2023-11-26T02:27:43,786 Created temporary directory: /tmp/pip-build-tracker-duhcm4xx
2023-11-26T02:27:43,788 Initialized build tracking at /tmp/pip-build-tracker-duhcm4xx
2023-11-26T02:27:43,788 Created build tracker: /tmp/pip-build-tracker-duhcm4xx
2023-11-26T02:27:43,788 Entered build tracker: /tmp/pip-build-tracker-duhcm4xx
2023-11-26T02:27:43,789 Created temporary directory: /tmp/pip-wheel-ssneg2um
2023-11-26T02:27:43,793 Created temporary directory: /tmp/pip-ephem-wheel-cache-z0ms8bq7
2023-11-26T02:27:43,817 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-11-26T02:27:43,820 2 location(s) to search for versions of ambermdrun:
2023-11-26T02:27:43,820 * https://pypi.org/simple/ambermdrun/
2023-11-26T02:27:43,820 * https://www.piwheels.org/simple/ambermdrun/
2023-11-26T02:27:43,821 Fetching project page and analyzing links: https://pypi.org/simple/ambermdrun/
2023-11-26T02:27:43,822 Getting page https://pypi.org/simple/ambermdrun/
2023-11-26T02:27:43,823 Found index url https://pypi.org/simple/
2023-11-26T02:27:43,872 Fetched page https://pypi.org/simple/ambermdrun/ as application/vnd.pypi.simple.v1+json
2023-11-26T02:27:43,874   Found link https://files.pythonhosted.org/packages/d6/db/18b74901842877c76f511fc9f2a0ed7f2ac8a09b72bc8926a79aa8e3613d/AmberMDrun-0.0.1.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.1
2023-11-26T02:27:43,875   Found link https://files.pythonhosted.org/packages/72/fa/7827263fc857e7ac22274ad3e8a13f417473309556ea106aed8ac61301b9/AmberMDrun-0.0.2.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.2
2023-11-26T02:27:43,876   Found link https://files.pythonhosted.org/packages/b4/d4/ba615c848cd91799c5be3f76cadb93a66892c729e88166d7d8282d093645/AmberMDrun-0.0.3.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.3
2023-11-26T02:27:43,876   Found link https://files.pythonhosted.org/packages/ed/d0/cf9b1bd460d898e4f264c3d2af7ef5838fa6c67044a2a798d4c1bf33bd96/AmberMDrun-0.0.4.zip (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.4
2023-11-26T02:27:43,877   Found link https://files.pythonhosted.org/packages/6b/db/79e3aaee51246a8df9c015c9f2774a29302956fb39e81a2d2fcb84efcacf/AmberMDrun-0.0.5.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.5
2023-11-26T02:27:43,877 Fetching project page and analyzing links: https://www.piwheels.org/simple/ambermdrun/
2023-11-26T02:27:43,877 Getting page https://www.piwheels.org/simple/ambermdrun/
2023-11-26T02:27:43,878 Found index url https://www.piwheels.org/simple/
2023-11-26T02:27:43,946 Fetched page https://www.piwheels.org/simple/ambermdrun/ as text/html
2023-11-26T02:27:43,949   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.5-cp311-cp311-linux_armv7l.whl#sha256=73a34492858be5d01779b82c05c41a2bb876ffe2de10bcb9d29bfb1effd1f460 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,950   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.5-cp311-cp311-linux_armv6l.whl#sha256=73a34492858be5d01779b82c05c41a2bb876ffe2de10bcb9d29bfb1effd1f460 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,950   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.3-cp311-cp311-linux_armv7l.whl#sha256=693969c632928d2134a15ee9fa785b3aa17d8c5030a6bd7ac4d6aa44ef836dd8 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,950   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.3-cp311-cp311-linux_armv6l.whl#sha256=693969c632928d2134a15ee9fa785b3aa17d8c5030a6bd7ac4d6aa44ef836dd8 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,950   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.3-cp39-cp39-linux_armv7l.whl#sha256=2cf4272b2c7bc0c08bfdc05d4ae26c24e4c9271aa6b54e75aa8483d86cbe04f4 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,951   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.3-cp39-cp39-linux_armv6l.whl#sha256=2cf4272b2c7bc0c08bfdc05d4ae26c24e4c9271aa6b54e75aa8483d86cbe04f4 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,951   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.2-cp39-cp39-linux_armv7l.whl#sha256=102c06dbbc37b52bacdbde48fd118a1e26403955f46644e6bcd94ddcc27f5df7 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,951   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.2-cp39-cp39-linux_armv6l.whl#sha256=102c06dbbc37b52bacdbde48fd118a1e26403955f46644e6bcd94ddcc27f5df7 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,951   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.1-cp39-cp39-linux_armv7l.whl#sha256=9d7e6f27bf8ed40c3dedf66ef4e92029d07387a88d52cc1879d0fb0cdceecb78 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,951   Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.1-cp39-cp39-linux_armv6l.whl#sha256=9d7e6f27bf8ed40c3dedf66ef4e92029d07387a88d52cc1879d0fb0cdceecb78 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6)
2023-11-26T02:27:43,952 Skipping link: not a file: https://www.piwheels.org/simple/ambermdrun/
2023-11-26T02:27:43,952 Skipping link: not a file: https://pypi.org/simple/ambermdrun/
2023-11-26T02:27:43,970 Given no hashes to check 1 links for project 'ambermdrun': discarding no candidates
2023-11-26T02:27:43,986 Collecting ambermdrun==0.0.5
2023-11-26T02:27:43,988   Created temporary directory: /tmp/pip-unpack-76hvi40j
2023-11-26T02:27:44,033   Downloading AmberMDrun-0.0.5.tar.gz (930 kB)
2023-11-26T02:27:44,866   Added ambermdrun==0.0.5 from https://files.pythonhosted.org/packages/6b/db/79e3aaee51246a8df9c015c9f2774a29302956fb39e81a2d2fcb84efcacf/AmberMDrun-0.0.5.tar.gz to build tracker '/tmp/pip-build-tracker-duhcm4xx'
2023-11-26T02:27:44,873   Created temporary directory: /tmp/pip-build-env-o7kf87bm
2023-11-26T02:27:44,883   Installing build dependencies: started
2023-11-26T02:27:44,884   Running command pip subprocess to install build dependencies
2023-11-26T02:27:46,074   Using pip 23.3.1 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9)
2023-11-26T02:27:46,609   Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2023-11-26T02:27:48,028   Collecting setuptools>=42
2023-11-26T02:27:48,044     Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.0.2-py3-none-any.whl (819 kB)
2023-11-26T02:27:48,285   Collecting wheel
2023-11-26T02:27:48,301     Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.3-py3-none-any.whl (65 kB)
2023-11-26T02:27:48,484   Collecting ninja
2023-11-26T02:27:48,500     Using cached https://www.piwheels.org/simple/ninja/ninja-1.11.1.1-cp39-cp39-linux_armv7l.whl (132 kB)
2023-11-26T02:27:49,130   Collecting cmake>=3.12
2023-11-26T02:27:49,146     Using cached https://www.piwheels.org/simple/cmake/cmake-3.27.7-cp39-cp39-linux_armv7l.whl (19.3 MB)
2023-11-26T02:27:51,925   Installing collected packages: ninja, cmake, wheel, setuptools
2023-11-26T02:27:51,980     Creating /tmp/pip-build-env-o7kf87bm/overlay/bin
2023-11-26T02:27:51,983     changing mode of /tmp/pip-build-env-o7kf87bm/overlay/bin/ninja to 755
2023-11-26T02:27:57,908     changing mode of /tmp/pip-build-env-o7kf87bm/overlay/bin/cmake to 755
2023-11-26T02:27:57,910     changing mode of /tmp/pip-build-env-o7kf87bm/overlay/bin/cpack to 755
2023-11-26T02:27:57,912     changing mode of /tmp/pip-build-env-o7kf87bm/overlay/bin/ctest to 755
2023-11-26T02:27:58,202     changing mode of /tmp/pip-build-env-o7kf87bm/overlay/bin/wheel to 755
2023-11-26T02:28:00,320   Successfully installed cmake-3.27.7 ninja-1.11.1.1 setuptools-69.0.2 wheel-0.41.3
2023-11-26T02:28:00,828   Installing build dependencies: finished with status 'done'
2023-11-26T02:28:00,833   Getting requirements to build wheel: started
2023-11-26T02:28:00,834   Running command Getting requirements to build wheel
2023-11-26T02:28:01,378   running egg_info
2023-11-26T02:28:01,384   writing AmberMDrun.egg-info/PKG-INFO
2023-11-26T02:28:01,387   writing dependency_links to AmberMDrun.egg-info/dependency_links.txt
2023-11-26T02:28:01,388   writing entry points to AmberMDrun.egg-info/entry_points.txt
2023-11-26T02:28:01,390   writing requirements to AmberMDrun.egg-info/requires.txt
2023-11-26T02:28:01,391   writing top-level names to AmberMDrun.egg-info/top_level.txt
2023-11-26T02:28:01,416   reading manifest file 'AmberMDrun.egg-info/SOURCES.txt'
2023-11-26T02:28:01,457   reading manifest template 'MANIFEST.in'
2023-11-26T02:28:01,486   adding license file 'LICENSE'
2023-11-26T02:28:01,504   writing manifest file 'AmberMDrun.egg-info/SOURCES.txt'
2023-11-26T02:28:01,567   Getting requirements to build wheel: finished with status 'done'
2023-11-26T02:28:01,576   Created temporary directory: /tmp/pip-modern-metadata-pou3x6cv
2023-11-26T02:28:01,579   Preparing metadata (pyproject.toml): started
2023-11-26T02:28:01,580   Running command Preparing metadata (pyproject.toml)
2023-11-26T02:28:02,109   running dist_info
2023-11-26T02:28:02,127   creating /tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info
2023-11-26T02:28:02,133   writing /tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/PKG-INFO
2023-11-26T02:28:02,136   writing dependency_links to /tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/dependency_links.txt
2023-11-26T02:28:02,137   writing entry points to /tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/entry_points.txt
2023-11-26T02:28:02,139   writing requirements to /tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/requires.txt
2023-11-26T02:28:02,140   writing top-level names to /tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/top_level.txt
2023-11-26T02:28:02,141   writing manifest file '/tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/SOURCES.txt'
2023-11-26T02:28:02,163   reading manifest file '/tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/SOURCES.txt'
2023-11-26T02:28:02,166   reading manifest template 'MANIFEST.in'
2023-11-26T02:28:02,185   adding license file 'LICENSE'
2023-11-26T02:28:02,198   writing manifest file '/tmp/pip-modern-metadata-pou3x6cv/AmberMDrun.egg-info/SOURCES.txt'
2023-11-26T02:28:02,199   creating '/tmp/pip-modern-metadata-pou3x6cv/AmberMDrun-0.0.5.dist-info'
2023-11-26T02:28:02,363   Preparing metadata (pyproject.toml): finished with status 'done'
2023-11-26T02:28:02,369   Source in /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207 has version 0.0.5, which satisfies requirement ambermdrun==0.0.5 from https://files.pythonhosted.org/packages/6b/db/79e3aaee51246a8df9c015c9f2774a29302956fb39e81a2d2fcb84efcacf/AmberMDrun-0.0.5.tar.gz
2023-11-26T02:28:02,370   Removed ambermdrun==0.0.5 from https://files.pythonhosted.org/packages/6b/db/79e3aaee51246a8df9c015c9f2774a29302956fb39e81a2d2fcb84efcacf/AmberMDrun-0.0.5.tar.gz from build tracker '/tmp/pip-build-tracker-duhcm4xx'
2023-11-26T02:28:02,376 Created temporary directory: /tmp/pip-unpack-7ha12w74
2023-11-26T02:28:02,376 Created temporary directory: /tmp/pip-unpack-v250vtz1
2023-11-26T02:28:02,379 Building wheels for collected packages: ambermdrun
2023-11-26T02:28:02,384   Created temporary directory: /tmp/pip-wheel-2e7d1h2k
2023-11-26T02:28:02,384   Destination directory: /tmp/pip-wheel-2e7d1h2k
2023-11-26T02:28:02,386   Building wheel for ambermdrun (pyproject.toml): started
2023-11-26T02:28:02,387   Running command Building wheel for ambermdrun (pyproject.toml)
2023-11-26T02:28:02,948   running bdist_wheel
2023-11-26T02:28:02,980   running build
2023-11-26T02:28:02,980   running build_py
2023-11-26T02:28:02,988   creating build
2023-11-26T02:28:02,989   creating build/lib.linux-armv7l-cpython-39
2023-11-26T02:28:02,989   creating build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:02,991   copying AmberMDrun/equil.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:02,992   copying AmberMDrun/__init__.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:02,994   copying AmberMDrun/pyamber.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:02,996   copying AmberMDrun/version.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:02,998   copying AmberMDrun/main.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:02,999   copying AmberMDrun/mmpbsa.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:03,003   running build_ext
2023-11-26T02:28:03,439   -- The CXX compiler identification is GNU 10.2.1
2023-11-26T02:28:03,522   -- Detecting CXX compiler ABI info
2023-11-26T02:28:03,853   -- Detecting CXX compiler ABI info - done
2023-11-26T02:28:03,920   -- Check for working CXX compiler: /usr/bin/c++ - skipped
2023-11-26T02:28:03,922   -- Detecting CXX compile features
2023-11-26T02:28:03,926   -- Detecting CXX compile features - done
2023-11-26T02:28:03,952   -- Performing Test COMPILER_SUPPORTS_CXX23
2023-11-26T02:28:04,053   -- Performing Test COMPILER_SUPPORTS_CXX23 - Failed
2023-11-26T02:28:04,057   -- Performing Test COMPILER_SUPPORTS_CXX20
2023-11-26T02:28:04,356   -- Performing Test COMPILER_SUPPORTS_CXX20 - Success
2023-11-26T02:28:04,359   -- Performing Test COMPILER_SUPPORTS_CXX17
2023-11-26T02:28:04,659   -- Performing Test COMPILER_SUPPORTS_CXX17 - Success
2023-11-26T02:28:04,659   -- current platform: Linux
2023-11-26T02:28:04,665   -- Performing Test CMAKE_HAVE_LIBC_PTHREAD
2023-11-26T02:28:04,976   -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
2023-11-26T02:28:04,977   -- Looking for pthread_create in pthreads
2023-11-26T02:28:05,196   -- Looking for pthread_create in pthreads - not found
2023-11-26T02:28:05,197   -- Looking for pthread_create in pthread
2023-11-26T02:28:05,448   -- Looking for pthread_create in pthread - found
2023-11-26T02:28:05,453   -- Found Threads: TRUE
2023-11-26T02:28:05,459   CMake Deprecation Warning at AmberMDrun/extern/pybind11/CMakeLists.txt:8 (cmake_minimum_required):
2023-11-26T02:28:05,460     Compatibility with CMake < 3.5 will be removed from a future version of
2023-11-26T02:28:05,460     CMake.

2023-11-26T02:28:05,460     Update the VERSION argument <min> value or use a ...<max> suffix to tell
2023-11-26T02:28:05,460     CMake that the project does not need compatibility with older versions.


2023-11-26T02:28:05,485   -- pybind11 v2.10.4
2023-11-26T02:28:05,496   CMake Warning (dev) at AmberMDrun/extern/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package):
2023-11-26T02:28:05,496     Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
2023-11-26T02:28:05,497     are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
2023-11-26T02:28:05,497     the cmake_policy command to set the policy and suppress this warning.

2023-11-26T02:28:05,497   Call Stack (most recent call first):
2023-11-26T02:28:05,497     AmberMDrun/extern/pybind11/tools/pybind11Tools.cmake:50 (find_package)
2023-11-26T02:28:05,497     AmberMDrun/extern/pybind11/tools/pybind11Common.cmake:180 (include)
2023-11-26T02:28:05,498     AmberMDrun/extern/pybind11/CMakeLists.txt:208 (include)
2023-11-26T02:28:05,498   This warning is for project developers.  Use -Wno-dev to suppress it.

2023-11-26T02:28:05,575   -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6")
2023-11-26T02:28:06,057   -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so
2023-11-26T02:28:06,063   -- Performing Test HAS_FLTO
2023-11-26T02:28:06,419   -- Performing Test HAS_FLTO - Success
2023-11-26T02:28:06,426   -- Configuring done (3.3s)
2023-11-26T02:28:06,463   -- Generating done (0.0s)
2023-11-26T02:28:06,488   -- Build files have been written to: /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/build/temp.linux-armv7l-cpython-39/AmberMDrun
2023-11-26T02:28:10,244   [1/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/fswatch.cpp.o
2023-11-26T02:28:18,213   [2/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o
2023-11-26T02:28:18,214   FAILED: AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o
2023-11-26T02:28:18,214   /usr/bin/c++  -I/tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include -I/tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/extern -static-libstdc++ -static-libgcc -O3 -DNDEBUG -std=gnu++2a -fPIC -MD -MT AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o -MF AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o.d -o AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o -c /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp
2023-11-26T02:28:18,214   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp: In function ‘std::string executeCMD2(const std::vector<std::__cxx11::basic_string<char> >&, bool)’:
2023-11-26T02:28:18,214   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:51:5: error: ‘pipe’ was not declared in this scope
2023-11-26T02:28:18,215      51 |     pipe(stdout_fds);
2023-11-26T02:28:18,215         |     ^~~~
2023-11-26T02:28:18,215   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:59:23: error: ‘fork’ was not declared in this scope
2023-11-26T02:28:18,216      59 |     const pid_t pid = fork();
2023-11-26T02:28:18,216         |                       ^~~~
2023-11-26T02:28:18,216   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:62:9: error: ‘close’ was not declared in this scope; did you mean ‘pclose’?
2023-11-26T02:28:18,216      62 |         close(stdout_fds[0]);
2023-11-26T02:28:18,217         |         ^~~~~
2023-11-26T02:28:18,217         |         pclose
2023-11-26T02:28:18,217   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:63:9: error: ‘dup2’ was not declared in this scope
2023-11-26T02:28:18,217      63 |         dup2(stdout_fds[1], 1);
2023-11-26T02:28:18,218         |         ^~~~
2023-11-26T02:28:18,218   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:84:9: error: ‘execvp’ was not declared in this scope
2023-11-26T02:28:18,218      84 |         execvp(vc[0], &vc[0]);
2023-11-26T02:28:18,218         |         ^~~~~~
2023-11-26T02:28:18,218   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:88:5: error: ‘close’ was not declared in this scope; did you mean ‘pclose’?
2023-11-26T02:28:18,219      88 |     close(stdout_fds[1]);
2023-11-26T02:28:18,219         |     ^~~~~
2023-11-26T02:28:18,219         |     pclose
2023-11-26T02:28:18,219   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:94:27: error: ‘read’ was not declared in this scope; did you mean ‘fread’?
2023-11-26T02:28:18,219      94 |         const ssize_t r = read(stdout_fds[0], buffer, buf_size);
2023-11-26T02:28:18,220         |                           ^~~~
2023-11-26T02:28:18,220         |                           fread
2023-11-26T02:28:18,220   /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/common.cpp:112:31: error: ‘read’ was not declared in this scope; did you mean ‘fread’?
2023-11-26T02:28:18,220     112 |             const ssize_t r = read(stderr_fds[0], buffer, buf_size);
2023-11-26T02:28:18,220         |                               ^~~~
2023-11-26T02:28:18,221         |                               fread
2023-11-26T02:28:24,725   [3/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/SystemInfo.cpp.o
2023-11-26T02:28:34,259   [4/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/format.cc.o
2023-11-26T02:28:34,515   [5/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/gamd.cpp.o
2023-11-26T02:28:34,611   [6/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/base.cpp.o
2023-11-26T02:28:34,611   In file included from /usr/include/c++/10/vector:72,
2023-11-26T02:28:34,612                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/SystemInfo.hpp:12,
2023-11-26T02:28:34,612                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/base.hpp:17,
2023-11-26T02:28:34,612                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/base.cpp:4:
2023-11-26T02:28:34,612   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
2023-11-26T02:28:34,612   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2023-11-26T02:28:34,612     426 |       vector<_Tp, _Alloc>::
2023-11-26T02:28:34,613         |       ^~~~~~~~~~~~~~~~~~~
2023-11-26T02:28:34,613   In file included from /usr/include/c++/10/vector:67,
2023-11-26T02:28:34,613                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/SystemInfo.hpp:12,
2023-11-26T02:28:34,613                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/base.hpp:17,
2023-11-26T02:28:34,613                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/base.cpp:4:
2023-11-26T02:28:34,613   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void tqdm::progress(int, int)’:
2023-11-26T02:28:34,613   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-11-26T02:28:34,613    1198 |    _M_realloc_insert(end(), __x);
2023-11-26T02:28:34,614         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2023-11-26T02:28:36,893   [7/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/md.cpp.o
2023-11-26T02:28:36,893   In file included from /usr/include/c++/10/vector:72,
2023-11-26T02:28:36,894                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/SystemInfo.hpp:12,
2023-11-26T02:28:36,894                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/base.hpp:17,
2023-11-26T02:28:36,894                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/md.hpp:8,
2023-11-26T02:28:36,894                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/md.cpp:4:
2023-11-26T02:28:36,894   /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]’:
2023-11-26T02:28:36,894   /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector<double>::iterator’ changed in GCC 7.1
2023-11-26T02:28:36,894     426 |       vector<_Tp, _Alloc>::
2023-11-26T02:28:36,894         |       ^~~~~~~~~~~~~~~~~~~
2023-11-26T02:28:36,895   In file included from /usr/include/c++/10/vector:67,
2023-11-26T02:28:36,895                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/SystemInfo.hpp:12,
2023-11-26T02:28:36,895                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/base.hpp:17,
2023-11-26T02:28:36,895                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/include/md.hpp:8,
2023-11-26T02:28:36,895                    from /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207/AmberMDrun/src/md.cpp:4:
2023-11-26T02:28:36,895   /usr/include/c++/10/bits/stl_vector.h: In member function ‘void tqdm::progress(int, int)’:
2023-11-26T02:28:36,895   /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator<double*, std::vector<double> >’ changed in GCC 7.1
2023-11-26T02:28:36,895    1198 |    _M_realloc_insert(end(), __x);
2023-11-26T02:28:36,895         |    ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
2023-11-26T02:28:36,896   ninja: build stopped: subcommand failed.
2023-11-26T02:28:36,913   Traceback (most recent call last):
2023-11-26T02:28:36,913     File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
2023-11-26T02:28:36,914       main()
2023-11-26T02:28:36,914     File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
2023-11-26T02:28:36,914       json_out['return_val'] = hook(**hook_input['kwargs'])
2023-11-26T02:28:36,914     File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
2023-11-26T02:28:36,915       return _build_backend().build_wheel(wheel_directory, config_settings,
2023-11-26T02:28:36,915     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in build_wheel
2023-11-26T02:28:36,916       return self._build_with_temp_dir(
2023-11-26T02:28:36,916     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 389, in _build_with_temp_dir
2023-11-26T02:28:36,916       self.run_setup()
2023-11-26T02:28:36,917     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 311, in run_setup
2023-11-26T02:28:36,917       exec(code, locals())
2023-11-26T02:28:36,917     File "<string>", line 126, in <module>
2023-11-26T02:28:36,918     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 103, in setup
2023-11-26T02:28:36,918       return distutils.core.setup(**attrs)
2023-11-26T02:28:36,919     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup
2023-11-26T02:28:36,919       return run_commands(dist)
2023-11-26T02:28:36,919     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
2023-11-26T02:28:36,919       dist.run_commands()
2023-11-26T02:28:36,920     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
2023-11-26T02:28:36,920       self.run_command(cmd)
2023-11-26T02:28:36,921     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command
2023-11-26T02:28:36,921       super().run_command(command)
2023-11-26T02:28:36,921     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-11-26T02:28:36,922       cmd_obj.run()
2023-11-26T02:28:36,922     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 369, in run
2023-11-26T02:28:36,923       self.run_command("build")
2023-11-26T02:28:36,923     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
2023-11-26T02:28:36,924       self.distribution.run_command(command)
2023-11-26T02:28:36,924     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command
2023-11-26T02:28:36,924       super().run_command(command)
2023-11-26T02:28:36,925     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-11-26T02:28:36,925       cmd_obj.run()
2023-11-26T02:28:36,926     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run
2023-11-26T02:28:36,926       self.run_command(cmd_name)
2023-11-26T02:28:36,926     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command
2023-11-26T02:28:36,927       self.distribution.run_command(command)
2023-11-26T02:28:36,927     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command
2023-11-26T02:28:36,928       super().run_command(command)
2023-11-26T02:28:36,928     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
2023-11-26T02:28:36,929       cmd_obj.run()
2023-11-26T02:28:36,929     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 88, in run
2023-11-26T02:28:36,929       _build_ext.run(self)
2023-11-26T02:28:36,930     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
2023-11-26T02:28:36,930       self.build_extensions()
2023-11-26T02:28:36,930     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
2023-11-26T02:28:36,931       self._build_extensions_serial()
2023-11-26T02:28:36,931     File "/tmp/pip-build-env-o7kf87bm/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
2023-11-26T02:28:36,931       self.build_extension(ext)
2023-11-26T02:28:36,931     File "<string>", line 119, in build_extension
2023-11-26T02:28:36,932     File "/usr/lib/python3.9/subprocess.py", line 528, in run
2023-11-26T02:28:36,932       raise CalledProcessError(retcode, process.args,
2023-11-26T02:28:36,932   subprocess.CalledProcessError: Command '['cmake', '--build', '.']' returned non-zero exit status 1.
2023-11-26T02:28:37,009   ERROR: Building wheel for ambermdrun (pyproject.toml) exited with 1
2023-11-26T02:28:37,026   [bold magenta]full command[/]: [blue]/usr/bin/python3 /home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py build_wheel /tmp/tmp6mh80ras[/]
2023-11-26T02:28:37,027   [bold magenta]cwd[/]: /tmp/pip-wheel-ssneg2um/ambermdrun_4e556384429f48d3ba3aaf4857777207
2023-11-26T02:28:37,027   Building wheel for ambermdrun (pyproject.toml): finished with status 'error'
2023-11-26T02:28:37,029   ERROR: Failed building wheel for ambermdrun
2023-11-26T02:28:37,032 Failed to build ambermdrun
2023-11-26T02:28:37,032 ERROR: Failed to build one or more wheels
2023-11-26T02:28:37,034 Exception information:
2023-11-26T02:28:37,034 Traceback (most recent call last):
2023-11-26T02:28:37,034   File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper
2023-11-26T02:28:37,034     status = run_func(*args)
2023-11-26T02:28:37,034   File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper
2023-11-26T02:28:37,034     return func(self, options, args)
2023-11-26T02:28:37,034   File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 181, in run
2023-11-26T02:28:37,034     raise CommandError("Failed to build one or more wheels")
2023-11-26T02:28:37,034 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2023-11-26T02:28:37,036 Removed build tracker: '/tmp/pip-build-tracker-duhcm4xx'