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LLNL / MemSurfer

MemSurfer is a software tool to compute bilayer membrane surfaces.
GNU General Public License v3.0
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cgal error installation from source OSX #21

Open zrollins opened 2 years ago

zrollins commented 2 years ago
  1. I installed MemSurfer from source utilizing the README protocol:

$ git clone --recursive git@github.com:LLNL/MemSurfer.git $ MEM_HOME=pwd/MemSurfer

  1. After installing dependencies,

$ export CC_COMPILER=which gcc $ export CXX_COMPILER=which g++ $ sh install_deps.sh

  1. I ran into the following issue with CGAL installation:

Installing MemSurfer's dependencies for () on (). platform = (Darwin)

Installation path = (/usr/local/anaconda3/pkgs/MemSurfer/external) Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1 Using gcc = (/usr/bin/gcc) [Apple clang version 12.0.0 (clang-1200.0.26.2)] Using g++ = (/usr/bin/g++) [Apple clang version 12.0.0 (clang-1200.0.26.2)] Using python = (/opt/anaconda3/bin/python3) [Python 3.7.6] (eigen-3.3.9) Already installed. Found (/usr/local/anaconda3/pkgs/MemSurfer/external/include/eigen3). (boost-1.66.0) Already installed. Found (/usr/local/anaconda3/pkgs/MemSurfer/external/lib/libboost_graph.a). (CGAL-4.13) Configuring (/usr/local/anaconda3/pkgs/MemSurfer/external/downloads/CGAL-4.13.tar/build-20220512-161945) (CGAL-4.13) Building and Installing (CGAL-4.13) Installation failed. Please see build logs in (/usr/local/anaconda3/pkgs/MemSurfer/external) for more information.

  1. Upon checking log file (for the make command) several errors are generated (only first two shown):

Consolidate compiler generated dependencies of target CGAL [ 16%] Building CXX object Installation/src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o In file included from /usr/local/anaconda3/pkgs/MemSurfer/external/downloads/CGAL-4.13.tar/build-20220512-161945/Installation/src/CGAL/all_files.cpp:1: In file included from /usr/local/anaconda3/pkgs/MemSurfer/external/downloads/CGAL-4.13.tar/Geomview/src/CGAL/Geomview_stream.cpp:28: In file included from /usr/local/anaconda3/pkgs/MemSurfer/external/downloads/CGAL-4.13.tar/Geomview/include/CGAL/IO/Geomview_stream.h:33: In file included from /usr/local/anaconda3/pkgs/MemSurfer/external/downloads/CGAL-4.13.tar/Kernel_23/include/CGAL/Bbox_2.h:33: In file included from /usr/local/include/boost/math/special_functions/next.hpp:13: In file included from /usr/local/include/boost/math/special_functions/math_fwd.hpp:29: In file included from /usr/local/include/boost/math/special_functions/detail/round_fwd.hpp:11: /usr/local/include/boost/math/tools/config.hpp:377:61: error: expected ';' at end of declaration inline T max BOOST_PREVENT_MACRO_SUBSTITUTION(T a, T b, T c) BOOST_MATH_NOEXCEPT(T) ^ /usr/local/include/boost/math/tools/config.hpp:377:82: error: use of undeclared identifier 'T' inline T max BOOST_PREVENT_MACRO_SUBSTITUTION(T a, T b, T c) BOOST_MATH_NOEXCEPT(T) ^ /usr/local/include/boost/math/tools/config.hpp:377:62: error: unknown type name 'noexcept' inline T max BOOST_PREVENT_MACRO_SUBSTITUTION(T a, T b, T c) BOOST_MATH_NOEXCEPT(T) ... fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[2]: [Installation/src/CGAL/CMakeFiles/CGAL.dir/all_files.cpp.o] Error 1 make[1]: [Installation/src/CGAL/CMakeFiles/CGAL.dir/all] Error 2

Can you help me with next steps in this installation?

bhatiaharsh commented 2 years ago

it looks like your C++ compiler is too old. can you please upgrade it and then retry.