2022-08-26T15:04:52,187 Created temporary directory: /tmp/pip-ephem-wheel-cache-7qw9gir_ 2022-08-26T15:04:52,192 Created temporary directory: /tmp/pip-build-tracker-9_rsqjj2 2022-08-26T15:04:52,193 Initialized build tracking at /tmp/pip-build-tracker-9_rsqjj2 2022-08-26T15:04:52,193 Created build tracker: /tmp/pip-build-tracker-9_rsqjj2 2022-08-26T15:04:52,194 Entered build tracker: /tmp/pip-build-tracker-9_rsqjj2 2022-08-26T15:04:52,195 Created temporary directory: /tmp/pip-wheel-bwcfyd1w 2022-08-26T15:04:52,262 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2022-08-26T15:04:52,270 2 location(s) to search for versions of pystochsim: 2022-08-26T15:04:52,270 * https://pypi.org/simple/pystochsim/ 2022-08-26T15:04:52,270 * https://www.piwheels.org/simple/pystochsim/ 2022-08-26T15:04:52,271 Fetching project page and analyzing links: https://pypi.org/simple/pystochsim/ 2022-08-26T15:04:52,272 Getting page https://pypi.org/simple/pystochsim/ 2022-08-26T15:04:52,276 Found index url https://pypi.org/simple 2022-08-26T15:04:52,389 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 2022-08-26T15:04:52,391 Found link https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz#sha256=9c19b2a1c2d1d17fdd6811ec31748f54bdf0cc321fc40b9344261c4ab2a8d7e5 (from https://pypi.org/simple/pystochsim/) (requires-python:>=3.6), version: 1.1.0 2022-08-26T15:04:52,392 Fetching project page and analyzing links: https://www.piwheels.org/simple/pystochsim/ 2022-08-26T15:04:52,392 Getting page https://www.piwheels.org/simple/pystochsim/ 2022-08-26T15:04:52,394 Found index url https://www.piwheels.org/simple 2022-08-26T15:04:52,602 Skipping link: No binaries permitted for pystochsim: https://www.piwheels.org/simple/pystochsim/pystochsim-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=92e9db83bd07e9f3cb3ae24e376554b7c560f25e28717b7e696bead47bcc2f24 (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2022-08-26T15:04:52,603 Skipping link: No binaries permitted for pystochsim: https://www.piwheels.org/simple/pystochsim/pystochsim-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=92e9db83bd07e9f3cb3ae24e376554b7c560f25e28717b7e696bead47bcc2f24 (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2022-08-26T15:04:52,604 Skipping link: not a file: https://www.piwheels.org/simple/pystochsim/ 2022-08-26T15:04:52,604 Skipping link: not a file: https://pypi.org/simple/pystochsim/ 2022-08-26T15:04:52,649 Given no hashes to check 1 links for project 'pystochsim': discarding no candidates 2022-08-26T15:04:52,690 Collecting pystochsim==1.1.0 2022-08-26T15:04:52,695 Created temporary directory: /tmp/pip-unpack-8lsk0gw1 2022-08-26T15:04:52,801 Downloading pystochsim-1.1.0.tar.gz (1.2 MB) 2022-08-26T15:04:55,677 Added pystochsim==1.1.0 from https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz#sha256=9c19b2a1c2d1d17fdd6811ec31748f54bdf0cc321fc40b9344261c4ab2a8d7e5 to build tracker '/tmp/pip-build-tracker-9_rsqjj2' 2022-08-26T15:04:55,681 Running setup.py (path:/tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/setup.py) egg_info for package pystochsim 2022-08-26T15:04:55,682 Created temporary directory: /tmp/pip-pip-egg-info-al0zzl8d 2022-08-26T15:04:55,683 Preparing metadata (setup.py): started 2022-08-26T15:04:55,685 Running command python setup.py egg_info 2022-08-26T15:05:02,420 running egg_info 2022-08-26T15:05:02,428 creating /tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info 2022-08-26T15:05:03,080 writing /tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info/PKG-INFO 2022-08-26T15:05:03,647 writing dependency_links to /tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info/dependency_links.txt 2022-08-26T15:05:07,021 writing top-level names to /tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info/top_level.txt 2022-08-26T15:05:07,024 writing manifest file '/tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info/SOURCES.txt' 2022-08-26T15:05:07,202 reading manifest file '/tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info/SOURCES.txt' 2022-08-26T15:05:07,205 reading manifest template 'MANIFEST.in' 2022-08-26T15:05:07,512 adding license file 'LICENSE' 2022-08-26T15:05:07,556 writing manifest file '/tmp/pip-pip-egg-info-al0zzl8d/pystochsim.egg-info/SOURCES.txt' 2022-08-26T15:05:07,784 Preparing metadata (setup.py): finished with status 'done' 2022-08-26T15:05:07,794 Source in /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5 has version 1.1.0, which satisfies requirement pystochsim==1.1.0 from https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz#sha256=9c19b2a1c2d1d17fdd6811ec31748f54bdf0cc321fc40b9344261c4ab2a8d7e5 2022-08-26T15:05:07,796 Removed pystochsim==1.1.0 from https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz#sha256=9c19b2a1c2d1d17fdd6811ec31748f54bdf0cc321fc40b9344261c4ab2a8d7e5 from build tracker '/tmp/pip-build-tracker-9_rsqjj2' 2022-08-26T15:05:07,808 Created temporary directory: /tmp/pip-unpack-z1xaxssn 2022-08-26T15:05:07,809 Building wheels for collected packages: pystochsim 2022-08-26T15:05:07,819 Created temporary directory: /tmp/pip-wheel-a3jz5c91 2022-08-26T15:05:07,819 Building wheel for pystochsim (setup.py): started 2022-08-26T15:05:07,821 Destination directory: /tmp/pip-wheel-a3jz5c91 2022-08-26T15:05:07,822 Running command python setup.py bdist_wheel 2022-08-26T15:05:14,001 running bdist_wheel 2022-08-26T15:05:14,267 running build 2022-08-26T15:05:14,267 running build_ext 2022-08-26T15:05:15,012 -- The C compiler identification is GNU 10.2.1 2022-08-26T15:05:15,709 -- The CXX compiler identification is GNU 10.2.1 2022-08-26T15:05:15,803 -- Detecting C compiler ABI info 2022-08-26T15:05:16,631 -- Detecting C compiler ABI info - done 2022-08-26T15:05:16,750 -- Check for working C compiler: /usr/bin/cc - skipped 2022-08-26T15:05:16,753 -- Detecting C compile features 2022-08-26T15:05:16,757 -- Detecting C compile features - done 2022-08-26T15:05:16,803 -- Detecting CXX compiler ABI info 2022-08-26T15:05:17,759 -- Detecting CXX compiler ABI info - done 2022-08-26T15:05:17,882 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2022-08-26T15:05:17,885 -- Detecting CXX compile features 2022-08-26T15:05:17,891 -- Detecting CXX compile features - done 2022-08-26T15:05:18,059 -- Using the multi-header code from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/ 2022-08-26T15:05:18,133 -- pybind11 v2.11.0 dev1 2022-08-26T15:05:18,391 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2022-08-26T15:05:20,778 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2022-08-26T15:05:20,798 -- Performing Test HAS_FLTO 2022-08-26T15:05:22,199 -- Performing Test HAS_FLTO - Success 2022-08-26T15:05:28,164 -- Found Python: /usr/bin/python3.9 (found version "3.9.2") found components: Interpreter 2022-08-26T15:05:28,183 -- Looking for pthread.h 2022-08-26T15:05:29,090 -- Looking for pthread.h - found 2022-08-26T15:05:29,095 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2022-08-26T15:05:29,994 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed 2022-08-26T15:05:29,997 -- Looking for pthread_create in pthreads 2022-08-26T15:05:30,702 -- Looking for pthread_create in pthreads - not found 2022-08-26T15:05:30,705 -- Looking for pthread_create in pthread 2022-08-26T15:05:31,556 -- Looking for pthread_create in pthread - found 2022-08-26T15:05:31,568 -- Found Threads: TRUE 2022-08-26T15:05:31,625 -- Configuring done 2022-08-26T15:05:32,142 -- Generating done 2022-08-26T15:05:32,204 CMake Warning: 2022-08-26T15:05:32,204 Manually-specified variables were not used by the project: 2022-08-26T15:05:32,205 EXAMPLE_VERSION_INFO 2022-08-26T15:05:32,213 -- Build files have been written to: /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/build/temp.linux-armv7l-cpython-39/pystochsim 2022-08-26T15:05:32,899 Scanning dependencies of target stochsim 2022-08-26T15:05:33,028 [ 2%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/factory.cpp.o 2022-08-26T15:06:22,112 [ 5%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/problem.cpp.o 2022-08-26T15:06:31,747 In file included from /usr/include/c++/10/vector:72, 2022-08-26T15:06:31,747 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.h:7, 2022-08-26T15:06:31,747 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/problem.h:3, 2022-08-26T15:06:31,748 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/problem.cpp:1: 2022-08-26T15:06:31,748 /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 = stochsim::Reaction; _Alloc = std::allocator]’: 2022-08-26T15:06:31,748 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-26T15:06:31,749 426 | vector<_Tp, _Alloc>:: 2022-08-26T15:06:31,749 | ^~~~~~~~~~~~~~~~~~~ 2022-08-26T15:06:32,518 /usr/include/c++/10/bits/vector.tcc: In member function ‘void stochsim::Problem::addReaction(stochsim::real, std::string)’: 2022-08-26T15:06:32,519 /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 2022-08-26T15:06:32,519 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2022-08-26T15:06:32,519 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:06:35,038 [ 7%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/reaction.cpp.o 2022-08-26T15:06:41,790 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.cpp: In member function ‘void stochsim::Reaction::computeGradPropensity(std::span, std::span) const’: 2022-08-26T15:06:41,791 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.cpp:131:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:06:41,791 131 | void Reaction::computeGradPropensity(std::span speciesNumber, 2022-08-26T15:06:41,791 | ^~~~~~~~ 2022-08-26T15:06:41,876 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.cpp: In member function ‘void stochsim::Reaction::addContributionMuHatSigmaHatSquare(stochsim::real, std::span, std::span) const’: 2022-08-26T15:06:41,876 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:06:41,877 152 | void Reaction::addContributionMuHatSigmaHatSquare(real propensity, 2022-08-26T15:06:41,877 | ^~~~~~~~ 2022-08-26T15:06:41,878 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:06:43,942 [ 10%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/reaction_parser.cpp.o 2022-08-26T15:06:56,981 [ 12%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/simulation.cpp.o 2022-08-26T15:07:06,050 [ 15%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/diagnostics/collect_tau.cpp.o 2022-08-26T15:07:11,377 In file included from /usr/include/c++/10/vector:72, 2022-08-26T15:07:11,377 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/diagnostic.h:8, 2022-08-26T15:07:11,378 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/collect_tau.h:3, 2022-08-26T15:07:11,378 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/collect_tau.cpp:1: 2022-08-26T15:07:11,378 /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]’: 2022-08-26T15:07:11,379 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-26T15:07:11,379 426 | vector<_Tp, _Alloc>:: 2022-08-26T15:07:11,379 | ^~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:11,461 In file included from /usr/include/c++/10/vector:67, 2022-08-26T15:07:11,462 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/diagnostic.h:8, 2022-08-26T15:07:11,462 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/collect_tau.h:3, 2022-08-26T15:07:11,463 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/collect_tau.cpp:1: 2022-08-26T15:07:11,463 /usr/include/c++/10/bits/stl_vector.h: In member function ‘virtual void stochsim::CollectTauDiagnostic::collect(int, stochsim::real, std::span)’: 2022-08-26T15:07:11,463 /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 2022-08-26T15:07:11,464 1198 | _M_realloc_insert(end(), __x); 2022-08-26T15:07:11,464 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-08-26T15:07:11,464 /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 2022-08-26T15:07:11,465 1198 | _M_realloc_insert(end(), __x); 2022-08-26T15:07:11,465 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2022-08-26T15:07:11,799 [ 17%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/diagnostics/diagnostic.cpp.o 2022-08-26T15:07:17,479 [ 20%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/diagnostics/mean_trajectory.cpp.o 2022-08-26T15:07:23,586 In file included from /usr/include/c++/10/vector:72, 2022-08-26T15:07:23,586 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/diagnostic.h:8, 2022-08-26T15:07:23,587 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/mean_trajectory.h:3, 2022-08-26T15:07:23,587 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/mean_trajectory.cpp:1: 2022-08-26T15:07:23,587 /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]’: 2022-08-26T15:07:23,588 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-26T15:07:23,588 509 | vector<_Tp, _Alloc>:: 2022-08-26T15:07:23,589 | ^~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:23,795 In file included from /usr/include/c++/10/vector:67, 2022-08-26T15:07:23,795 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/diagnostic.h:8, 2022-08-26T15:07:23,796 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/mean_trajectory.h:3, 2022-08-26T15:07:23,796 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/mean_trajectory.cpp:1: 2022-08-26T15:07:23,796 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘stochsim::MeanTrajectoryDiagnostic::MeanTrajectoryDiagnostic(std::vector >, stochsim::real, int)’: 2022-08-26T15:07:23,797 /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 2022-08-26T15:07:23,797 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-26T15:07:23,797 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:23,798 /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 2022-08-26T15:07:23,798 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-26T15:07:23,798 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:23,880 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/mean_trajectory.cpp:15:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-26T15:07:23,880 15 | } 2022-08-26T15:07:23,880 | ^ 2022-08-26T15:07:23,881 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/diagnostics/mean_trajectory.cpp:15:1: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-26T15:07:24,415 [ 22%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/R0_leaping.cpp.o 2022-08-26T15:07:32,667 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R0_leaping.cpp: In static member function ‘static void stochsim::R0Leaping::sampleNumFirings(int, std::span, std::span, std::mt19937&)’: 2022-08-26T15:07:32,667 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R0_leaping.cpp:43:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:32,668 43 | void R0Leaping::sampleNumFirings(int L, 2022-08-26T15:07:32,668 | ^~~~~~~~~ 2022-08-26T15:07:33,584 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R0_leaping.cpp: In member function ‘virtual void stochsim::R0Leaping::advance()’: 2022-08-26T15:07:33,584 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R0_leaping.cpp:35:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:33,585 35 | sampleNumFirings(L_, cumPropensities_, numFirings_, gen_); 2022-08-26T15:07:33,585 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:34,233 [ 25%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/R1_leaping.cpp.o 2022-08-26T15:07:43,853 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R1_leaping.cpp: In static member function ‘static void stochsim::R1Leaping::sampleNumFirings(int, std::span, std::span, std::span, std::mt19937&)’: 2022-08-26T15:07:43,853 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R1_leaping.cpp:57:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:43,854 57 | void R1Leaping::sampleNumFirings(int L, 2022-08-26T15:07:43,854 | ^~~~~~~~~ 2022-08-26T15:07:44,044 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R1_leaping.cpp: In member function ‘virtual void stochsim::R1Leaping::advance()’: 2022-08-26T15:07:44,045 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:44,045 45 | sampleNumFirings(L_, sortedReactionsIndices_, propensities_, numFirings_, gen_); 2022-08-26T15:07:44,045 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:44,046 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:44,952 [ 27%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/R_leaping.cpp.o 2022-08-26T15:07:57,607 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp: In member function ‘virtual void stochsim::RLeaping::advance()’: 2022-08-26T15:07:57,608 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:57,608 106 | r.addContributionMuHatSigmaHatSquare(a, muHat, sigmaHatSq); 2022-08-26T15:07:57,609 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:57,609 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:57,609 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:57,610 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp:149:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:57,610 149 | R0Leaping::sampleNumFirings(L, cumPropensities_, numFirings_, gen_); 2022-08-26T15:07:57,610 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:57,611 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:57,611 153 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices_, 2022-08-26T15:07:57,612 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:57,612 154 | propensities_, numFirings_, gen_); 2022-08-26T15:07:57,612 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:07:57,612 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:07:58,837 [ 30%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/solver.cpp.o 2022-08-26T15:08:02,462 [ 32%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/ssa.cpp.o 2022-08-26T15:08:11,415 [ 35%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/tau_leaping.cpp.o 2022-08-26T15:08:21,269 In file included from /usr/include/c++/10/vector:72, 2022-08-26T15:08:21,270 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.h:7, 2022-08-26T15:08:21,270 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/solver.h:3, 2022-08-26T15:08:21,271 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/tau_leaping.h:3, 2022-08-26T15:08:21,271 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/tau_leaping.cpp:1: 2022-08-26T15:08:21,271 /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]’: 2022-08-26T15:08:21,272 /usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2022-08-26T15:08:21,272 509 | vector<_Tp, _Alloc>:: 2022-08-26T15:08:21,272 | ^~~~~~~~~~~~~~~~~~~ 2022-08-26T15:08:21,506 In file included from /usr/include/c++/10/vector:67, 2022-08-26T15:08:21,507 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.h:7, 2022-08-26T15:08:21,507 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/solver.h:3, 2022-08-26T15:08:21,507 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/tau_leaping.h:3, 2022-08-26T15:08:21,508 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/tau_leaping.cpp:1: 2022-08-26T15:08:21,508 /usr/include/c++/10/bits/stl_vector.h: In member function ‘stochsim::real stochsim::TauLeaping::estimateLargestTau() const’: 2022-08-26T15:08:21,508 /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 2022-08-26T15:08:21,509 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-26T15:08:21,509 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:08:21,510 /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 2022-08-26T15:08:21,510 960 | _M_fill_insert(end(), __new_size - size(), __x); 2022-08-26T15:08:21,510 | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:08:26,295 [ 37%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/utils/algorithms.cpp.o 2022-08-26T15:08:36,143 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/utils/algorithms.cpp: In function ‘void stochsim::utils::argsortDecreasingOrder(std::span, std::span)’: 2022-08-26T15:08:36,144 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/utils/algorithms.cpp:23:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:08:36,144 23 | void argsortDecreasingOrder(std::span a, std::span indices) 2022-08-26T15:08:36,144 | ^~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:08:36,380 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/utils/algorithms.cpp: In function ‘size_t stochsim::utils::choose(std::span, std::mt19937&)’: 2022-08-26T15:08:36,380 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/utils/algorithms.cpp:9:8: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:08:36,380 9 | size_t choose(std::span cumulativeProbs, std::mt19937& gen) 2022-08-26T15:08:36,381 | ^~~~~~ 2022-08-26T15:08:36,775 [ 40%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/utils/exceptions.cpp.o 2022-08-26T15:08:40,718 [ 42%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/utils/strprintf.cpp.o 2022-08-26T15:08:44,761 [ 45%] Linking CXX static library libstochsim.a 2022-08-26T15:08:46,350 [ 45%] Built target stochsim 2022-08-26T15:08:46,578 Scanning dependencies of target run_simulation 2022-08-26T15:08:46,700 [ 47%] Building CXX object apps/CMakeFiles/run_simulation.dir/run_simulation.cpp.o 2022-08-26T15:09:18,742 In file included from /usr/include/c++/10/map:60, 2022-08-26T15:09:18,743 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-26T15:09:18,743 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-26T15:09:18,743 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/json.hpp:35, 2022-08-26T15:09:18,743 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/factory.h:9, 2022-08-26T15:09:18,744 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/apps/run_simulation.cpp:1: 2022-08-26T15:09:18,744 /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<> > >]’: 2022-08-26T15:09:18,744 /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 2022-08-26T15:09:18,745 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2022-08-26T15:09:18,745 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:19,003 In file included from /usr/include/c++/10/map:61, 2022-08-26T15:09:19,003 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-26T15:09:19,004 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-26T15:09:19,004 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/json.hpp:35, 2022-08-26T15:09:19,004 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/factory.h:9, 2022-08-26T15:09:19,005 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/apps/run_simulation.cpp:1: 2022-08-26T15:09:19,005 /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<> > >]’: 2022-08-26T15:09:19,005 /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 2022-08-26T15:09:19,006 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-26T15:09:19,006 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:19,006 502 | std::tuple(__k), 2022-08-26T15:09:19,007 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:19,007 503 | std::tuple<>()); 2022-08-26T15:09:19,007 | ~~~~~~~~~~~~~~~ 2022-08-26T15:09:19,143 /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<>]’: 2022-08-26T15:09:19,144 /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 2022-08-26T15:09:19,144 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-26T15:09:19,144 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:19,145 502 | std::tuple(__k), 2022-08-26T15:09:19,145 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:19,145 503 | std::tuple<>()); 2022-08-26T15:09:19,145 | ~~~~~~~~~~~~~~~ 2022-08-26T15:09:26,377 /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]’: 2022-08-26T15:09:26,378 /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 2022-08-26T15:09:26,378 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-26T15:09:26,379 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:26,379 502 | std::tuple(__k), 2022-08-26T15:09:26,379 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:09:26,380 503 | std::tuple<>()); 2022-08-26T15:09:26,380 | ~~~~~~~~~~~~~~~ 2022-08-26T15:09:34,382 [ 50%] Linking CXX executable run_simulation 2022-08-26T15:09:36,558 [ 50%] Built target run_simulation 2022-08-26T15:09:36,985 Scanning dependencies of target pystochsim 2022-08-26T15:09:37,123 [ 52%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/bindings.cpp.o 2022-08-26T15:10:04,651 [ 55%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/problem.cpp.o 2022-08-26T15:10:38,697 [ 57%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/run.cpp.o 2022-08-26T15:11:11,177 [ 60%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/solvers.cpp.o 2022-08-26T15:11:47,319 [ 62%] Linking CXX shared module ../../../../lib.linux-armv7l-cpython-39/pystochsim.cpython-39-arm-linux-gnueabihf.so 2022-08-26T15:12:35,940 [ 62%] Built target pystochsim 2022-08-26T15:12:36,201 Scanning dependencies of target gtest 2022-08-26T15:12:36,325 [ 65%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o 2022-08-26T15:13:52,531 [ 67%] Linking CXX static library ../../../../lib/libgtest.a 2022-08-26T15:13:53,024 [ 67%] Built target gtest 2022-08-26T15:13:53,199 Scanning dependencies of target gtest_main 2022-08-26T15:13:53,320 [ 70%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o 2022-08-26T15:14:00,288 [ 72%] Linking CXX static library ../../../../lib/libgtest_main.a 2022-08-26T15:14:00,655 [ 72%] Built target gtest_main 2022-08-26T15:14:01,036 Scanning dependencies of target test_stochsim 2022-08-26T15:14:01,162 [ 75%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/main.cpp.o 2022-08-26T15:14:14,719 [ 77%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/diagnostics.cpp.o 2022-08-26T15:14:38,016 [ 80%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/exceptions.cpp.o 2022-08-26T15:14:54,813 [ 82%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/factory.cpp.o 2022-08-26T15:15:34,966 In file included from /usr/include/c++/10/map:60, 2022-08-26T15:15:34,967 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-26T15:15:34,967 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-26T15:15:34,968 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/json.hpp:35, 2022-08-26T15:15:34,968 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/factory.h:9, 2022-08-26T15:15:34,968 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/factory.cpp:1: 2022-08-26T15:15:34,968 /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<> > >]’: 2022-08-26T15:15:34,969 /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 2022-08-26T15:15:34,969 2458 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2022-08-26T15:15:34,969 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:35,230 In file included from /usr/include/c++/10/map:61, 2022-08-26T15:15:35,231 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2022-08-26T15:15:35,231 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/adl_serializer.hpp:14, 2022-08-26T15:15:35,232 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/extern/json/include/nlohmann/json.hpp:35, 2022-08-26T15:15:35,232 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/factory.h:9, 2022-08-26T15:15:35,232 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/factory.cpp:1: 2022-08-26T15:15:35,232 /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<> > >]’: 2022-08-26T15:15:35,233 /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 2022-08-26T15:15:35,233 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-26T15:15:35,233 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:35,234 502 | std::tuple(__k), 2022-08-26T15:15:35,234 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:35,234 503 | std::tuple<>()); 2022-08-26T15:15:35,235 | ~~~~~~~~~~~~~~~ 2022-08-26T15:15:35,374 /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<>]’: 2022-08-26T15:15:35,374 /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 2022-08-26T15:15:35,375 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-26T15:15:35,375 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:35,375 502 | std::tuple(__k), 2022-08-26T15:15:35,376 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:35,376 503 | std::tuple<>()); 2022-08-26T15:15:35,376 | ~~~~~~~~~~~~~~~ 2022-08-26T15:15:42,494 /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]’: 2022-08-26T15:15:42,494 /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 2022-08-26T15:15:42,495 501 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2022-08-26T15:15:42,495 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:42,495 502 | std::tuple(__k), 2022-08-26T15:15:42,496 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:15:42,496 503 | std::tuple<>()); 2022-08-26T15:15:42,496 | ~~~~~~~~~~~~~~~ 2022-08-26T15:15:54,250 [ 85%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/R_leaping.cpp.o 2022-08-26T15:16:13,222 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/R_leaping.cpp: In member function ‘virtual void R1_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2022-08-26T15:16:13,222 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:13,223 40 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices, propensities, numFirings, gen); 2022-08-26T15:16:13,223 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:13,224 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:13,592 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/R_leaping.cpp: In member function ‘virtual void R0_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2022-08-26T15:16:13,592 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/R_leaping.cpp:21:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:13,593 21 | R0Leaping::sampleNumFirings(L, cumPropensities, numFirings, gen); 2022-08-26T15:16:13,593 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:14,956 [ 87%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/reaction.cpp.o 2022-08-26T15:16:40,150 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_third_order_Test::TestBody()’: 2022-08-26T15:16:40,151 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:40,151 181 | reaction.computeGradPropensity(numSpecies, gradients); 2022-08-26T15:16:40,151 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:40,152 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:43,249 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_second_order_Test::TestBody()’: 2022-08-26T15:16:43,249 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:43,250 167 | reaction.computeGradPropensity(numSpecies, gradients); 2022-08-26T15:16:43,250 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:43,251 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:43,842 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_first_order_Test::TestBody()’: 2022-08-26T15:16:43,843 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:43,843 151 | reaction.computeGradPropensity(numSpecies, gradients); 2022-08-26T15:16:43,843 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:43,844 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:44,985 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp: In member function ‘virtual void reaction_muHat_sigmaHatSquare_Test::TestBody()’: 2022-08-26T15:16:44,986 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:44,987 200 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2022-08-26T15:16:44,987 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:44,987 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:44,988 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:44,999 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:45,000 218 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2022-08-26T15:16:45,000 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2022-08-26T15:16:45,000 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:45,001 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2022-08-26T15:16:57,225 [ 90%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/reaction_parser.cpp.o 2022-08-26T15:17:29,759 [ 92%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/ssa.cpp.o 2022-08-26T15:17:46,690 In file included from /usr/include/c++/10/vector:67, 2022-08-26T15:17:46,690 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/reaction.h:7, 2022-08-26T15:17:46,691 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/solver.h:3, 2022-08-26T15:17:46,691 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/source/stochsim/solvers/ssa.h:3, 2022-08-26T15:17:46,691 from /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/ssa.cpp:1: 2022-08-26T15:17:46,692 /usr/include/c++/10/bits/stl_vector.h: In constructor ‘std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = stochsim::Reaction; _Alloc = std::allocator]’: 2022-08-26T15:17:46,692 /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 2022-08-26T15:17:46,692 625 | vector(initializer_list __l, 2022-08-26T15:17:46,693 | ^~~~~~ 2022-08-26T15:17:47,390 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/ssa.cpp: In member function ‘virtual void ssa_decay_Test::TestBody()’: 2022-08-26T15:17:47,390 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/ssa.cpp:16:17: note: parameter passing for argument of type ‘std::initializer_list’ changed in GCC 7.1 2022-08-26T15:17:47,391 16 | {n0}); 2022-08-26T15:17:47,391 | ^ 2022-08-26T15:17:48,290 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/ssa.cpp: In member function ‘virtual void ssa_equilibrium_Test::TestBody()’: 2022-08-26T15:17:48,291 /tmp/pip-wheel-bwcfyd1w/pystochsim_6ec1e26095574e55b06bcea7a70ff6e5/tests/units/ssa.cpp:47:20: note: parameter passing for argument of type ‘std::initializer_list’ changed in GCC 7.1 2022-08-26T15:17:48,291 47 | {n0, 0}); 2022-08-26T15:17:48,292 | ^ 2022-08-26T15:17:50,644 [ 95%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/tau_leaping.cpp.o 2022-08-26T15:18:12,630 [ 97%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/utils.cpp.o 2022-08-26T15:18:33,162 [100%] Linking CXX executable test_stochsim 2022-08-26T15:18:36,421 [100%] Built target test_stochsim 2022-08-26T15:18:37,283 /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. 2022-08-26T15:18:37,283 warnings.warn( 2022-08-26T15:18:37,941 installing to build/bdist.linux-armv7l/wheel 2022-08-26T15:18:37,941 running install 2022-08-26T15:18:38,003 running install_lib 2022-08-26T15:18:38,650 creating build/bdist.linux-armv7l 2022-08-26T15:18:38,651 creating build/bdist.linux-armv7l/wheel 2022-08-26T15:18:38,653 copying build/lib.linux-armv7l-cpython-39/pystochsim.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel 2022-08-26T15:18:38,679 running install_egg_info 2022-08-26T15:18:40,008 running egg_info 2022-08-26T15:18:40,655 writing pystochsim.egg-info/PKG-INFO 2022-08-26T15:18:41,216 writing dependency_links to pystochsim.egg-info/dependency_links.txt 2022-08-26T15:18:44,573 writing top-level names to pystochsim.egg-info/top_level.txt 2022-08-26T15:18:44,661 reading manifest file 'pystochsim.egg-info/SOURCES.txt' 2022-08-26T15:18:44,835 reading manifest template 'MANIFEST.in' 2022-08-26T15:18:45,207 adding license file 'LICENSE' 2022-08-26T15:18:45,270 writing manifest file 'pystochsim.egg-info/SOURCES.txt' 2022-08-26T15:18:45,275 Copying pystochsim.egg-info to build/bdist.linux-armv7l/wheel/pystochsim-1.1.0-py3.9.egg-info 2022-08-26T15:18:45,297 running install_scripts 2022-08-26T15:18:45,444 adding license file "LICENSE" (matched pattern "LICEN[CS]E*") 2022-08-26T15:18:45,453 creating build/bdist.linux-armv7l/wheel/pystochsim-1.1.0.dist-info/WHEEL 2022-08-26T15:18:45,458 creating '/tmp/pip-wheel-a3jz5c91/pystochsim-1.1.0-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2022-08-26T15:18:45,581 adding 'pystochsim.cpython-39-arm-linux-gnueabihf.so' 2022-08-26T15:18:45,591 adding 'pystochsim-1.1.0.dist-info/LICENSE' 2022-08-26T15:18:45,593 adding 'pystochsim-1.1.0.dist-info/METADATA' 2022-08-26T15:18:45,595 adding 'pystochsim-1.1.0.dist-info/WHEEL' 2022-08-26T15:18:45,596 adding 'pystochsim-1.1.0.dist-info/top_level.txt' 2022-08-26T15:18:45,598 adding 'pystochsim-1.1.0.dist-info/RECORD' 2022-08-26T15:18:45,604 removing build/bdist.linux-armv7l/wheel 2022-08-26T15:18:45,885 Building wheel for pystochsim (setup.py): finished with status 'done' 2022-08-26T15:18:45,896 Created wheel for pystochsim: filename=pystochsim-1.1.0-cp39-cp39-linux_armv7l.whl size=103289 sha256=062427fe2a74ec34a7481340aaca1e703a59e91473321a009b31d84876b4fe61 2022-08-26T15:18:45,898 Stored in directory: /tmp/pip-ephem-wheel-cache-7qw9gir_/wheels/2e/b5/40/b205f5a6d3369c4e900ff89616762016f7c213f0ce07ca272b 2022-08-26T15:18:45,919 Successfully built pystochsim 2022-08-26T15:18:45,934 Removed build tracker: '/tmp/pip-build-tracker-9_rsqjj2'