I/Applications/FEniCS.app/Contents/Resources/include/vtk-5.10 > -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/. > -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include > -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > -o > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i > /Applications/FEniCS.app/Contents/Resources/include/dolfin/la/LinearAlgebraObject.h:36: > Warning 520: Derived class 'LinearAlgebraObject' of 'dolfin::Variable' is > not similarly marked as a smart pointer. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:63: > Warning 402: Base class 'Hierarchical< Function >' is incomplete. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/swig/function/pre.i:219: > Warning 402: Only forward declaration 'Hierarchical< Function >' was found. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:64: > Warning 520: Derived class 'Function' of 'dolfin::GenericFunction' is not > similarly marked as a smart pointer. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:64: > Warning 520: Derived class 'Function' of 'ufc::function' is not similarly > marked as a smart pointer. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:64: > Warning 520: Derived class 'Function' of 'dolfin::Variable' is not > similarly marked as a smart pointer. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/FunctionSpace.h:53: > Warning 402: Base class 'Hierarchical< FunctionSpace >' is incomplete. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/swig/function/pre.i:218: > Warning 402: Only forward declaration 'Hierarchical< FunctionSpace >' was > found. > /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/FunctionSpace.h:54: > Warning 520: Derived class 'FunctionSpace' of 'dolfin::Variable' is not > similarly marked as a smart pointer. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:170: > Warning 315: Nothing known about 'std::cos'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:171: > Warning 315: Nothing known about 'std::sin'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:172: > Warning 315: Nothing known about 'std::tan'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:173: > Warning 315: Nothing known about 'std::acos'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:174: > Warning 315: Nothing known about 'std::asin'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:175: > Warning 315: Nothing known about 'std::atan'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:176: > Warning 315: Nothing known about 'std::atan2'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:177: > Warning 315: Nothing known about 'std::cosh'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:178: > Warning 315: Nothing known about 'std::sinh'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:179: > Warning 315: Nothing known about 'std::tanh'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:180: > Warning 315: Nothing known about 'std::exp'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:181: > Warning 315: Nothing known about 'std::frexp'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:182: > Warning 315: Nothing known about 'std::ldexp'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:183: > Warning 315: Nothing known about 'std::log'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:184: > Warning 315: Nothing known about 'std::log10'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:185: > Warning 315: Nothing known about 'std::modf'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:186: > Warning 315: Nothing known about 'std::pow'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:187: > Warning 315: Nothing known about 'std::sqrt'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:188: > Warning 315: Nothing known about 'std::ceil'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:189: > Warning 315: Nothing known about 'std::fabs'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:190: > Warning 315: Nothing known about 'std::floor'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:191: > Warning 315: Nothing known about 'std::fmod'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:192: > Warning 315: Nothing known about 'std::max'. > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:193: > Warning 315: Nothing known about 'std::min'. > cd > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > && /Applications/FEniCS.app/Contents/Resources/bin/cmake -E cmake_depends > "Unix Makefiles" > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/DependInfo.cmake > --color= > Dependee > "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/DependInfo.cmake" > is newer than depender > "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/depend.internal". > Dependee > "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/CMakeDirectoryInformation.cmake" > is newer than depender > "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/depend.internal". > Scanning dependencies of target > _dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > /Applications/Xcode.app/Contents/Developer/usr/bin/make -f > CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/build.make > CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/build > /Applications/FEniCS.app/Contents/Resources/bin/cmake -E > cmake_progress_report > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles > 2 > [100%] Building CXX object > CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx.o > /usr/bin/g++ -DBOOST_UBLAS_NDEBUG -DDOLFIN_LA_INDEX_SIZE=4 > -DDOLFIN_SIZE_T=8 -DDOLFIN_VERSION=\"1.5.0\" -DHAS_CHOLMOD -DHAS_HDF5 > -DHAS_MPI -DHAS_PETSC -DHAS_SCOTCH -DHAS_SLEPC -DHAS_TRILINOS -DHAS_UMFPACK > -DHAS_VTK -DHAS_ZLIB -DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MICRO=2 > -DNUMPY_VERSION_MINOR=6 > -D_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990_EXPORTS > -std=c++11 -Wno-deprecated -O2 -fPIC -isystem > /Applications/FEniCS.app/Contents/Resources/include -isystem > /usr/include/libxml2 -isystem /Applications/FEniCS.app/Contents/Resources > -isystem /Applications/FEniCS.app/Contents/Resources/include/suitesparse > -isystem /Applications/FEniCS.app/Contents/Resources/include/eigen3 > -isystem > /Applications/FEniCS.app/Contents/Resources/lib/cmake/Trilinos/../../../include/trilinos > -isystem /Applications/FEniCS.app/Contents/Resources/include/trilinos > -isystem /Applications/FEniCS.app/Contents/Resources/include/vtk-5.10 > -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/. > -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include > -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 > -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 > -o > CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx.o > -c > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx > /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx:4183:3: > warning: expression result unused; should this cast be to 'void'? > [-Wunused-value] > (void *)clientdata; > ^ ~ > 1 warning generated. > make[2]: *** No rule to make target > `/Users/johannr/fenics-1.5.0/local/lib/libboost_filesystem.dylib', needed > by `_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.so'. > Stop. > make[1]: *** > [CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/all] > Error 2 > make: *** [all] Error 2 > > --- > > On Wed, Jan 21, 2015 at 3:32 AM, Johannes Ring <[email protected]> wrote: > >> On Wed, Jan 21, 2015 at 12:34 AM, Jan Blechta >> <[email protected]> wrote: >> > [Please, keep [email protected] in CC.] >> > >> > On Tue, 20 Jan 2015 18:10:36 -0500 >> > Adrian Butscher <[email protected]> wrote: >> > >> >> Hi, >> >> >> >> My apologies: >> >> >> >> FEniCS = Stable release 1.5.0, the one that is immediately accessible >> >> on the downloads page, i.e. without going to “older releases.” >> >> >> >> Before giving the contents of the log file, let me mention that a >> >> fellow FEniCS user has told me that the older release 1.4 does not >> >> have the problem I’ve described. So I installed the older version >> >> and tried out the demos — they work fine! >> > >> > Yes, it really looks like a bug in a binary package. See below. >> > Thanks for reporting it! >> > >> >> >> >> The contents of the 1.5.0 log file are here: >> >> >> >> -------------------- >> >> >> >> -- The C compiler identification is Clang 6.0.0 >> >> -- The CXX compiler identification is Clang 6.0.0 >> >> -- Check for working C compiler: /usr/bin/gcc >> >> -- Check for working C compiler: /usr/bin/gcc -- works >> >> -- Detecting C compiler ABI info >> >> -- Detecting C compiler ABI info - done >> >> -- Check for working CXX compiler: /usr/bin/g++ >> >> -- Check for working CXX compiler: /usr/bin/g++ -- works >> >> -- Detecting CXX compiler ABI info >> >> -- Detecting CXX compiler ABI info - done >> >> -- Found SWIG: /Applications/FEniCS.app/Contents/Resources/bin/swig >> >> (found version "2.0.8") -- Configuring done >> >> -- Generating done >> >> CMake Warning: >> >> Manually-specified variables were not used by the project: >> >> >> >> DEBUG >> >> >> >> >> >> -- Build files have been written >> >> to: >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /Applications/FEniCS.app/Contents/Resources/bin/cmake >> >> >> -H/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> >> >> -B/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> >> --check-build-system CMakeFiles/Makefile.cmake >> >> 0 /Applications/FEniCS.app/Contents/Resources/bin/cmake -E >> >> cmake_progress_start >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/progress.marks >> /Applications/Xcode.app/Contents/Developer/usr/bin/make >> >> -f CMakeFiles/Makefile2 >> >> all /Applications/Xcode.app/Contents/Developer/usr/bin/make -f >> >> >> CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/build.make >> >> >> CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/depend >> /Applications/FEniCS.app/Contents/Resources/bin/cmake >> >> -E >> >> cmake_progress_report >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles >> >> 1 [ 50%] Swig >> >> source /Applications/FEniCS.app/Contents/Resources/bin/cmake -E >> >> make_directory >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /Applications/FEniCS.app/Contents/Resources/bin/swig >> >> -python -module >> >> dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 -shadow >> >> -modern -modernargs -fastdispatch -fvirtual -nosafecstrings >> >> -noproxydel -fastproxy -fastinit -fastunpack -fastquery -nobuildnone >> >> -DDOLFIN_VERSION="1.5.0" -DBOOST_UBLAS_NDEBUG -DDOLFIN_SIZE_T=8 >> >> -DDOLFIN_LA_INDEX_SIZE=4 -DHAS_HDF5 -DHAS_TRILINOS -DHAS_SLEPC >> >> -DHAS_PETSC -DHAS_UMFPACK -DHAS_CHOLMOD -DHAS_SCOTCH -DHAS_ZLIB >> >> -DHAS_MPI -DHAS_VTK -DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MINOR=6 >> >> -DNUMPY_VERSION_MICRO=2 -c++ -fcompact -O -I. -small >> >> -outdir >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> >> -c++ -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/usr/include/libxml2 >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/Applications/FEniCS.app/Contents/Resources >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/Applications/FEniCS.app/Contents/Resources/include/suitesparse >> >> -I/Applications/FEniCS.app/Contents/Resources/include/suitesparse >> >> -I/Applications/FEniCS.app/Contents/Resources/include -I/usr/include >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/Applications/FEniCS.app/Contents/Resources/include/eigen3 >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> >> -I/Applications/FEniCS.app/Contents/Resources/lib/cmake/Trilinos/../../../include/trilinos >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/Applications/FEniCS.app/Contents/Resources/include/trilinos >> >> -I/Applications/FEniCS.app/Contents/Resources/include/suitesparse >> >> -I/Applications/FEniCS.app/Contents/Resources/include >> >> -I/Applications/FEniCS.app/Contents/Resources/include/vtk-5.10 >> >> >> -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/. >> >> >> -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include >> >> >> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 >> >> >> -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> >> -o >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/la/LinearAlgebraObject.h:36: >> >> Warning 520: Derived class 'LinearAlgebraObject' of >> >> 'dolfin::Variable' is not similarly marked as a smart >> >> pointer. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:63: >> >> Warning 402: Base class 'Hierarchical< Function >' is >> >> incomplete. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/swig/function/pre.i:219: >> >> Warning 402: Only forward declaration 'Hierarchical< Function >' was >> >> found. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:64: >> >> Warning 520: Derived class 'Function' of 'dolfin::GenericFunction' is >> >> not similarly marked as a smart >> >> pointer. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:64: >> >> Warning 520: Derived class 'Function' of 'ufc::function' is not >> >> similarly marked as a smart >> >> pointer. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/Function.h:64: >> >> Warning 520: Derived class 'Function' of 'dolfin::Variable' is not >> >> similarly marked as a smart >> >> pointer. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/FunctionSpace.h:53: >> >> Warning 402: Base class 'Hierarchical< FunctionSpace >' is >> >> incomplete. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/swig/function/pre.i:218: >> >> Warning 402: Only forward declaration 'Hierarchical< FunctionSpace >' >> >> was >> >> found. >> /Applications/FEniCS.app/Contents/Resources/include/dolfin/function/FunctionSpace.h:54: >> >> Warning 520: Derived class 'FunctionSpace' of 'dolfin::Variable' is >> >> not similarly marked as a smart >> >> pointer. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:170: >> >> Warning 315: Nothing known about >> >> 'std::cos'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:171: >> >> Warning 315: Nothing known about >> >> 'std::sin'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:172: >> >> Warning 315: Nothing known about >> >> 'std::tan'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:173: >> >> Warning 315: Nothing known about >> >> 'std::acos'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:174: >> >> Warning 315: Nothing known about >> >> 'std::asin'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:175: >> >> Warning 315: Nothing known about >> >> 'std::atan'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:176: >> >> Warning 315: Nothing known about >> >> 'std::atan2'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:177: >> >> Warning 315: Nothing known about >> >> 'std::cosh'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:178: >> >> Warning 315: Nothing known about >> >> 'std::sinh'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:179: >> >> Warning 315: Nothing known about >> >> 'std::tanh'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:180: >> >> Warning 315: Nothing known about >> >> 'std::exp'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:181: >> >> Warning 315: Nothing known about >> >> 'std::frexp'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:182: >> >> Warning 315: Nothing known about >> >> 'std::ldexp'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:183: >> >> Warning 315: Nothing known about >> >> 'std::log'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:184: >> >> Warning 315: Nothing known about >> >> 'std::log10'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:185: >> >> Warning 315: Nothing known about >> >> 'std::modf'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:186: >> >> Warning 315: Nothing known about >> >> 'std::pow'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:187: >> >> Warning 315: Nothing known about >> >> 'std::sqrt'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:188: >> >> Warning 315: Nothing known about >> >> 'std::ceil'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:189: >> >> Warning 315: Nothing known about >> >> 'std::fabs'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:190: >> >> Warning 315: Nothing known about >> >> 'std::floor'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:191: >> >> Warning 315: Nothing known about >> >> 'std::fmod'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:192: >> >> Warning 315: Nothing known about >> >> 'std::max'. >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.i:193: >> >> Warning 315: Nothing known about 'std::min'. >> >> cd >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> >> && /Applications/FEniCS.app/Contents/Resources/bin/cmake -E >> >> cmake_depends "Unix >> >> Makefiles" >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/DependInfo.cmake >> >> --color= Dependee >> >> >> "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/DependInfo.cmake" >> >> is newer than depender >> >> >> "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/depend.internal". >> >> Dependee >> >> >> "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/CMakeDirectoryInformation.cmake" >> >> is newer than depender >> >> >> "/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/depend.internal". >> >> Scanning dependencies of target >> >> _dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> /Applications/Xcode.app/Contents/Developer/usr/bin/make >> >> -f >> >> >> CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/build.make >> >> >> CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/build >> /Applications/FEniCS.app/Contents/Resources/bin/cmake >> >> -E >> >> cmake_progress_report >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/CMakeFiles >> >> 2 [100%] Building CXX object >> >> >> CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx.o >> /usr/bin/g++ >> >> -DBOOST_UBLAS_NDEBUG -DDOLFIN_LA_INDEX_SIZE=4 -DDOLFIN_SIZE_T=8 >> >> -DDOLFIN_VERSION=\"1.5.0\" -DHAS_CHOLMOD -DHAS_HDF5 -DHAS_MPI >> >> -DHAS_PETSC -DHAS_SCOTCH -DHAS_SLEPC -DHAS_TRILINOS -DHAS_UMFPACK >> >> -DHAS_VTK -DHAS_ZLIB -DNUMPY_VERSION_MAJOR=1 -DNUMPY_VERSION_MICRO=2 >> >> -DNUMPY_VERSION_MINOR=6 >> >> -D_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990_EXPORTS >> >> -std=c++11 -Wno-deprecated -O2 -fPIC >> >> -isystem /Applications/FEniCS.app/Contents/Resources/include >> >> -isystem /usr/include/libxml2 >> >> -isystem /Applications/FEniCS.app/Contents/Resources >> >> -isystem >> /Applications/FEniCS.app/Contents/Resources/include/suitesparse >> >> -isystem /Applications/FEniCS.app/Contents/Resources/include/eigen3 >> >> -isystem >> /Applications/FEniCS.app/Contents/Resources/lib/cmake/Trilinos/../../../include/trilinos >> >> -isystem /Applications/FEniCS.app/Contents/Resources/include/trilinos >> >> -isystem /Applications/FEniCS.app/Contents/Resources/include/vtk-5.10 >> >> >> -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/. >> >> >> -I/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy/core/include >> >> >> -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 >> >> >> -I/private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990 >> >> -o >> >> >> CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx.o >> >> -c >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx >> /private/var/folders/67/55yyvb51557frm02pm1ry_8c0000gn/T/tmpJGlVhp2015-1-20-16-26_instant_66528264d07361d64663d27c215c1ab47b1af0a5/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990PYTHON_wrap.cxx:4183:3: >> >> warning: expression result unused; should this cast be to 'void'? >> >> [-Wunused-value] (void *)clientdata; ^ ~ 1 warning generated. >> >> make[2]: *** No rule to make target >> >> `/Users/johannr/fenics-1.5.0/local/lib/libboost_filesystem.dylib', >> > >> > Johannes, it looks like there is a wrong hardcoded path to >> > libboost_filesystem.dylib. >> >> Yes, that is the correct. The post install script that fixes the paths >> was missing an update. This is fixed now and I have uploaded new >> packages for OS X 10.10 and 10.9: >> >> >> http://fenicsproject.org/pub/software/fenics/fenics-1.5.0-p1-osx10.10.dmg >> >> http://fenicsproject.org/pub/software/fenics/fenics-1.5.0-p1-osx10.9.dmg >> >> Please let me know if this fixes the problem. >> >> Johannes >> >> > Jan >> > >> >> needed by >> >> `_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.so'. >> >> Stop. make[1]: *** >> >> >> [CMakeFiles/_dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990.dir/all] >> >> Error 2 make: *** [all] Error 2 >> >> >> >> ------------------------------------ >> >> >> >> >> >> On Jan 20, 2015, at 17:39, Jan Blechta <[email protected]> >> >> wrote: >> >> >> >> > On Tue, 20 Jan 2015 17:28:22 -0500 >> >> > Adrian Butscher <[email protected]> wrote: >> >> > >> >> >> Hi, >> >> >> >> >> >> I’m running the lastest FEniCS on my Mac running osx 10.9.5. I >> >> > >> >> > Which one is it? Stable release 1.5.0? >> >> > >> >> >> installed FEniCS using the .dmg provided on the FEniCS website and >> >> >> I’m using the FEniCS shell provided by the FEniCS.app. I.e. I >> >> >> don’t think I’m doing anything outside of the ordinary use-case. >> >> >> I’m having a bug that other users have experienced in the past, >> >> >> and the solutions I’ve found online so far are not clear to me >> >> >> (and seem a bit out of date). My apologies if I am re-asking a >> >> >> question that has already been answered. >> >> >> >> >> >> The problem arises with the demo_poisson.py file though I think it >> >> >> will occur whenever the Expression command is used. (In >> >> >> particular, it does NOT occur when using the demo_cahn-hilliard.py >> >> >> file, as someone else on this forum discovered.) Here’s the >> >> >> output from python: >> >> >> >> >> >> Calling DOLFIN just-in-time (JIT) compiler, this may take some >> >> >> time. In instant.recompile: The module did not compile with >> >> >> command 'make VERBOSE=1', see >> >> >> >> '/Users/butscher/.instant/error/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/compile.log' >> >> >> Traceback (most recent call last): File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/share/dolfin/demo/documented/poisson/python/demo_poisson.py", >> >> >> line 54, in <module> f = Expression("10*exp(-(pow(x[0] - 0.5, 2) + >> >> >> pow(x[1] - 0.5, 2)) / 0.02)") File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/functions/expression.py", >> >> >> line 602, in __new__ mpi_comm=mpi_comm) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", >> >> >> line 217, in compile_expressions mpi_comm=mpi_comm) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/expressions.py", >> >> >> line 145, in compile_expression_code mpi_comm=mpi_comm) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", >> >> >> line 64, in mpi_jit return local_jit(*args, **kwargs) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.py", >> >> >> line 458, in compile_extension_module **instant_kwargs) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/build.py", >> >> >> line 563, in build_module recompile(modulename, module_path, >> >> >> new_compilation_checksum, build_system) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/build.py", >> >> >> line 165, in recompile instant_error(msg % (cmd, >> >> >> compile_log_filename_dest)) File >> >> >> >> "/Applications/FEniCS.app/Contents/Resources/lib/python2.7/site-packages/instant/output.py", >> >> >> line 85, in instant_error raise RuntimeError(text) RuntimeError: In >> >> >> instant.recompile: The module did not compile with command 'make >> >> >> VERBOSE=1', see >> >> >> >> '/Users/butscher/.instant/error/dolfin_compile_code_e71a4e0b9db4c7b3c4379cadd4a0fbc66cf1c990/compile.log’ >> >> > >> >> > Please, post contents of this file otherwise we can barely help you. >> >> > >> >> > Jan >> >> > >> >> >> >> >> >> If someone knows, please advise me on how to fix this problem. >> >> >> Many thanks. >> >> >> >> >> >> Adrian >> >> >> _______________________________________________ >> >> >> fenics-support mailing list >> >> >> [email protected] >> >> >> http://fenicsproject.org/mailman/listinfo/fenics-support >> >> > >> > >> > _______________________________________________ >> > fenics-support mailing list >> > [email protected] >> > http://fenicsproject.org/mailman/listinfo/fenics-support >> > >
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