2025-09-11T04:43:24,763 Created temporary directory: /tmp/pip-build-tracker-vdncxemh 2025-09-11T04:43:24,764 Initialized build tracking at /tmp/pip-build-tracker-vdncxemh 2025-09-11T04:43:24,764 Created build tracker: /tmp/pip-build-tracker-vdncxemh 2025-09-11T04:43:24,764 Entered build tracker: /tmp/pip-build-tracker-vdncxemh 2025-09-11T04:43:24,765 Created temporary directory: /tmp/pip-wheel-eird_56h 2025-09-11T04:43:24,768 Created temporary directory: /tmp/pip-ephem-wheel-cache-dwavob34 2025-09-11T04:43:24,829 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-11T04:43:24,832 2 location(s) to search for versions of pystochsim: 2025-09-11T04:43:24,832 * https://pypi.org/simple/pystochsim/ 2025-09-11T04:43:24,832 * https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:43:24,832 Fetching project page and analyzing links: https://pypi.org/simple/pystochsim/ 2025-09-11T04:43:24,833 Getting page https://pypi.org/simple/pystochsim/ 2025-09-11T04:43:24,834 Found index url https://pypi.org/simple/ 2025-09-11T04:43:24,982 Fetched page https://pypi.org/simple/pystochsim/ as application/vnd.pypi.simple.v1+json 2025-09-11T04:43:24,984 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 2025-09-11T04:43:24,984 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 2025-09-11T04:43:24,985 Fetching project page and analyzing links: https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:43:24,985 Getting page https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:43:24,986 Found index url https://www.piwheels.org/simple/ 2025-09-11T04:43:25,074 Fetched page https://www.piwheels.org/simple/pystochsim/ as text/html 2025-09-11T04:43:25,077 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) 2025-09-11T04:43:25,077 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) 2025-09-11T04:43:25,077 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) 2025-09-11T04:43:25,077 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) 2025-09-11T04:43:25,077 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) 2025-09-11T04:43:25,078 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) 2025-09-11T04:43:25,078 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) 2025-09-11T04:43:25,078 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) 2025-09-11T04:43:25,078 Skipping link: not a file: https://www.piwheels.org/simple/pystochsim/ 2025-09-11T04:43:25,078 Skipping link: not a file: https://pypi.org/simple/pystochsim/ 2025-09-11T04:43:25,102 Given no hashes to check 1 links for project 'pystochsim': discarding no candidates 2025-09-11T04:43:25,104 Collecting pystochsim==1.0.0 2025-09-11T04:43:25,105 Created temporary directory: /tmp/pip-unpack-jxj77ce7 2025-09-11T04:43:25,253 Downloading pystochsim-1.0.0.tar.gz (1.2 MB) 2025-09-11T04:43:25,975 Added pystochsim==1.0.0 from https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz to build tracker '/tmp/pip-build-tracker-vdncxemh' 2025-09-11T04:43:25,976 Running setup.py (path:/tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/setup.py) egg_info for package pystochsim 2025-09-11T04:43:25,977 Created temporary directory: /tmp/pip-pip-egg-info-_jg2r3j3 2025-09-11T04:43:25,977 Preparing metadata (setup.py): started 2025-09-11T04:43:25,978 Running command python setup.py egg_info 2025-09-11T04:43:27,321 running egg_info 2025-09-11T04:43:27,412 creating /tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info 2025-09-11T04:43:27,413 writing /tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info/PKG-INFO 2025-09-11T04:43:27,414 writing dependency_links to /tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info/dependency_links.txt 2025-09-11T04:43:27,415 writing top-level names to /tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info/top_level.txt 2025-09-11T04:43:27,415 writing manifest file '/tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:43:27,589 reading manifest file '/tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:43:27,590 reading manifest template 'MANIFEST.in' 2025-09-11T04:43:27,641 adding license file 'LICENSE' 2025-09-11T04:43:27,656 writing manifest file '/tmp/pip-pip-egg-info-_jg2r3j3/pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:43:27,787 Preparing metadata (setup.py): finished with status 'done' 2025-09-11T04:43:27,792 Source in /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb has version 1.0.0, which satisfies requirement pystochsim==1.0.0 from https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz 2025-09-11T04:43:27,792 Removed pystochsim==1.0.0 from https://files.pythonhosted.org/packages/08/4f/07ff0c61259abdba9a979cb58c1d52eb991d7ffacf6d323dc56e85cdd3d7/pystochsim-1.0.0.tar.gz from build tracker '/tmp/pip-build-tracker-vdncxemh' 2025-09-11T04:43:27,796 Created temporary directory: /tmp/pip-unpack-auonw5m_ 2025-09-11T04:43:27,797 Created temporary directory: /tmp/pip-unpack-0dch39kd 2025-09-11T04:43:27,797 Building wheels for collected packages: pystochsim 2025-09-11T04:43:27,798 Created temporary directory: /tmp/pip-wheel-7qqkns5m 2025-09-11T04:43:27,799 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 2025-09-11T04:43:27,800 Building wheel for pystochsim (setup.py): started 2025-09-11T04:43:27,801 Destination directory: /tmp/pip-wheel-7qqkns5m 2025-09-11T04:43:27,801 Running command python setup.py bdist_wheel 2025-09-11T04:43:29,054 running bdist_wheel 2025-09-11T04:43:29,444 running build 2025-09-11T04:43:29,444 running build_ext 2025-09-11T04:43:29,502 CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): 2025-09-11T04:43:29,502 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:43:29,503 CMake. 2025-09-11T04:43:29,503 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:43:29,503 to tell CMake that the project requires at least but has been updated 2025-09-11T04:43:29,503 to work with policies introduced by or earlier. 2025-09-11T04:43:29,784 -- The C compiler identification is GNU 14.2.0 2025-09-11T04:43:30,132 -- The CXX compiler identification is GNU 14.2.0 2025-09-11T04:43:30,177 -- Detecting C compiler ABI info 2025-09-11T04:43:30,632 -- Detecting C compiler ABI info - done 2025-09-11T04:43:30,704 -- Check for working C compiler: /usr/bin/cc - skipped 2025-09-11T04:43:30,706 -- Detecting C compile features 2025-09-11T04:43:30,708 -- Detecting C compile features - done 2025-09-11T04:43:30,768 -- Detecting CXX compiler ABI info 2025-09-11T04:43:31,260 -- Detecting CXX compiler ABI info - done 2025-09-11T04:43:31,342 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2025-09-11T04:43:31,344 -- Detecting CXX compile features 2025-09-11T04:43:31,348 -- Detecting CXX compile features - done 2025-09-11T04:43:31,386 CMake Deprecation Warning at extern/json/CMakeLists.txt:1 (cmake_minimum_required): 2025-09-11T04:43:31,386 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:43:31,386 CMake. 2025-09-11T04:43:31,386 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:43:31,387 to tell CMake that the project requires at least but has been updated 2025-09-11T04:43:31,387 to work with policies introduced by or earlier. 2025-09-11T04:43:31,425 -- Using the multi-header code from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/ 2025-09-11T04:43:31,433 CMake Deprecation Warning at extern/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2025-09-11T04:43:31,433 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:43:31,433 CMake. 2025-09-11T04:43:31,433 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:43:31,433 to tell CMake that the project requires at least but has been updated 2025-09-11T04:43:31,433 to work with policies introduced by or earlier. 2025-09-11T04:43:31,451 -- pybind11 v2.11.0 dev1 2025-09-11T04:43:31,458 CMake Warning (dev) at extern/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package): 2025-09-11T04:43:31,458 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2025-09-11T04:43:31,458 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2025-09-11T04:43:31,458 the cmake_policy command to set the policy and suppress this warning. 2025-09-11T04:43:31,458 Call Stack (most recent call first): 2025-09-11T04:43:31,458 extern/pybind11/tools/pybind11Tools.cmake:50 (find_package) 2025-09-11T04:43:31,459 extern/pybind11/tools/pybind11Common.cmake:180 (include) 2025-09-11T04:43:31,459 extern/pybind11/CMakeLists.txt:200 (include) 2025-09-11T04:43:31,459 This warning is for project developers. Use -Wno-dev to suppress it. 2025-09-11T04:43:31,531 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.13.5", minimum required is "3.6") 2025-09-11T04:43:31,627 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so 2025-09-11T04:43:31,638 -- Performing Test HAS_FLTO 2025-09-11T04:43:32,346 -- Performing Test HAS_FLTO - Success 2025-09-11T04:43:32,370 CMake Deprecation Warning at tests/extern/googletest/CMakeLists.txt:4 (cmake_minimum_required): 2025-09-11T04:43:32,370 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:43:32,370 CMake. 2025-09-11T04:43:32,370 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:43:32,370 to tell CMake that the project requires at least but has been updated 2025-09-11T04:43:32,371 to work with policies introduced by or earlier. 2025-09-11T04:43:32,383 CMake Deprecation Warning at tests/extern/googletest/googletest/CMakeLists.txt:49 (cmake_minimum_required): 2025-09-11T04:43:32,383 Compatibility with CMake < 3.10 will be removed from a future version of 2025-09-11T04:43:32,383 CMake. 2025-09-11T04:43:32,384 Update the VERSION argument value. Or, use the ... syntax 2025-09-11T04:43:32,384 to tell CMake that the project requires at least but has been updated 2025-09-11T04:43:32,384 to work with policies introduced by or earlier. 2025-09-11T04:43:33,023 -- Found Python: /usr/bin/python3 (found version "3.13.5") found components: Interpreter 2025-09-11T04:43:33,029 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2025-09-11T04:43:33,526 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success 2025-09-11T04:43:33,531 -- Found Threads: TRUE 2025-09-11T04:43:33,542 -- Configuring done (4.0s) 2025-09-11T04:43:33,640 -- Generating done (0.1s) 2025-09-11T04:43:33,640 CMake Warning: 2025-09-11T04:43:33,641 Manually-specified variables were not used by the project: 2025-09-11T04:43:33,641 EXAMPLE_VERSION_INFO 2025-09-11T04:43:33,641 -- Build files have been written to: /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/build/temp.linux-armv7l-cpython-313/pystochsim 2025-09-11T04:43:33,944 [ 2%] Building CXX object source/ssm/CMakeFiles/ssm.dir/factory.cpp.o 2025-09-11T04:43:57,505 [ 5%] Building CXX object source/ssm/CMakeFiles/ssm.dir/problem.cpp.o 2025-09-11T04:44:03,600 [ 7%] Building CXX object source/ssm/CMakeFiles/ssm.dir/reaction.cpp.o 2025-09-11T04:44:06,428 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/reaction.cpp: In member function ‘void ssm::Reaction::computeGradPropensity(std::span, std::span) const’: 2025-09-11T04:44:06,428 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/reaction.cpp:131:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:06,428 131 | void Reaction::computeGradPropensity(std::span speciesNumber, 2025-09-11T04:44:06,429 | ^~~~~~~~ 2025-09-11T04:44:06,478 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/reaction.cpp: In member function ‘void ssm::Reaction::addContributionMuHatSigmaHatSquare(ssm::real, std::span, std::span) const’: 2025-09-11T04:44:06,479 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:06,479 152 | void Reaction::addContributionMuHatSigmaHatSquare(real propensity, 2025-09-11T04:44:06,479 | ^~~~~~~~ 2025-09-11T04:44:06,479 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/reaction.cpp:152:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:07,434 [ 10%] Building CXX object source/ssm/CMakeFiles/ssm.dir/reaction_parser.cpp.o 2025-09-11T04:44:14,500 [ 12%] Building CXX object source/ssm/CMakeFiles/ssm.dir/simulation.cpp.o 2025-09-11T04:44:18,283 [ 15%] Building CXX object source/ssm/CMakeFiles/ssm.dir/diagnostics/collect_tau.cpp.o 2025-09-11T04:44:21,190 [ 17%] Building CXX object source/ssm/CMakeFiles/ssm.dir/diagnostics/diagnostic.cpp.o 2025-09-11T04:44:23,779 [ 20%] Building CXX object source/ssm/CMakeFiles/ssm.dir/diagnostics/mean_trajectory.cpp.o 2025-09-11T04:44:26,940 [ 22%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/R0_leaping.cpp.o 2025-09-11T04:44:30,165 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R0_leaping.cpp: In static member function ‘static void ssm::R0Leaping::sampleNumFirings(int, std::span, std::span, std::mt19937&)’: 2025-09-11T04:44:30,165 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R0_leaping.cpp:43:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:30,166 43 | void R0Leaping::sampleNumFirings(int L, 2025-09-11T04:44:30,166 | ^~~~~~~~~ 2025-09-11T04:44:30,403 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R0_leaping.cpp: In member function ‘virtual void ssm::R0Leaping::advance()’: 2025-09-11T04:44:30,404 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R0_leaping.cpp:35:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:30,404 35 | sampleNumFirings(L_, cumPropensities_, numFirings_, gen_); 2025-09-11T04:44:30,404 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:30,800 [ 25%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/R1_leaping.cpp.o 2025-09-11T04:44:35,163 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R1_leaping.cpp: In static member function ‘static void ssm::R1Leaping::sampleNumFirings(int, std::span, std::span, std::span, std::mt19937&)’: 2025-09-11T04:44:35,163 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R1_leaping.cpp:57:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:35,163 57 | void R1Leaping::sampleNumFirings(int L, 2025-09-11T04:44:35,163 | ^~~~~~~~~ 2025-09-11T04:44:35,414 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R1_leaping.cpp: In member function ‘virtual void ssm::R1Leaping::advance()’: 2025-09-11T04:44:35,414 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:35,415 45 | sampleNumFirings(L_, sortedReactionsIndices_, propensities_, numFirings_, gen_); 2025-09-11T04:44:35,415 | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:35,415 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R1_leaping.cpp:45:21: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:35,857 [ 27%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/R_leaping.cpp.o 2025-09-11T04:44:41,022 In function ‘void ssm::computeMuHatSigmaHatSq(std::span, std::span, std::span, std::span)’, 2025-09-11T04:44:41,022 inlined from ‘virtual void ssm::RLeaping::advance()’ at /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:136:27: 2025-09-11T04:44:41,022 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:41,022 106 | r.addContributionMuHatSigmaHatSquare(a, muHat, sigmaHatSq); 2025-09-11T04:44:41,022 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:41,023 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:41,023 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:106:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:41,024 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp: In member function ‘virtual void ssm::RLeaping::advance()’: 2025-09-11T04:44:41,024 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:149:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:41,024 149 | R0Leaping::sampleNumFirings(L, cumPropensities_, numFirings_, gen_); 2025-09-11T04:44:41,024 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:41,025 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:41,025 153 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices_, 2025-09-11T04:44:41,025 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:41,025 154 | propensities_, numFirings_, gen_); 2025-09-11T04:44:41,026 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:41,026 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/solvers/R_leaping.cpp:153:40: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:41,706 [ 30%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/solver.cpp.o 2025-09-11T04:44:43,318 [ 32%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/ssa.cpp.o 2025-09-11T04:44:46,931 [ 35%] Building CXX object source/ssm/CMakeFiles/ssm.dir/solvers/tau_leaping.cpp.o 2025-09-11T04:44:54,235 [ 37%] Building CXX object source/ssm/CMakeFiles/ssm.dir/utils/algorithms.cpp.o 2025-09-11T04:44:58,165 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/utils/algorithms.cpp: In function ‘void ssm::utils::argsortDecreasingOrder(std::span, std::span)’: 2025-09-11T04:44:58,165 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/utils/algorithms.cpp:23:6: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:58,165 23 | void argsortDecreasingOrder(std::span a, std::span indices) 2025-09-11T04:44:58,165 | ^~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:44:58,309 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/utils/algorithms.cpp: In function ‘size_t ssm::utils::choose(std::span, std::mt19937&)’: 2025-09-11T04:44:58,309 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/utils/algorithms.cpp:9:8: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:44:58,309 9 | size_t choose(std::span cumulativeProbs, std::mt19937& gen) 2025-09-11T04:44:58,309 | ^~~~~~ 2025-09-11T04:44:58,486 [ 40%] Building CXX object source/ssm/CMakeFiles/ssm.dir/utils/exceptions.cpp.o 2025-09-11T04:45:00,153 [ 42%] Building CXX object source/ssm/CMakeFiles/ssm.dir/utils/strprintf.cpp.o 2025-09-11T04:45:01,798 [ 45%] Linking CXX static library libssm.a 2025-09-11T04:45:02,282 [ 45%] Built target ssm 2025-09-11T04:45:02,406 [ 47%] Building CXX object apps/CMakeFiles/run_simulation.dir/run_simulation.cpp.o 2025-09-11T04:45:16,931 In file included from /usr/include/c++/14/map:62, 2025-09-11T04:45:16,932 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2025-09-11T04:45:16,932 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/adl_serializer.hpp:14, 2025-09-11T04:45:16,932 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/json.hpp:35, 2025-09-11T04:45:16,932 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/factory.h:9, 2025-09-11T04:45:16,932 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/apps/run_simulation.cpp:1: 2025-09-11T04:45:16,932 /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<> > >]’: 2025-09-11T04:45:16,932 /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 2025-09-11T04:45:16,933 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-11T04:45:16,933 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:18,568 In file included from /usr/include/c++/14/map:63: 2025-09-11T04:45:18,568 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<> > >]’, 2025-09-11T04:45:18,568 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-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/input/json_sax.hpp:442:76: 2025-09-11T04:45:18,569 /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 2025-09-11T04:45:18,569 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:45:18,569 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:18,569 514 | std::tuple(__k), 2025-09-11T04:45:18,569 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:18,569 515 | std::tuple<>()); 2025-09-11T04:45:18,569 | ~~~~~~~~~~~~~~~ 2025-09-11T04:45:18,993 /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<> > >]’: 2025-09-11T04:45:18,993 /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 2025-09-11T04:45:18,993 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:45:18,993 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:18,993 514 | std::tuple(__k), 2025-09-11T04:45:18,994 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:18,994 515 | std::tuple<>()); 2025-09-11T04:45:18,994 | ~~~~~~~~~~~~~~~ 2025-09-11T04:45:22,920 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<> > >]’, 2025-09-11T04:45:22,920 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-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/input/json_sax.hpp:247:72, 2025-09-11T04:45:22,920 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-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/input/parser.hpp:418:21: 2025-09-11T04:45:22,921 /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 2025-09-11T04:45:22,921 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:45:22,921 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:22,921 514 | std::tuple(__k), 2025-09-11T04:45:22,921 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:45:22,921 515 | std::tuple<>()); 2025-09-11T04:45:22,921 | ~~~~~~~~~~~~~~~ 2025-09-11T04:45:26,148 [ 50%] Linking CXX executable run_simulation 2025-09-11T04:45:26,857 [ 50%] Built target run_simulation 2025-09-11T04:45:26,975 [ 52%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/bindings.cpp.o 2025-09-11T04:45:39,965 [ 55%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/problem.cpp.o 2025-09-11T04:45:56,472 [ 57%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/run.cpp.o 2025-09-11T04:46:14,022 [ 60%] Building CXX object source/bindings/CMakeFiles/pystochsim.dir/solvers.cpp.o 2025-09-11T04:46:31,682 [ 62%] Linking CXX shared module /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/build/lib.linux-armv7l-cpython-313/pystochsim.cpython-313-arm-linux-gnueabihf.so 2025-09-11T04:46:32,851 lto-wrapper: warning: using serial compilation of 3 LTRANS jobs 2025-09-11T04:46:32,851 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2025-09-11T04:46:54,251 [ 62%] Built target pystochsim 2025-09-11T04:46:54,379 [ 65%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest.dir/src/gtest-all.cc.o 2025-09-11T04:47:35,161 [ 67%] Linking CXX static library ../../../../lib/libgtest.a 2025-09-11T04:47:35,513 [ 67%] Built target gtest 2025-09-11T04:47:35,630 [ 70%] Building CXX object tests/extern/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o 2025-09-11T04:47:40,140 [ 72%] Linking CXX static library ../../../../lib/libgtest_main.a 2025-09-11T04:47:40,439 [ 72%] Built target gtest_main 2025-09-11T04:47:40,556 [ 75%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/main.cpp.o 2025-09-11T04:47:46,750 [ 77%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/diagnostics.cpp.o 2025-09-11T04:47:57,213 [ 80%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/exceptions.cpp.o 2025-09-11T04:48:04,882 [ 82%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/factory.cpp.o 2025-09-11T04:48:21,594 In file included from /usr/include/c++/14/map:62, 2025-09-11T04:48:21,594 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/conversions/from_json.hpp:15, 2025-09-11T04:48:21,594 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/adl_serializer.hpp:14, 2025-09-11T04:48:21,594 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/json.hpp:35, 2025-09-11T04:48:21,594 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/source/ssm/factory.h:9, 2025-09-11T04:48:21,594 from /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/factory.cpp:1: 2025-09-11T04:48:21,595 /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<> > >]’: 2025-09-11T04:48:21,595 /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 2025-09-11T04:48:21,595 2456 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: 2025-09-11T04:48:21,595 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:22,714 In file included from /usr/include/c++/14/map:63: 2025-09-11T04:48:22,714 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<> > >]’, 2025-09-11T04:48:22,715 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-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/input/json_sax.hpp:442:76: 2025-09-11T04:48:22,715 /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 2025-09-11T04:48:22,715 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:48:22,715 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:22,715 514 | std::tuple(__k), 2025-09-11T04:48:22,715 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:22,715 515 | std::tuple<>()); 2025-09-11T04:48:22,715 | ~~~~~~~~~~~~~~~ 2025-09-11T04:48:23,109 /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<> > >]’: 2025-09-11T04:48:23,109 /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 2025-09-11T04:48:23,109 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:48:23,109 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:23,110 514 | std::tuple(__k), 2025-09-11T04:48:23,110 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:23,110 515 | std::tuple<>()); 2025-09-11T04:48:23,110 | ~~~~~~~~~~~~~~~ 2025-09-11T04:48:26,707 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<> > >]’, 2025-09-11T04:48:26,707 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-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/input/json_sax.hpp:247:72, 2025-09-11T04:48:26,707 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-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/extern/json/include/nlohmann/detail/input/parser.hpp:418:21: 2025-09-11T04:48:26,707 /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 2025-09-11T04:48:26,707 513 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, 2025-09-11T04:48:26,708 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:26,708 514 | std::tuple(__k), 2025-09-11T04:48:26,708 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:26,708 515 | std::tuple<>()); 2025-09-11T04:48:26,708 | ~~~~~~~~~~~~~~~ 2025-09-11T04:48:30,957 [ 85%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/R_leaping.cpp.o 2025-09-11T04:48:39,248 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/R_leaping.cpp: In member function ‘virtual void R1_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2025-09-11T04:48:39,248 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:39,248 40 | R1Leaping::sampleNumFirings(L, sortedReactionsIndices, propensities, numFirings, gen); 2025-09-11T04:48:39,248 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:39,249 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/R_leaping.cpp:40:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:39,441 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/R_leaping.cpp: In member function ‘virtual void R0_sampling_numFirings_sum_up_to_L_Test::TestBody()’: 2025-09-11T04:48:39,441 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/R_leaping.cpp:21:36: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:39,442 21 | R0Leaping::sampleNumFirings(L, cumPropensities, numFirings, gen); 2025-09-11T04:48:39,442 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:39,964 [ 87%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/reaction.cpp.o 2025-09-11T04:48:50,565 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_third_order_Test::TestBody()’: 2025-09-11T04:48:50,566 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:50,566 181 | reaction.computeGradPropensity(numSpecies, gradients); 2025-09-11T04:48:50,566 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:50,566 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:181:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,166 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_first_order_Test::TestBody()’: 2025-09-11T04:48:52,166 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,166 151 | reaction.computeGradPropensity(numSpecies, gradients); 2025-09-11T04:48:52,166 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:52,166 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:151:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,500 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp: In member function ‘virtual void reaction_grad_propensity_second_order_Test::TestBody()’: 2025-09-11T04:48:52,500 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,500 167 | reaction.computeGradPropensity(numSpecies, gradients); 2025-09-11T04:48:52,500 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:52,501 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:167:35: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,950 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp: In member function ‘virtual void reaction_muHat_sigmaHatSquare_Test::TestBody()’: 2025-09-11T04:48:52,950 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,950 200 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2025-09-11T04:48:52,950 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:52,950 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,951 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:200:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,955 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,955 218 | r.addContributionMuHatSigmaHatSquare(propensities[0], muHat, sigmaHatSq); 2025-09-11T04:48:52,955 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-11T04:48:52,956 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:52,956 /tmp/pip-wheel-eird_56h/pystochsim_dd77b1c6baa54fe3b3fe14ca6d55d3eb/tests/units/reaction.cpp:218:45: note: parameter passing for argument of type ‘std::span’ changed in GCC 7.1 2025-09-11T04:48:57,583 [ 90%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/reaction_parser.cpp.o 2025-09-11T04:49:12,722 [ 92%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/ssa.cpp.o 2025-09-11T04:49:24,470 [ 95%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/tau_leaping.cpp.o 2025-09-11T04:49:35,120 [ 97%] Building CXX object tests/units/CMakeFiles/test_ssm.dir/utils.cpp.o 2025-09-11T04:49:43,985 [100%] Linking CXX executable test_ssm 2025-09-11T04:49:44,929 [100%] Built target test_ssm 2025-09-11T04:49:45,151 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated. 2025-09-11T04:49:45,152 !! 2025-09-11T04:49:45,152 ******************************************************************************** 2025-09-11T04:49:45,152 Please avoid running ``setup.py`` directly. 2025-09-11T04:49:45,152 Instead, use pypa/build, pypa/installer or other 2025-09-11T04:49:45,152 standards-based tools. 2025-09-11T04:49:45,152 By 2025-Oct-31, you need to update your project and remove deprecated calls 2025-09-11T04:49:45,153 or your builds will no longer be supported. 2025-09-11T04:49:45,153 See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details. 2025-09-11T04:49:45,153 ******************************************************************************** 2025-09-11T04:49:45,153 !! 2025-09-11T04:49:45,153 self.initialize_options() 2025-09-11T04:49:45,254 installing to build/bdist.linux-armv7l/wheel 2025-09-11T04:49:45,255 running install 2025-09-11T04:49:45,281 running install_lib 2025-09-11T04:49:45,383 creating build/bdist.linux-armv7l/wheel 2025-09-11T04:49:45,384 copying build/lib.linux-armv7l-cpython-313/pystochsim.cpython-313-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/. 2025-09-11T04:49:45,386 running install_egg_info 2025-09-11T04:49:45,494 running egg_info 2025-09-11T04:49:45,599 writing pystochsim.egg-info/PKG-INFO 2025-09-11T04:49:45,601 writing dependency_links to pystochsim.egg-info/dependency_links.txt 2025-09-11T04:49:45,601 writing top-level names to pystochsim.egg-info/top_level.txt 2025-09-11T04:49:45,706 reading manifest file 'pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:49:45,737 reading manifest template 'MANIFEST.in' 2025-09-11T04:49:45,817 adding license file 'LICENSE' 2025-09-11T04:49:45,842 writing manifest file 'pystochsim.egg-info/SOURCES.txt' 2025-09-11T04:49:45,843 Copying pystochsim.egg-info to build/bdist.linux-armv7l/wheel/./pystochsim-1.0.0-py3.13.egg-info 2025-09-11T04:49:45,845 running install_scripts 2025-09-11T04:49:45,908 creating build/bdist.linux-armv7l/wheel/pystochsim-1.0.0.dist-info/WHEEL 2025-09-11T04:49:45,910 creating '/tmp/pip-wheel-7qqkns5m/pystochsim-1.0.0-cp313-cp313-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2025-09-11T04:49:45,968 adding 'pystochsim.cpython-313-arm-linux-gnueabihf.so' 2025-09-11T04:49:45,971 adding 'pystochsim-1.0.0.dist-info/licenses/LICENSE' 2025-09-11T04:49:45,972 adding 'pystochsim-1.0.0.dist-info/METADATA' 2025-09-11T04:49:45,972 adding 'pystochsim-1.0.0.dist-info/WHEEL' 2025-09-11T04:49:45,973 adding 'pystochsim-1.0.0.dist-info/top_level.txt' 2025-09-11T04:49:45,974 adding 'pystochsim-1.0.0.dist-info/RECORD' 2025-09-11T04:49:45,974 removing build/bdist.linux-armv7l/wheel 2025-09-11T04:49:46,115 Building wheel for pystochsim (setup.py): finished with status 'done' 2025-09-11T04:49:46,117 Created wheel for pystochsim: filename=pystochsim-1.0.0-cp313-cp313-linux_armv7l.whl size=107987 sha256=e526a41dc8cbfb5a86dd8143fe3a8ed3c0e93e5de284e6fb3a5b1e13844a702c 2025-09-11T04:49:46,118 Stored in directory: /tmp/pip-ephem-wheel-cache-dwavob34/wheels/62/17/c6/cf4c8ae757f0ca63200e49826d82e63ca645bcf966b6ace54f 2025-09-11T04:49:46,126 Successfully built pystochsim 2025-09-11T04:49:46,128 Removed build tracker: '/tmp/pip-build-tracker-vdncxemh'