2025-09-11T04:46:58,762 Created temporary directory: /tmp/pip-build-tracker-_w686_w2 2025-09-11T04:46:58,763 Initialized build tracking at /tmp/pip-build-tracker-_w686_w2 2025-09-11T04:46:58,763 Created build tracker: /tmp/pip-build-tracker-_w686_w2 2025-09-11T04:46:58,763 Entered build tracker: /tmp/pip-build-tracker-_w686_w2 2025-09-11T04:46:58,763 Created temporary directory: /tmp/pip-wheel-hyh3cl7c 2025-09-11T04:46:58,767 Created temporary directory: /tmp/pip-ephem-wheel-cache-k21upvg3 2025-09-11T04:46:58,829 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-11T04:46:58,832 2 location(s) to search for versions of pystochsim: 2025-09-11T04:46:58,832 * https://pypi.org/simple/pystochsim/ 2025-09-11T04:46:58,832 * https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:46:58,832 Fetching project page and analyzing links: https://pypi.org/simple/pystochsim/ 2025-09-11T04:46:58,832 Getting page https://pypi.org/simple/pystochsim/ 2025-09-11T04:46:58,834 Found index url https://pypi.org/simple/ 2025-09-11T04:46:58,909 Fetched page https://pypi.org/simple/pystochsim/ as application/vnd.pypi.simple.v1+json 2025-09-11T04:46:58,911 Found link https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz (from https://pypi.org/simple/pystochsim/) (requires-python:>=3.6), version: 1.0.0 2025-09-11T04:46:58,911 Found link https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz (from https://pypi.org/simple/pystochsim/) (requires-python:>=3.6), version: 1.1.0 2025-09-11T04:46:58,911 Fetching project page and analyzing links: https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:46:58,912 Getting page https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:46:58,913 Found index url https://www.piwheels.org/simple/ 2025-09-11T04:46:59,004 Fetched page https://www.piwheels.org/simple/pystochsim/ as text/html 2025-09-11T04:46:59,007 Skipping link: No binaries permitted for pystochsim: https://archive1.piwheels.org/simple/pystochsim/pystochsim-1.1.0-cp311-cp311-linux_armv6l.whl#sha256=370fb234eacb92d55bc33a5a997a84209b7c67348cfe78011882817fc529cbb5 (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2025-09-11T04:46:59,007 Skipping link: No binaries permitted for pystochsim: https://archive1.piwheels.org/simple/pystochsim/pystochsim-1.1.0-cp311-cp311-linux_armv7l.whl#sha256=370fb234eacb92d55bc33a5a997a84209b7c67348cfe78011882817fc529cbb5 (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2025-09-11T04:46:59,007 Skipping link: No binaries permitted for pystochsim: https://archive1.piwheels.org/simple/pystochsim/pystochsim-1.1.0-cp39-cp39-linux_armv6l.whl#sha256=062427fe2a74ec34a7481340aaca1e703a59e91473321a009b31d84876b4fe61 (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2025-09-11T04:46:59,007 Skipping link: No binaries permitted for pystochsim: https://archive1.piwheels.org/simple/pystochsim/pystochsim-1.1.0-cp39-cp39-linux_armv7l.whl#sha256=062427fe2a74ec34a7481340aaca1e703a59e91473321a009b31d84876b4fe61 (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2025-09-11T04:46:59,008 Skipping link: No binaries permitted for pystochsim: https://archive1.piwheels.org/simple/pystochsim/pystochsim-1.0.0-cp311-cp311-linux_armv6l.whl#sha256=757fd665e29c2960f43b5ebb53927dd9c7656b6a8b93500064e2077982df15ec (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2025-09-11T04:46:59,008 Skipping link: No binaries permitted for pystochsim: https://archive1.piwheels.org/simple/pystochsim/pystochsim-1.0.0-cp311-cp311-linux_armv7l.whl#sha256=757fd665e29c2960f43b5ebb53927dd9c7656b6a8b93500064e2077982df15ec (from https://www.piwheels.org/simple/pystochsim/) (requires-python:>=3.6) 2025-09-11T04:46:59,008 Skipping link: No binaries permitted for pystochsim: https://archive1.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) 2025-09-11T04:46:59,008 Skipping link: No binaries permitted for pystochsim: https://archive1.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) 2025-09-11T04:46:59,008 Skipping link: not a file: https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:46:59,008 Skipping link: not a file: https://pypi.org/simple/pystochsim/ 2025-09-11T04:46:59,032 Given no hashes to check 1 links for project 'pystochsim': discarding no candidates 2025-09-11T04:46:59,033 Collecting pystochsim==1.1.0 2025-09-11T04:46:59,035 Created temporary directory: /tmp/pip-unpack-n0ltbm9f 2025-09-11T04:46:59,184 Downloading pystochsim-1.1.0.tar.gz (1.2 MB) 2025-09-11T04:47:00,138 Added pystochsim==1.1.0 from https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz to build tracker '/tmp/pip-build-tracker-_w686_w2' 2025-09-11T04:47:00,139 Running setup.py (path:/tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/setup.py) egg_info for package pystochsim 2025-09-11T04:47:00,139 Created temporary directory: /tmp/pip-pip-egg-info-atn7xxzp 2025-09-11T04:47:00,140 Preparing metadata (setup.py): started 2025-09-11T04:47:00,141 Running command python setup.py egg_info 2025-09-11T04:47:01,440 running egg_info 2025-09-11T04:47:01,536 creating /tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info 2025-09-11T04:47:01,536 writing /tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info/PKG-INFO 2025-09-11T04:47:01,538 writing dependency_links to /tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info/dependency_links.txt 2025-09-11T04:47:01,538 writing top-level names to /tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info/top_level.txt 2025-09-11T04:47:01,539 writing manifest file '/tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:47:01,717 reading manifest file '/tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:47:01,718 reading manifest template 'MANIFEST.in' 2025-09-11T04:47:01,768 adding license file 'LICENSE' 2025-09-11T04:47:01,784 writing manifest file '/tmp/pip-pip-egg-info-atn7xxzp/pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:47:01,913 Preparing metadata (setup.py): finished with status 'done' 2025-09-11T04:47:01,918 Source in /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88 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 2025-09-11T04:47:01,918 Removed pystochsim==1.1.0 from https://files.pythonhosted.org/packages/a6/5c/7613c6bac1ee52964e761e325353878d5f6ccd739f03b2012eae8c741260/pystochsim-1.1.0.tar.gz from build tracker '/tmp/pip-build-tracker-_w686_w2' 2025-09-11T04:47:01,923 Created temporary directory: /tmp/pip-unpack-m4mva1ep 2025-09-11T04:47:01,923 Created temporary directory: /tmp/pip-unpack-f4fu_s25 2025-09-11T04:47:01,923 Building wheels for collected packages: pystochsim 2025-09-11T04:47:01,925 Created temporary directory: /tmp/pip-wheel-icerjv81 2025-09-11T04:47:01,925 DEPRECATION: Building 'pystochsim' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pystochsim'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-11T04:47:01,927 Building wheel for pystochsim (setup.py): started 2025-09-11T04:47:01,928 Destination directory: /tmp/pip-wheel-icerjv81 2025-09-11T04:47:01,928 Running command python setup.py bdist_wheel 2025-09-11T04:47:03,126 running bdist_wheel 2025-09-11T04:47:03,487 running build 2025-09-11T04:47:03,487 running build_ext 2025-09-11T04:47:03,547 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): 2025-09-11T04:47:03,547 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:47:03,547 CMake. 2025-09-11T04:47:03,548 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:47:03,548 to tell CMake that the project requires at least but has been updated 2025-09-11T04:47:03,548 to work with policies introduced by or earlier. 2025-09-11T04:47:03,831 -- The C compiler identification is GNU 14.2.0 2025-09-11T04:47:04,167 -- The CXX compiler identification is GNU 14.2.0 2025-09-11T04:47:04,211 -- Detecting C compiler ABI info 2025-09-11T04:47:04,643 -- Detecting C compiler ABI info - done 2025-09-11T04:47:04,726 -- Check for working C compiler: /usr/bin/cc - skipped 2025-09-11T04:47:04,728 -- Detecting C compile features 2025-09-11T04:47:04,731 -- Detecting C compile features - done 2025-09-11T04:47:04,800 -- Detecting CXX compiler ABI info 2025-09-11T04:47:05,333 -- Detecting CXX compiler ABI info - done 2025-09-11T04:47:05,407 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2025-09-11T04:47:05,409 -- Detecting CXX compile features 2025-09-11T04:47:05,413 -- Detecting CXX compile features - done 2025-09-11T04:47:05,453 CMake Deprecation Warning at extern/json/CMakeLists.txt:1 (cmake_minimum_required): 2025-09-11T04:47:05,453 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:47:05,453 CMake. 2025-09-11T04:47:05,454 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:47:05,454 to tell CMake that the project requires at least but has been updated 2025-09-11T04:47:05,454 to work with policies introduced by or earlier. 2025-09-11T04:47:05,490 -- Using the multi-header code from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/ 2025-09-11T04:47:05,497 CMake Deprecation Warning at extern/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2025-09-11T04:47:05,498 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:47:05,498 CMake. 2025-09-11T04:47:05,498 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:47:05,498 to tell CMake that the project requires at least but has been updated 2025-09-11T04:47:05,498 to work with policies introduced by or earlier. 2025-09-11T04:47:05,515 -- pybind11 v2.11.0 dev1 2025-09-11T04:47:05,522 CMake Warning (dev) at extern/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package): 2025-09-11T04:47:05,522 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T04:47:05,522 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T04:47:05,523 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T04:47:05,523 Call Stack (most recent call first): 2025-09-11T04:47:05,523 extern/pybind11/tools/pybind11Tools.cmake:50 (find_package) 2025-09-11T04:47:05,523 extern/pybind11/tools/pybind11Common.cmake:180 (include) 2025-09-11T04:47:05,523 extern/pybind11/CMakeLists.txt:200 (include) 2025-09-11T04:47:05,523 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T04:47:05,595 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.13.5", minimum required is "3.6") 2025-09-11T04:47:05,702 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so 2025-09-11T04:47:05,713 -- Performing Test HAS_FLTO 2025-09-11T04:47:06,432 -- Performing Test HAS_FLTO - Success 2025-09-11T04:47:06,455 CMake Deprecation Warning at tests/extern/googletest/CMakeLists.txt:4 (cmake_minimum_required): 2025-09-11T04:47:06,455 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:47:06,455 CMake. 2025-09-11T04:47:06,456 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:47:06,456 to tell CMake that the project requires at least but has been updated 2025-09-11T04:47:06,456 to work with policies introduced by or earlier. 2025-09-11T04:47:06,469 CMake Deprecation Warning at tests/extern/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): 2025-09-11T04:47:06,470 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:47:06,470 CMake. 2025-09-11T04:47:06,470 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:47:06,470 to tell CMake that the project requires at least but has been updated 2025-09-11T04:47:06,470 to work with policies introduced by or earlier. 2025-09-11T04:47:07,208 -- Found Python: /usr/bin/python3 (found version "3.13.5") found components: Interpreter 2025-09-11T04:47:07,214 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2025-09-11T04:47:07,719 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success 2025-09-11T04:47:07,725 -- Found Threads: TRUE 2025-09-11T04:47:07,736 -- Configuring done (4.2s) 2025-09-11T04:47:07,826 -- Generating done (0.1s) 2025-09-11T04:47:07,826 CMake Warning: 2025-09-11T04:47:07,827 Manually-specified variables were not used by the project: 2025-09-11T04:47:07,827 EXAMPLE_VERSION_INFO 2025-09-11T04:47:07,829 -- Build files have been written to: /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/build/temp.linux-armv7l-cpython-313/pystochsim 2025-09-11T04:47:08,156 [ 2%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/factory.cpp.o 2025-09-11T04:47:31,754 [ 5%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/problem.cpp.o 2025-09-11T04:47:38,317 [ 7%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/reaction.cpp.o 2025-09-11T04:47:41,230 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/reaction.cpp: In member function ‘void stochsim::Reaction::computeGradPropensity(std::span, std::span) const’: 2025-09-11T04:47:41,230 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/reaction.cpp:131:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:47:41,231 131 | void Reaction::computeGradPropensity(std::span speciesNumber, 2025-09-11T04:47:41,231 | ^~~~~~~~ 2025-09-11T04:47:41,282 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/reaction.cpp: In member function ‘void stochsim::Reaction::addContributionMuHatSigmaHatSquare(stochsim::real, std::span, std::span) const’: 2025-09-11T04:47:41,282 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:47:41,282 152 | void Reaction::addContributionMuHatSigmaHatSquare(real propensity, 2025-09-11T04:47:41,282 | ^~~~~~~~ 2025-09-11T04:47:41,283 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:47:42,234 [ 10%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/reaction_parser.cpp.o 2025-09-11T04:47:49,321 [ 12%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/simulation.cpp.o 2025-09-11T04:47:53,142 [ 15%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/diagnostics/collect_tau.cpp.o 2025-09-11T04:47:56,023 [ 17%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/diagnostics/diagnostic.cpp.o 2025-09-11T04:47:58,628 [ 20%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/diagnostics/mean_trajectory.cpp.o 2025-09-11T04:48:01,822 [ 22%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/R0_leaping.cpp.o 2025-09-11T04:48:05,276 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R0_leaping.cpp: In static member function ‘static void stochsim::R0Leaping::sampleNumFirings(int, std::span, std::span, std::mt19937&)’: 2025-09-11T04:48:05,276 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R0_leaping.cpp:43:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:05,276 43 | void R0Leaping::sampleNumFirings(int L, 2025-09-11T04:48:05,276 | ^~~~~~~~~ 2025-09-11T04:48:05,512 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R0_leaping.cpp: In member function ‘virtual void stochsim::R0Leaping::advance()’: 2025-09-11T04:48:05,513 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R0_leaping.cpp:35:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:05,513 35 | sampleNumFirings(L_, cumPropensities_, numFirings_, gen_); 2025-09-11T04:48:05,513 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:05,908 [ 25%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/R1_leaping.cpp.o 2025-09-11T04:48:09,864 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R1_leaping.cpp: In static member function ‘static void stochsim::R1Leaping::sampleNumFirings(int, std::span, std::span, std::span, std::mt19937&)’: 2025-09-11T04:48:09,865 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R1_leaping.cpp:57:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:09,865 57 | void R1Leaping::sampleNumFirings(int L, 2025-09-11T04:48:09,865 | ^~~~~~~~~ 2025-09-11T04:48:10,099 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R1_leaping.cpp: In member function ‘virtual void stochsim::R1Leaping::advance()’: 2025-09-11T04:48:10,099 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:10,099 45 | sampleNumFirings(L_, sortedReactionsIndices_, propensities_, numFirings_, gen_); 2025-09-11T04:48:10,099 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:10,100 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:10,527 [ 27%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/R_leaping.cpp.o 2025-09-11T04:48:15,715 In function ‘void stochsim::computeMuHatSigmaHatSq(std::span, std::span, std::span, std::span)’, 2025-09-11T04:48:15,716 inlined from ‘virtual void stochsim::RLeaping::advance()’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:136:27: 2025-09-11T04:48:15,716 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:15,716 106 | r.addContributionMuHatSigmaHatSquare(a, muHat, sigmaHatSq); 2025-09-11T04:48:15,716 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:15,716 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:15,716 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:15,717 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp: In member function ‘virtual void stochsim::RLeaping::advance()’: 2025-09-11T04:48:15,717 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:149:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:15,717 149 | R0Leaping::sampleNumFirings(L, cumPropensities_, numFirings_, gen_); 2025-09-11T04:48:15,717 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:15,717 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:15,717 153 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices_, 2025-09-11T04:48:15,718 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:15,718 154 | propensities_, numFirings_, gen_); 2025-09-11T04:48:15,718 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:15,718 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:16,408 [ 30%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/solver.cpp.o 2025-09-11T04:48:17,896 [ 32%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/ssa.cpp.o 2025-09-11T04:48:21,458 [ 35%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/solvers/tau_leaping.cpp.o 2025-09-11T04:48:28,784 [ 37%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/utils/algorithms.cpp.o 2025-09-11T04:48:32,706 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/utils/algorithms.cpp: In function ‘void stochsim::utils::argsortDecreasingOrder(std::span, std::span)’: 2025-09-11T04:48:32,706 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/utils/algorithms.cpp:23:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:32,706 23 | void argsortDecreasingOrder(std::span a, std::span indices) 2025-09-11T04:48:32,706 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:32,852 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/utils/algorithms.cpp: In function ‘size_t stochsim::utils::choose(std::span, std::mt19937&)’: 2025-09-11T04:48:32,852 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/utils/algorithms.cpp:9:8: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:32,852 9 | size_t choose(std::span cumulativeProbs, std::mt19937& gen) 2025-09-11T04:48:32,852 | ^~~~~~ 2025-09-11T04:48:33,033 [ 40%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/utils/exceptions.cpp.o 2025-09-11T04:48:34,666 [ 42%] Building CXX object source/stochsim/CMakeFiles/stochsim.dir/utils/strprintf.cpp.o 2025-09-11T04:48:36,316 [ 45%] Linking CXX static library libstochsim.a 2025-09-11T04:48:36,815 [ 45%] Built target stochsim 2025-09-11T04:48:36,933 [ 47%] Building CXX object apps/CMakeFiles/run_simulation.dir/run_simulation.cpp.o 2025-09-11T04:48:52,574 In file included from /usr/include/c++/14/map:62, 2025-09-11T04:48:52,574 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2025-09-11T04:48:52,574 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/adl_serializer.hpp:14, 2025-09-11T04:48:52,574 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/json.hpp:35, 2025-09-11T04:48:52,574 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/factory.h:9, 2025-09-11T04:48:52,574 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/apps/run_simulation.cpp:1: 2025-09-11T04:48:52,575 /usr/include/c++/14/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(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<> > >]’: 2025-09-11T04:48:52,575 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-11T04:48:52,575 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-11T04:48:52,575 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:54,388 In file included from /usr/include/c++/14/map:63: 2025-09-11T04:48:54,388 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<> > >]’, 2025-09-11T04:48:54,388 inlined from ‘bool nlohmann::json_abi_v3_11_1::detail::json_sax_dom_callback_parser::key(string_t&) [with BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>]’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/input/json_sax.hpp:442:76: 2025-09-11T04:48:54,388 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-11T04:48:54,388 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:48:54,389 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:54,389 514 | std::tuple(__k), 2025-09-11T04:48:54,389 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:54,389 515 | std::tuple<>()); 2025-09-11T04:48:54,389 | ~~~~~~~~~~~~~~~ 2025-09-11T04:48:54,860 /usr/include/c++/14/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<> > >]’: 2025-09-11T04:48:54,860 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-11T04:48:54,860 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:48:54,861 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:54,861 514 | std::tuple(__k), 2025-09-11T04:48:54,861 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:54,861 515 | std::tuple<>()); 2025-09-11T04:48:54,861 | ~~~~~~~~~~~~~~~ 2025-09-11T04:48:59,202 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<> > >]’, 2025-09-11T04:48:59,202 inlined from ‘bool nlohmann::json_abi_v3_11_1::detail::json_sax_dom_parser::key(string_t&) [with BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>]’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/input/json_sax.hpp:247:72, 2025-09-11T04:48:59,202 inlined from ‘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]’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/input/parser.hpp:418:21: 2025-09-11T04:48:59,202 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-11T04:48:59,202 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:48:59,203 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:59,203 514 | std::tuple(__k), 2025-09-11T04:48:59,203 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:59,203 515 | std::tuple<>()); 2025-09-11T04:48:59,203 | ~~~~~~~~~~~~~~~ 2025-09-11T04:49:02,575 [ 50%] Linking CXX executable run_simulation 2025-09-11T04:49:03,226 [ 50%] Built target run_simulation 2025-09-11T04:49:03,343 [ 52%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/bindings.cpp.o 2025-09-11T04:49:17,726 [ 55%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/problem.cpp.o 2025-09-11T04:49:35,972 [ 57%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/run.cpp.o 2025-09-11T04:49:52,117 [ 60%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/solvers.cpp.o 2025-09-11T04:50:09,913 [ 62%] Linking CXX shared module /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/build/lib.linux-armv7l-cpython-313/pystochsim.cpython-313-arm-linux-gnueabihf.so 2025-09-11T04:50:11,093 lto-wrapper: warning: using serial compilation of 3 LTRANS jobs 2025-09-11T04:50:11,093 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2025-09-11T04:50:32,587 [ 62%] Built target pystochsim 2025-09-11T04:50:32,705 [ 65%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o 2025-09-11T04:51:13,557 [ 67%] Linking CXX static library ../../../../lib/libgtest.a 2025-09-11T04:51:13,906 [ 67%] Built target gtest 2025-09-11T04:51:14,034 [ 70%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o 2025-09-11T04:51:18,588 [ 72%] Linking CXX static library ../../../../lib/libgtest_main.a 2025-09-11T04:51:18,895 [ 72%] Built target gtest_main 2025-09-11T04:51:19,014 [ 75%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/main.cpp.o 2025-09-11T04:51:25,435 [ 77%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/diagnostics.cpp.o 2025-09-11T04:51:36,075 [ 80%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/exceptions.cpp.o 2025-09-11T04:51:44,559 [ 82%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/factory.cpp.o 2025-09-11T04:52:00,979 In file included from /usr/include/c++/14/map:62, 2025-09-11T04:52:00,980 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2025-09-11T04:52:00,980 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/adl_serializer.hpp:14, 2025-09-11T04:52:00,980 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/json.hpp:35, 2025-09-11T04:52:00,980 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/source/stochsim/factory.h:9, 2025-09-11T04:52:00,980 from /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/factory.cpp:1: 2025-09-11T04:52:00,980 /usr/include/c++/14/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(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<> > >]’: 2025-09-11T04:52:00,980 /usr/include/c++/14/bits/stl_tree.h:2456:7: 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 2025-09-11T04:52:00,981 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-11T04:52:00,981 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:02,106 In file included from /usr/include/c++/14/map:63: 2025-09-11T04:52:02,106 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<> > >]’, 2025-09-11T04:52:02,106 inlined from ‘bool nlohmann::json_abi_v3_11_1::detail::json_sax_dom_callback_parser::key(string_t&) [with BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>]’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/input/json_sax.hpp:442:76: 2025-09-11T04:52:02,106 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-11T04:52:02,106 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:52:02,106 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:02,106 514 | std::tuple(__k), 2025-09-11T04:52:02,107 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:02,107 515 | std::tuple<>()); 2025-09-11T04:52:02,107 | ~~~~~~~~~~~~~~~ 2025-09-11T04:52:02,498 /usr/include/c++/14/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<> > >]’: 2025-09-11T04:52:02,498 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-11T04:52:02,499 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:52:02,499 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:02,499 514 | std::tuple(__k), 2025-09-11T04:52:02,499 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:02,499 515 | std::tuple<>()); 2025-09-11T04:52:02,499 | ~~~~~~~~~~~~~~~ 2025-09-11T04:52:06,107 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<> > >]’, 2025-09-11T04:52:06,107 inlined from ‘bool nlohmann::json_abi_v3_11_1::detail::json_sax_dom_parser::key(string_t&) [with BasicJsonType = nlohmann::json_abi_v3_11_1::basic_json<>]’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/input/json_sax.hpp:247:72, 2025-09-11T04:52:06,107 inlined from ‘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]’ at /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/extern/json/include/nlohmann/detail/input/parser.hpp:418:21: 2025-09-11T04:52:06,107 /usr/include/c++/14/bits/stl_map.h:513:44: 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 2025-09-11T04:52:06,107 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:52:06,108 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:06,108 514 | std::tuple(__k), 2025-09-11T04:52:06,108 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:06,108 515 | std::tuple<>()); 2025-09-11T04:52:06,108 | ~~~~~~~~~~~~~~~ 2025-09-11T04:52:10,333 [ 85%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/R_leaping.cpp.o 2025-09-11T04:52:18,751 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/R_leaping.cpp: In member function ‘virtual void R1_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2025-09-11T04:52:18,751 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:18,751 40 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices, propensities, numFirings, gen); 2025-09-11T04:52:18,751 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:18,751 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:18,943 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/R_leaping.cpp: In member function ‘virtual void R0_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2025-09-11T04:52:18,943 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/R_leaping.cpp:21:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:18,943 21 | R0Leaping::sampleNumFirings(L, cumPropensities, numFirings, gen); 2025-09-11T04:52:18,943 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:19,462 [ 87%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/reaction.cpp.o 2025-09-11T04:52:31,111 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_third_order_Test::TestBody()’: 2025-09-11T04:52:31,111 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:31,111 181 | reaction.computeGradPropensity(numSpecies, gradients); 2025-09-11T04:52:31,111 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:31,111 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:32,873 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_first_order_Test::TestBody()’: 2025-09-11T04:52:32,873 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:32,873 151 | reaction.computeGradPropensity(numSpecies, gradients); 2025-09-11T04:52:32,873 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:32,873 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,235 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_second_order_Test::TestBody()’: 2025-09-11T04:52:33,235 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,235 167 | reaction.computeGradPropensity(numSpecies, gradients); 2025-09-11T04:52:33,235 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:33,235 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,730 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp: In member function ‘virtual void reaction_muHat_sigmaHatSquare_Test::TestBody()’: 2025-09-11T04:52:33,730 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,730 200 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2025-09-11T04:52:33,731 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:33,731 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,731 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,735 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,735 218 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2025-09-11T04:52:33,735 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:52:33,735 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:33,735 /tmp/pip-wheel-hyh3cl7c/pystochsim_558eb9f36efd4ab78faa3926e324ae88/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:52:38,678 [ 90%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/reaction_parser.cpp.o 2025-09-11T04:52:53,814 [ 92%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/ssa.cpp.o 2025-09-11T04:53:04,482 [ 95%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/tau_leaping.cpp.o 2025-09-11T04:53:15,036 [ 97%] Building CXX object tests/units/CMakeFiles/test_stochsim.dir/utils.cpp.o 2025-09-11T04:53:23,865 [100%] Linking CXX executable test_stochsim 2025-09-11T04:53:24,750 [100%] Built target test_stochsim 2025-09-11T04:53:24,962 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-11T04:53:24,963 !! 2025-09-11T04:53:24,963 ******************************************************************************** 2025-09-11T04:53:24,963 Please avoid running ``setup.py`` directly. 2025-09-11T04:53:24,963 Instead, use pypa/build, pypa/installer or other 2025-09-11T04:53:24,963 standards-based tools. 2025-09-11T04:53:24,963 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-11T04:53:24,963 or your builds will no longer be supported. 2025-09-11T04:53:24,964 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-11T04:53:24,964 ******************************************************************************** 2025-09-11T04:53:24,964 !! 2025-09-11T04:53:24,964 self.initialize_options() 2025-09-11T04:53:25,051 installing to build/bdist.linux-armv7l/wheel 2025-09-11T04:53:25,051 running install 2025-09-11T04:53:25,075 running install_lib 2025-09-11T04:53:25,160 creating build/bdist.linux-armv7l/wheel 2025-09-11T04:53:25,161 copying build/lib.linux-armv7l-cpython-313/pystochsim.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-09-11T04:53:25,163 running install_egg_info 2025-09-11T04:53:25,251 running egg_info 2025-09-11T04:53:25,333 writing pystochsim.egg-info/PKG-INFO 2025-09-11T04:53:25,335 writing dependency_links to pystochsim.egg-info/dependency_links.txt 2025-09-11T04:53:25,336 writing top-level names to pystochsim.egg-info/top_level.txt 2025-09-11T04:53:25,433 reading manifest file 'pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:53:25,459 reading manifest template 'MANIFEST.in' 2025-09-11T04:53:25,525 adding license file 'LICENSE' 2025-09-11T04:53:25,546 writing manifest file 'pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:53:25,547 Copying pystochsim.egg-info to build/bdist.linux-armv7l/wheel/./pystochsim-1.1.0-py3.13.egg-info 2025-09-11T04:53:25,549 running install_scripts 2025-09-11T04:53:25,605 creating build/bdist.linux-armv7l/wheel/pystochsim-1.1.0.dist-info/WHEEL 2025-09-11T04:53:25,606 creating '/tmp/pip-wheel-icerjv81/pystochsim-1.1.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-11T04:53:25,661 adding 'pystochsim.cpython-313-arm-linux-gnueabihf.so' 2025-09-11T04:53:25,664 adding 'pystochsim-1.1.0.dist-info/licenses/LICENSE' 2025-09-11T04:53:25,665 adding 'pystochsim-1.1.0.dist-info/METADATA' 2025-09-11T04:53:25,666 adding 'pystochsim-1.1.0.dist-info/WHEEL' 2025-09-11T04:53:25,667 adding 'pystochsim-1.1.0.dist-info/top_level.txt' 2025-09-11T04:53:25,668 adding 'pystochsim-1.1.0.dist-info/RECORD' 2025-09-11T04:53:25,668 removing build/bdist.linux-armv7l/wheel 2025-09-11T04:53:25,782 Building wheel for pystochsim (setup.py): finished with status 'done' 2025-09-11T04:53:25,785 Created wheel for pystochsim: filename=pystochsim-1.1.0-cp313-cp313-linux_armv7l.whl size=108186 sha256=db343fe50741dc1e40b1c17b30b326aa507ca4ea5533a4e6b85086baab8acc88 2025-09-11T04:53:25,785 Stored in directory: /tmp/pip-ephem-wheel-cache-k21upvg3/wheels/19/0c/2c/95d9eff8c4ed49ef66a2beb7ca57baba5191c53ea8391be591 2025-09-11T04:53:25,843 Successfully built pystochsim 2025-09-11T04:53:25,847 Removed build tracker: '/tmp/pip-build-tracker-_w686_w2'