2022-08-25T21:31:20,311 Created temporary directory: /tmp/pip-ephem-wheel-cache-ndq0s2f4 2022-08-25T21:31:20,316 Created temporary directory: /tmp/pip-build-tracker-o6c0eu2d 2022-08-25T21:31:20,317 Initialized build tracking at /tmp/pip-build-tracker-o6c0eu2d 2022-08-25T21:31:20,318 Created build tracker: /tmp/pip-build-tracker-o6c0eu2d 2022-08-25T21:31:20,318 Entered build tracker: /tmp/pip-build-tracker-o6c0eu2d 2022-08-25T21:31:20,319 Created temporary directory: /tmp/pip-wheel-pwbb7xwr 2022-08-25T21:31:20,394 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-08-25T21:31:20,402 2 location(s) to search for versions of pystochsim: 2022-08-25T21:31:20,402 * https://pypi.org/simple/pystochsim/ 2022-08-25T21:31:20,402 * https://www.piwheels.org/simple/pystochsim/ 2022-08-25T21:31:20,403 Fetching project page and analyzing links: https://pypi.org/simple/pystochsim/ 2022-08-25T21:31:20,404 Getting page https://pypi.org/simple/pystochsim/ 2022-08-25T21:31:20,408 Found index url https://pypi.org/simple 2022-08-25T21:31:20,524 Found link https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz#sha256=8b22365ebcca59a6de8e05da0ad2a616b10728ada44b5acd6e1a62fcce727b55 (from https://pypi.org/simple/pystochsim/) (requires-python:>=3.6), version: 1.0.0 2022-08-25T21:31:20,525 Fetching project page and analyzing links: https://www.piwheels.org/simple/pystochsim/ 2022-08-25T21:31:20,526 Getting page https://www.piwheels.org/simple/pystochsim/ 2022-08-25T21:31:20,528 Found index url https://www.piwheels.org/simple 2022-08-25T21:31:20,847 Skipping link: not a file: https://www.piwheels.org/simple/pystochsim/ 2022-08-25T21:31:20,848 Skipping link: not a file: https://pypi.org/simple/pystochsim/ 2022-08-25T21:31:20,892 Given no hashes to check 1 links for project 'pystochsim': discarding no candidates 2022-08-25T21:31:20,934 Collecting pystochsim==1.0.0 2022-08-25T21:31:20,938 Created temporary directory: /tmp/pip-unpack-3h7r8t61 2022-08-25T21:31:21,041 Downloading pystochsim-1.0.0.tar.gz (1.2 MB) 2022-08-25T21:31:23,887 Added pystochsim==1.0.0 from https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz#sha256=8b22365ebcca59a6de8e05da0ad2a616b10728ada44b5acd6e1a62fcce727b55 to build tracker '/tmp/pip-build-tracker-o6c0eu2d' 2022-08-25T21:31:23,891 Running setup.py (path:/tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/setup.py) egg_info for package pystochsim 2022-08-25T21:31:23,892 Created temporary directory: /tmp/pip-pip-egg-info-8c473ju6 2022-08-25T21:31:23,892 Preparing metadata (setup.py): started 2022-08-25T21:31:23,894 Running command python setup.py egg_info 2022-08-25T21:31:30,525 running egg_info 2022-08-25T21:31:30,532 creating /tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info 2022-08-25T21:31:31,188 writing /tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info/PKG-INFO 2022-08-25T21:31:31,750 writing dependency_links to /tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info/dependency_links.txt 2022-08-25T21:31:35,106 writing top-level names to /tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info/top_level.txt 2022-08-25T21:31:35,109 writing manifest file '/tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info/SOURCES.txt' 2022-08-25T21:31:35,306 reading manifest file '/tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info/SOURCES.txt' 2022-08-25T21:31:35,309 reading manifest template 'MANIFEST.in' 2022-08-25T21:31:35,621 adding license file 'LICENSE' 2022-08-25T21:31:35,664 writing manifest file '/tmp/pip-pip-egg-info-8c473ju6/pystochsim.egg-info/SOURCES.txt' 2022-08-25T21:31:35,889 Preparing metadata (setup.py): finished with status 'done' 2022-08-25T21:31:35,899 Source in /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f has version 1.0.0, which satisfies requirement pystochsim==1.0.0 from https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz#sha256=8b22365ebcca59a6de8e05da0ad2a616b10728ada44b5acd6e1a62fcce727b55 2022-08-25T21:31:35,901 Removed pystochsim==1.0.0 from https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz#sha256=8b22365ebcca59a6de8e05da0ad2a616b10728ada44b5acd6e1a62fcce727b55 from build tracker '/tmp/pip-build-tracker-o6c0eu2d' 2022-08-25T21:31:35,913 Created temporary directory: /tmp/pip-unpack-pb5pb5zx 2022-08-25T21:31:35,915 Building wheels for collected packages: pystochsim 2022-08-25T21:31:35,924 Created temporary directory: /tmp/pip-wheel-gr3dlp1u 2022-08-25T21:31:35,925 Building wheel for pystochsim (setup.py): started 2022-08-25T21:31:35,926 Destination directory: /tmp/pip-wheel-gr3dlp1u 2022-08-25T21:31:35,927 Running command python setup.py bdist_wheel 2022-08-25T21:31:41,970 running bdist_wheel 2022-08-25T21:31:42,258 running build 2022-08-25T21:31:42,258 running build_ext 2022-08-25T21:31:43,003 -- The C compiler identification is GNU 10.2.1 2022-08-25T21:31:43,702 -- The CXX compiler identification is GNU 10.2.1 2022-08-25T21:31:43,797 -- Detecting C compiler ABI info 2022-08-25T21:31:44,628 -- Detecting C compiler ABI info - done 2022-08-25T21:31:44,755 -- Check for working C compiler: /usr/bin/cc - skipped 2022-08-25T21:31:44,758 -- Detecting C compile features 2022-08-25T21:31:44,763 -- Detecting C compile features - done 2022-08-25T21:31:44,809 -- Detecting CXX compiler ABI info 2022-08-25T21:31:45,761 -- Detecting CXX compiler ABI info - done 2022-08-25T21:31:45,882 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2022-08-25T21:31:45,885 -- Detecting CXX compile features 2022-08-25T21:31:45,891 -- Detecting CXX compile features - done 2022-08-25T21:31:46,060 -- Using the multi-header code from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/ 2022-08-25T21:31:46,135 -- pybind11 v2.11.0 dev1 2022-08-25T21:31:46,289 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2022-08-25T21:31:48,575 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2022-08-25T21:31:48,593 -- Performing Test HAS_FLTO 2022-08-25T21:31:50,005 -- Performing Test HAS_FLTO - Success 2022-08-25T21:31:55,296 -- Found Python: /usr/bin/python3.9 (found version "3.9.2") found components: Interpreter 2022-08-25T21:31:55,315 -- Looking for pthread.h 2022-08-25T21:31:56,230 -- Looking for pthread.h - found 2022-08-25T21:31:56,235 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2022-08-25T21:31:57,143 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed 2022-08-25T21:31:57,147 -- Looking for pthread_create in pthreads 2022-08-25T21:31:57,879 -- Looking for pthread_create in pthreads - not found 2022-08-25T21:31:57,882 -- Looking for pthread_create in pthread 2022-08-25T21:31:58,754 -- Looking for pthread_create in pthread - found 2022-08-25T21:31:58,766 -- Found Threads: TRUE 2022-08-25T21:31:58,822 -- Configuring done 2022-08-25T21:31:59,329 -- Generating done 2022-08-25T21:31:59,387 CMake Warning: 2022-08-25T21:31:59,388 Manually-specified variables were not used by the project: 2022-08-25T21:31:59,389 EXAMPLE_VERSION_INFO 2022-08-25T21:31:59,396 -- Build files have been written to: /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/build/temp.linux-armv7l-cpython-39/pystochsim 2022-08-25T21:32:00,070 Scanning dependencies of target ssm 2022-08-25T21:32:00,199 [ 2%] Building CXX object source/ssm/CMakeFiles/ssm.dir/factory.cpp.o 2022-08-25T21:32:49,219 [ 5%] Building CXX object source/ssm/CMakeFiles/ssm.dir/problem.cpp.o 2022-08-25T21:32:58,841 In file included from /usr/include/c++/10/vector:72, 2022-08-25T21:32:58,842 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.h:7, 2022-08-25T21:32:58,842 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/problem.h:3, 2022-08-25T21:32:58,842 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/problem.cpp:1: 2022-08-25T21:32:58,843 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, std::vector >, std::vector >, std::vector >, std::vector >, std::vector >}; _Tp = ssm::Reaction; _Alloc = std::allocator]’: 2022-08-25T21:32:58,843 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-25T21:32:58,843 426 | vector<_Tp, _Alloc>:: 2022-08-25T21:32:58,844 | ^~~~~~~~~~~~~~~~~~~ 2022-08-25T21:32:59,611 /usr/include/c++/10/bits/vector.tcc: In member function ‘void ssm::Problem::addReaction(ssm::real, std::string)’: 2022-08-25T21:32:59,611 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:32:59,612 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-25T21:32:59,612 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:33:02,120 [ 7%] Building CXX object source/ssm/CMakeFiles/ssm.dir/reaction.cpp.o 2022-08-25T21:33:08,873 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.cpp: In member function ‘void ssm::Reaction::computeGradPropensity(std::span, std::span) const’: 2022-08-25T21:33:08,873 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.cpp:131:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:33:08,874 131 | void Reaction::computeGradPropensity(std::span speciesNumber, 2022-08-25T21:33:08,874 | ^~~~~~~~ 2022-08-25T21:33:08,958 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.cpp: In member function ‘void ssm::Reaction::addContributionMuHatSigmaHatSquare(ssm::real, std::span, std::span) const’: 2022-08-25T21:33:08,959 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:33:08,959 152 | void Reaction::addContributionMuHatSigmaHatSquare(real propensity, 2022-08-25T21:33:08,960 | ^~~~~~~~ 2022-08-25T21:33:08,960 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:33:11,059 [ 10%] Building CXX object source/ssm/CMakeFiles/ssm.dir/reaction_parser.cpp.o 2022-08-25T21:33:24,136 [ 12%] Building CXX object source/ssm/CMakeFiles/ssm.dir/simulation.cpp.o 2022-08-25T21:33:33,124 [ 15%] Building CXX object source/ssm/CMakeFiles/ssm.dir/diagnostics/collect_tau.cpp.o 2022-08-25T21:33:38,498 In file included from /usr/include/c++/10/vector:72, 2022-08-25T21:33:38,498 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/diagnostic.h:8, 2022-08-25T21:33:38,499 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/collect_tau.h:3, 2022-08-25T21:33:38,499 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/collect_tau.cpp:1: 2022-08-25T21:33:38,499 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2022-08-25T21:33:38,500 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-25T21:33:38,500 426 | vector<_Tp, _Alloc>:: 2022-08-25T21:33:38,501 | ^~~~~~~~~~~~~~~~~~~ 2022-08-25T21:33:38,582 In file included from /usr/include/c++/10/vector:67, 2022-08-25T21:33:38,583 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/diagnostic.h:8, 2022-08-25T21:33:38,583 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/collect_tau.h:3, 2022-08-25T21:33:38,584 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/collect_tau.cpp:1: 2022-08-25T21:33:38,584 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual void ssm::CollectTauDiagnostic::collect(int, ssm::real, std::span)’: 2022-08-25T21:33:38,584 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:33:38,585 1198 | _M_realloc_insert(end(), __x); 2022-08-25T21:33:38,585 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-08-25T21:33:38,585 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:33:38,586 1198 | _M_realloc_insert(end(), __x); 2022-08-25T21:33:38,586 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-08-25T21:33:38,919 [ 17%] Building CXX object source/ssm/CMakeFiles/ssm.dir/diagnostics/diagnostic.cpp.o 2022-08-25T21:33:44,592 [ 20%] Building CXX object source/ssm/CMakeFiles/ssm.dir/diagnostics/mean_trajectory.cpp.o 2022-08-25T21:33:50,629 In file included from /usr/include/c++/10/vector:72, 2022-08-25T21:33:50,630 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/diagnostic.h:8, 2022-08-25T21:33:50,630 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/mean_trajectory.h:3, 2022-08-25T21:33:50,631 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/mean_trajectory.cpp:1: 2022-08-25T21:33:50,631 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = long long int; _Alloc = std::allocator]’: 2022-08-25T21:33:50,631 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-25T21:33:50,631 509 | vector<_Tp, _Alloc>:: 2022-08-25T21:33:50,632 | ^~~~~~~~~~~~~~~~~~~ 2022-08-25T21:33:50,840 In file included from /usr/include/c++/10/vector:67, 2022-08-25T21:33:50,841 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/diagnostic.h:8, 2022-08-25T21:33:50,841 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/mean_trajectory.h:3, 2022-08-25T21:33:50,841 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/mean_trajectory.cpp:1: 2022-08-25T21:33:50,841 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘ssm::MeanTrajectoryDiagnostic::MeanTrajectoryDiagnostic(std::vector >, ssm::real, int)’: 2022-08-25T21:33:50,842 /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:33:50,842 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-25T21:33:50,842 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:33:50,843 /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:33:50,844 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-25T21:33:50,844 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:33:50,929 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/mean_trajectory.cpp:15:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-25T21:33:50,929 15 | } 2022-08-25T21:33:50,930 | ^ 2022-08-25T21:33:50,931 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/diagnostics/mean_trajectory.cpp:15:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-25T21:33:51,455 [ 22%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/R0_leaping.cpp.o 2022-08-25T21:33:59,669 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R0_leaping.cpp: In static member function ‘static void ssm::R0Leaping::sampleNumFirings(int, std::span, std::span, std::mt19937&)’: 2022-08-25T21:33:59,669 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R0_leaping.cpp:43:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:33:59,670 43 | void R0Leaping::sampleNumFirings(int L, 2022-08-25T21:33:59,670 | ^~~~~~~~~ 2022-08-25T21:34:00,584 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R0_leaping.cpp: In member function ‘virtual void ssm::R0Leaping::advance()’: 2022-08-25T21:34:00,584 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R0_leaping.cpp:35:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:00,585 35 | sampleNumFirings(L_, cumPropensities_, numFirings_, gen_); 2022-08-25T21:34:00,585 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:01,236 [ 25%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/R1_leaping.cpp.o 2022-08-25T21:34:10,831 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R1_leaping.cpp: In static member function ‘static void ssm::R1Leaping::sampleNumFirings(int, std::span, std::span, std::span, std::mt19937&)’: 2022-08-25T21:34:10,832 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R1_leaping.cpp:57:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:10,832 57 | void R1Leaping::sampleNumFirings(int L, 2022-08-25T21:34:10,832 | ^~~~~~~~~ 2022-08-25T21:34:11,022 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R1_leaping.cpp: In member function ‘virtual void ssm::R1Leaping::advance()’: 2022-08-25T21:34:11,023 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:11,023 45 | sampleNumFirings(L_, sortedReactionsIndices_, propensities_, numFirings_, gen_); 2022-08-25T21:34:11,023 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:11,024 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:11,943 [ 27%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/R_leaping.cpp.o 2022-08-25T21:34:24,580 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp: In member function ‘virtual void ssm::RLeaping::advance()’: 2022-08-25T21:34:24,580 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:24,581 106 | r.addContributionMuHatSigmaHatSquare(a, muHat, sigmaHatSq); 2022-08-25T21:34:24,581 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:24,581 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:24,582 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:24,582 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp:149:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:24,582 149 | R0Leaping::sampleNumFirings(L, cumPropensities_, numFirings_, gen_); 2022-08-25T21:34:24,583 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:24,583 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:24,583 153 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices_, 2022-08-25T21:34:24,584 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:24,584 154 | propensities_, numFirings_, gen_); 2022-08-25T21:34:24,584 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:24,585 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:34:25,804 [ 30%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/solver.cpp.o 2022-08-25T21:34:29,456 [ 32%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/ssa.cpp.o 2022-08-25T21:34:38,347 [ 35%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/tau_leaping.cpp.o 2022-08-25T21:34:48,178 In file included from /usr/include/c++/10/vector:72, 2022-08-25T21:34:48,179 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.h:7, 2022-08-25T21:34:48,179 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/solver.h:3, 2022-08-25T21:34:48,179 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/tau_leaping.h:3, 2022-08-25T21:34:48,180 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/tau_leaping.cpp:1: 2022-08-25T21:34:48,180 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator]’: 2022-08-25T21:34:48,180 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-25T21:34:48,181 509 | vector<_Tp, _Alloc>:: 2022-08-25T21:34:48,181 | ^~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:48,415 In file included from /usr/include/c++/10/vector:67, 2022-08-25T21:34:48,415 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.h:7, 2022-08-25T21:34:48,416 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/solver.h:3, 2022-08-25T21:34:48,416 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/tau_leaping.h:3, 2022-08-25T21:34:48,416 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/tau_leaping.cpp:1: 2022-08-25T21:34:48,417 /usr/include/c++/10/bits/stl_vector.h: In member function ‘ssm::real ssm::TauLeaping::estimateLargestTau() const’: 2022-08-25T21:34:48,417 /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:34:48,417 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-25T21:34:48,418 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:48,418 /usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2022-08-25T21:34:48,418 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-25T21:34:48,419 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:34:53,169 [ 37%] Building CXX object source/ssm/CMakeFiles/ssm.dir/utils/algorithms.cpp.o 2022-08-25T21:35:03,078 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/utils/algorithms.cpp: In function ‘void ssm::utils::argsortDecreasingOrder(std::span, std::span)’: 2022-08-25T21:35:03,079 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/utils/algorithms.cpp:23:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:35:03,079 23 | void argsortDecreasingOrder(std::span a, std::span indices) 2022-08-25T21:35:03,080 | ^~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:03,318 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/utils/algorithms.cpp: In function ‘size_t ssm::utils::choose(std::span, std::mt19937&)’: 2022-08-25T21:35:03,318 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/utils/algorithms.cpp:9:8: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:35:03,319 9 | size_t choose(std::span cumulativeProbs, std::mt19937& gen) 2022-08-25T21:35:03,319 | ^~~~~~ 2022-08-25T21:35:03,714 [ 40%] Building CXX object source/ssm/CMakeFiles/ssm.dir/utils/exceptions.cpp.o 2022-08-25T21:35:07,670 [ 42%] Building CXX object source/ssm/CMakeFiles/ssm.dir/utils/strprintf.cpp.o 2022-08-25T21:35:11,683 [ 45%] Linking CXX static library libssm.a 2022-08-25T21:35:13,312 [ 45%] Built target ssm 2022-08-25T21:35:13,542 Scanning dependencies of target run_simulation 2022-08-25T21:35:13,663 [ 47%] Building CXX object apps/CMakeFiles/run_simulation.dir/run_simulation.cpp.o 2022-08-25T21:35:45,728 In file included from /usr/include/c++/10/map:60, 2022-08-25T21:35:45,728 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-25T21:35:45,729 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-25T21:35:45,729 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/json.hpp:35, 2022-08-25T21:35:45,729 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/factory.h:9, 2022-08-25T21:35:45,729 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/apps/run_simulation.cpp:1: 2022-08-25T21:35:45,730 /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >; _Compare = std::less; _Alloc = std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > >]’: 2022-08-25T21:35:45,730 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:35:45,730 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2022-08-25T21:35:45,731 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:45,989 In file included from /usr/include/c++/10/map:61, 2022-08-25T21:35:45,989 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-25T21:35:45,989 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-25T21:35:45,990 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/json.hpp:35, 2022-08-25T21:35:45,990 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/factory.h:9, 2022-08-25T21:35:45,990 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/apps/run_simulation.cpp:1: 2022-08-25T21:35:45,991 /usr/include/c++/10/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::json_abi_v3_11_1::basic_json<>; _Compare = std::less; _Alloc = std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > >]’: 2022-08-25T21:35:45,991 /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:35:45,991 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-25T21:35:45,992 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:45,992 502 | std::tuple(__k), 2022-08-25T21:35:45,992 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:45,992 503 | std::tuple<>()); 2022-08-25T21:35:45,993 | ~~~~~~~~~~~~~~~ 2022-08-25T21:35:46,131 /usr/include/c++/10/bits/stl_map.h: In member function ‘bool nlohmann::json_abi_v3_11_1::detail::json_sax_dom_callback_parser::key(nlohmann::json_abi_v3_11_1::detail::json_sax_dom_callback_parser::string_t&) [with BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>]’: 2022-08-25T21:35:46,131 /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:35:46,132 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-25T21:35:46,132 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:46,132 502 | std::tuple(__k), 2022-08-25T21:35:46,133 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:46,133 503 | std::tuple<>()); 2022-08-25T21:35:46,133 | ~~~~~~~~~~~~~~~ 2022-08-25T21:35:53,305 /usr/include/c++/10/bits/stl_map.h: In member function ‘bool nlohmann::json_abi_v3_11_1::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::json_abi_v3_11_1::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>; InputAdapterType = nlohmann::json_abi_v3_11_1::detail::input_stream_adapter]’: 2022-08-25T21:35:53,306 /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:35:53,306 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-25T21:35:53,306 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:53,307 502 | std::tuple(__k), 2022-08-25T21:35:53,307 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:35:53,307 503 | std::tuple<>()); 2022-08-25T21:35:53,308 | ~~~~~~~~~~~~~~~ 2022-08-25T21:36:01,363 [ 50%] Linking CXX executable run_simulation 2022-08-25T21:36:03,549 [ 50%] Built target run_simulation 2022-08-25T21:36:03,953 Scanning dependencies of target pystochsim 2022-08-25T21:36:04,084 [ 52%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/bindings.cpp.o 2022-08-25T21:36:31,367 [ 55%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/problem.cpp.o 2022-08-25T21:37:05,109 [ 57%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/run.cpp.o 2022-08-25T21:37:37,776 [ 60%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/solvers.cpp.o 2022-08-25T21:38:13,672 [ 62%] Linking CXX shared module ../../../../lib.linux-armv7l-cpython-39/pystochsim.cpython-39-arm-linux-gnueabihf.so 2022-08-25T21:39:02,458 [ 62%] Built target pystochsim 2022-08-25T21:39:02,715 Scanning dependencies of target gtest 2022-08-25T21:39:02,839 [ 65%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o 2022-08-25T21:40:19,212 [ 67%] Linking CXX static library ../../../../lib/libgtest.a 2022-08-25T21:40:19,700 [ 67%] Built target gtest 2022-08-25T21:40:19,874 Scanning dependencies of target gtest_main 2022-08-25T21:40:19,995 [ 70%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o 2022-08-25T21:40:26,929 [ 72%] Linking CXX static library ../../../../lib/libgtest_main.a 2022-08-25T21:40:27,285 [ 72%] Built target gtest_main 2022-08-25T21:40:27,685 Scanning dependencies of target test_ssm 2022-08-25T21:40:27,818 [ 75%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/main.cpp.o 2022-08-25T21:40:41,395 [ 77%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/diagnostics.cpp.o 2022-08-25T21:41:04,605 [ 80%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/exceptions.cpp.o 2022-08-25T21:41:21,252 [ 82%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/factory.cpp.o 2022-08-25T21:42:01,525 In file included from /usr/include/c++/10/map:60, 2022-08-25T21:42:01,526 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-25T21:42:01,526 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-25T21:42:01,526 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/json.hpp:35, 2022-08-25T21:42:01,527 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/factory.h:9, 2022-08-25T21:42:01,527 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/factory.cpp:1: 2022-08-25T21:42:01,527 /usr/include/c++/10/bits/stl_tree.h: In function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >; _KeyOfValue = std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >; _Compare = std::less; _Alloc = std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > >]’: 2022-08-25T21:42:01,528 /usr/include/c++/10/bits/stl_tree.h:2458:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:42:01,528 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2022-08-25T21:42:01,528 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:01,788 In file included from /usr/include/c++/10/map:61, 2022-08-25T21:42:01,788 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-25T21:42:01,788 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-25T21:42:01,789 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/extern/json/include/nlohmann/json.hpp:35, 2022-08-25T21:42:01,789 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/factory.h:9, 2022-08-25T21:42:01,789 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/factory.cpp:1: 2022-08-25T21:42:01,790 /usr/include/c++/10/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = nlohmann::json_abi_v3_11_1::basic_json<>; _Compare = std::less; _Alloc = std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > >]’: 2022-08-25T21:42:01,790 /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:42:01,790 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-25T21:42:01,791 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:01,791 502 | std::tuple(__k), 2022-08-25T21:42:01,791 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:01,792 503 | std::tuple<>()); 2022-08-25T21:42:01,792 | ~~~~~~~~~~~~~~~ 2022-08-25T21:42:01,926 /usr/include/c++/10/bits/stl_map.h: In member function ‘bool nlohmann::json_abi_v3_11_1::detail::json_sax_dom_callback_parser::key(nlohmann::json_abi_v3_11_1::detail::json_sax_dom_callback_parser::string_t&) [with BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>]’: 2022-08-25T21:42:01,927 /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:42:01,927 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-25T21:42:01,927 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:01,928 502 | std::tuple(__k), 2022-08-25T21:42:01,928 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:01,928 503 | std::tuple<>()); 2022-08-25T21:42:01,929 | ~~~~~~~~~~~~~~~ 2022-08-25T21:42:09,018 /usr/include/c++/10/bits/stl_map.h: In member function ‘bool nlohmann::json_abi_v3_11_1::detail::parser::sax_parse_internal(SAX*) [with SAX = nlohmann::json_abi_v3_11_1::detail::json_sax_dom_parser >; BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>; InputAdapterType = nlohmann::json_abi_v3_11_1::detail::iterator_input_adapter]’: 2022-08-25T21:42:09,018 /usr/include/c++/10/bits/stl_map.h:501:37: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, nlohmann::json_abi_v3_11_1::basic_json<> >, std::_Select1st, nlohmann::json_abi_v3_11_1::basic_json<> > >, std::less, std::allocator, nlohmann::json_abi_v3_11_1::basic_json<> > > >::const_iterator’ changed in GCC 7.1 2022-08-25T21:42:09,019 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-25T21:42:09,019 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:09,019 502 | std::tuple(__k), 2022-08-25T21:42:09,020 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:09,020 503 | std::tuple<>()); 2022-08-25T21:42:09,020 | ~~~~~~~~~~~~~~~ 2022-08-25T21:42:21,035 [ 85%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/R_leaping.cpp.o 2022-08-25T21:42:39,737 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/R_leaping.cpp: In member function ‘virtual void R1_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2022-08-25T21:42:39,738 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:42:39,738 40 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices, propensities, numFirings, gen); 2022-08-25T21:42:39,739 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:39,739 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:42:40,104 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/R_leaping.cpp: In member function ‘virtual void R0_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2022-08-25T21:42:40,104 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/R_leaping.cpp:21:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:42:40,105 21 | R0Leaping::sampleNumFirings(L, cumPropensities, numFirings, gen); 2022-08-25T21:42:40,105 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:42:41,424 [ 87%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/reaction.cpp.o 2022-08-25T21:43:06,635 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_third_order_Test::TestBody()’: 2022-08-25T21:43:06,636 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:06,636 181 | reaction.computeGradPropensity(numSpecies, gradients); 2022-08-25T21:43:06,636 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:43:06,637 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:09,724 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_second_order_Test::TestBody()’: 2022-08-25T21:43:09,724 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:09,724 167 | reaction.computeGradPropensity(numSpecies, gradients); 2022-08-25T21:43:09,725 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:43:09,725 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:10,314 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_first_order_Test::TestBody()’: 2022-08-25T21:43:10,314 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:10,315 151 | reaction.computeGradPropensity(numSpecies, gradients); 2022-08-25T21:43:10,315 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:43:10,316 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:11,455 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp: In member function ‘virtual void reaction_muHat_sigmaHatSquare_Test::TestBody()’: 2022-08-25T21:43:11,456 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:11,456 200 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2022-08-25T21:43:11,456 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:43:11,457 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:11,457 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:11,469 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:11,469 218 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2022-08-25T21:43:11,469 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-25T21:43:11,470 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:11,470 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-25T21:43:23,604 [ 90%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/reaction_parser.cpp.o 2022-08-25T21:43:56,032 [ 92%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/ssa.cpp.o 2022-08-25T21:44:12,866 In file included from /usr/include/c++/10/vector:67, 2022-08-25T21:44:12,867 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/reaction.h:7, 2022-08-25T21:44:12,867 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/solver.h:3, 2022-08-25T21:44:12,868 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/source/ssm/solvers/ssa.h:3, 2022-08-25T21:44:12,868 from /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/ssa.cpp:1: 2022-08-25T21:44:12,868 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = ssm::Reaction; _Alloc = std::allocator]’: 2022-08-25T21:44:12,869 /usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type ‘std::initializer_list’ changed in GCC 7.1 2022-08-25T21:44:12,869 625 | vector(initializer_list __l, 2022-08-25T21:44:12,869 | ^~~~~~ 2022-08-25T21:44:13,559 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/ssa.cpp: In member function ‘virtual void ssa_decay_Test::TestBody()’: 2022-08-25T21:44:13,559 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/ssa.cpp:16:17: note: parameter passing for argument of type ‘std::initializer_list’ changed in GCC 7.1 2022-08-25T21:44:13,560 16 | {n0}); 2022-08-25T21:44:13,560 | ^ 2022-08-25T21:44:14,455 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/ssa.cpp: In member function ‘virtual void ssa_equilibrium_Test::TestBody()’: 2022-08-25T21:44:14,456 /tmp/pip-wheel-pwbb7xwr/pystochsim_d9381e9bc38c4e4d8c1aa6100a02328f/tests/units/ssa.cpp:47:20: note: parameter passing for argument of type ‘std::initializer_list’ changed in GCC 7.1 2022-08-25T21:44:14,456 47 | {n0, 0}); 2022-08-25T21:44:14,457 | ^ 2022-08-25T21:44:16,736 [ 95%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/tau_leaping.cpp.o 2022-08-25T21:44:38,741 [ 97%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/utils.cpp.o 2022-08-25T21:44:59,349 [100%] Linking CXX executable test_ssm 2022-08-25T21:45:02,448 [100%] Built target test_ssm 2022-08-25T21:45:03,316 /usr/local/lib/python3.9/dist-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools. 2022-08-25T21:45:03,317 warnings.warn( 2022-08-25T21:45:03,979 installing to build/bdist.linux-armv7l/wheel 2022-08-25T21:45:03,980 running install 2022-08-25T21:45:04,042 running install_lib 2022-08-25T21:45:04,705 creating build/bdist.linux-armv7l 2022-08-25T21:45:04,706 creating build/bdist.linux-armv7l/wheel 2022-08-25T21:45:04,708 copying build/lib.linux-armv7l-cpython-39/pystochsim.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2022-08-25T21:45:04,724 running install_egg_info 2022-08-25T21:45:06,073 running egg_info 2022-08-25T21:45:06,732 writing pystochsim.egg-info/PKG-INFO 2022-08-25T21:45:07,293 writing dependency_links to pystochsim.egg-info/dependency_links.txt 2022-08-25T21:45:10,629 writing top-level names to pystochsim.egg-info/top_level.txt 2022-08-25T21:45:10,731 reading manifest file 'pystochsim.egg-info/SOURCES.txt' 2022-08-25T21:45:10,900 reading manifest template 'MANIFEST.in' 2022-08-25T21:45:11,280 adding license file 'LICENSE' 2022-08-25T21:45:11,343 writing manifest file 'pystochsim.egg-info/SOURCES.txt' 2022-08-25T21:45:11,348 Copying pystochsim.egg-info to build/bdist.linux-armv7l/wheel/pystochsim-1.0.0-py3.9.egg-info 2022-08-25T21:45:11,372 running install_scripts 2022-08-25T21:45:11,521 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-08-25T21:45:11,531 creating build/bdist.linux-armv7l/wheel/pystochsim-1.0.0.dist-info/WHEEL 2022-08-25T21:45:11,536 creating '/tmp/pip-wheel-gr3dlp1u/pystochsim-1.0.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-08-25T21:45:11,661 adding 'pystochsim.cpython-39-arm-linux-gnueabihf.so' 2022-08-25T21:45:11,671 adding 'pystochsim-1.0.0.dist-info/LICENSE' 2022-08-25T21:45:11,672 adding 'pystochsim-1.0.0.dist-info/METADATA' 2022-08-25T21:45:11,674 adding 'pystochsim-1.0.0.dist-info/WHEEL' 2022-08-25T21:45:11,676 adding 'pystochsim-1.0.0.dist-info/top_level.txt' 2022-08-25T21:45:11,678 adding 'pystochsim-1.0.0.dist-info/RECORD' 2022-08-25T21:45:11,683 removing build/bdist.linux-armv7l/wheel 2022-08-25T21:45:11,965 Building wheel for pystochsim (setup.py): finished with status 'done' 2022-08-25T21:45:11,976 Created wheel for pystochsim: filename=pystochsim-1.0.0-cp39-cp39-linux_armv7l.whl size=103099 sha256=92e9db83bd07e9f3cb3ae24e376554b7c560f25e28717b7e696bead47bcc2f24 2022-08-25T21:45:11,978 Stored in directory: /tmp/pip-ephem-wheel-cache-ndq0s2f4/wheels/74/10/bc/50b3160a51a9ec98cea5c767946bcddf6f499954a3da9ab301 2022-08-25T21:45:11,999 Successfully built pystochsim 2022-08-25T21:45:12,014 Removed build tracker: '/tmp/pip-build-tracker-o6c0eu2d'