2023-12-05T17:32:28,091 Created temporary directory: /tmp/pip-build-tracker-ra52w089 2023-12-05T17:32:28,092 Initialized build tracking at /tmp/pip-build-tracker-ra52w089 2023-12-05T17:32:28,093 Created build tracker: /tmp/pip-build-tracker-ra52w089 2023-12-05T17:32:28,093 Entered build tracker: /tmp/pip-build-tracker-ra52w089 2023-12-05T17:32:28,094 Created temporary directory: /tmp/pip-wheel-w4n0vemf 2023-12-05T17:32:28,099 Created temporary directory: /tmp/pip-ephem-wheel-cache-oqb37an1 2023-12-05T17:32:28,142 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-05T17:32:28,145 2 location(s) to search for versions of ambermdrun: 2023-12-05T17:32:28,145 * https://pypi.org/simple/ambermdrun/ 2023-12-05T17:32:28,145 * https://www.piwheels.org/simple/ambermdrun/ 2023-12-05T17:32:28,146 Fetching project page and analyzing links: https://pypi.org/simple/ambermdrun/ 2023-12-05T17:32:28,146 Getting page https://pypi.org/simple/ambermdrun/ 2023-12-05T17:32:28,148 Found index url https://pypi.org/simple/ 2023-12-05T17:32:28,199 Fetched page https://pypi.org/simple/ambermdrun/ as application/vnd.pypi.simple.v1+json 2023-12-05T17:32:28,201 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 2023-12-05T17:32:28,202 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 2023-12-05T17:32:28,203 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 2023-12-05T17:32:28,203 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 2023-12-05T17:32:28,204 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 2023-12-05T17:32:28,204 Found link https://files.pythonhosted.org/packages/59/b5/852f6b3877971d39fe9f07b6606d1de1128c1fe478801d96a315f0830d05/AmberMDrun-0.0.6.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.6), version: 0.0.6 2023-12-05T17:32:28,205 Fetching project page and analyzing links: https://www.piwheels.org/simple/ambermdrun/ 2023-12-05T17:32:28,205 Getting page https://www.piwheels.org/simple/ambermdrun/ 2023-12-05T17:32:28,206 Found index url https://www.piwheels.org/simple/ 2023-12-05T17:32:28,270 Fetched page https://www.piwheels.org/simple/ambermdrun/ as text/html 2023-12-05T17:32:28,275 Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.6-cp311-cp311-linux_armv7l.whl#sha256=d47771cfc657f2728fc1a164181a58ce47beae176e7b46b5fa592569340f9a52 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6) 2023-12-05T17:32:28,275 Skipping link: No binaries permitted for ambermdrun: https://www.piwheels.org/simple/ambermdrun/AmberMDrun-0.0.6-cp311-cp311-linux_armv6l.whl#sha256=d47771cfc657f2728fc1a164181a58ce47beae176e7b46b5fa592569340f9a52 (from https://www.piwheels.org/simple/ambermdrun/) (requires-python:>=3.6) 2023-12-05T17:32:28,275 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) 2023-12-05T17:32:28,275 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) 2023-12-05T17:32:28,275 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) 2023-12-05T17:32:28,276 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) 2023-12-05T17:32:28,276 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) 2023-12-05T17:32:28,276 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) 2023-12-05T17:32:28,276 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) 2023-12-05T17:32:28,276 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) 2023-12-05T17:32:28,277 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) 2023-12-05T17:32:28,277 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) 2023-12-05T17:32:28,277 Skipping link: not a file: https://www.piwheels.org/simple/ambermdrun/ 2023-12-05T17:32:28,277 Skipping link: not a file: https://pypi.org/simple/ambermdrun/ 2023-12-05T17:32:28,295 Given no hashes to check 1 links for project 'ambermdrun': discarding no candidates 2023-12-05T17:32:28,312 Collecting ambermdrun==0.0.6 2023-12-05T17:32:28,314 Created temporary directory: /tmp/pip-unpack-ms3ckx62 2023-12-05T17:32:28,361 Downloading AmberMDrun-0.0.6.tar.gz (930 kB) 2023-12-05T17:32:29,455 Added ambermdrun==0.0.6 from https://files.pythonhosted.org/packages/59/b5/852f6b3877971d39fe9f07b6606d1de1128c1fe478801d96a315f0830d05/AmberMDrun-0.0.6.tar.gz to build tracker '/tmp/pip-build-tracker-ra52w089' 2023-12-05T17:32:29,465 Created temporary directory: /tmp/pip-build-env-35wn5dwo 2023-12-05T17:32:29,480 Installing build dependencies: started 2023-12-05T17:32:29,482 Running command pip subprocess to install build dependencies 2023-12-05T17:32:30,912 Using pip 23.3.1 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-12-05T17:32:31,438 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-12-05T17:32:32,875 Collecting setuptools>=42 2023-12-05T17:32:32,891 Using cached https://www.piwheels.org/simple/setuptools/setuptools-69.0.2-py3-none-any.whl (819 kB) 2023-12-05T17:32:33,137 Collecting wheel 2023-12-05T17:32:33,152 Using cached https://www.piwheels.org/simple/wheel/wheel-0.42.0-py3-none-any.whl (65 kB) 2023-12-05T17:32:33,336 Collecting ninja 2023-12-05T17:32:33,353 Using cached https://www.piwheels.org/simple/ninja/ninja-1.11.1.1-cp39-cp39-linux_armv7l.whl (132 kB) 2023-12-05T17:32:33,986 Collecting cmake>=3.12 2023-12-05T17:32:34,002 Using cached https://www.piwheels.org/simple/cmake/cmake-3.27.9-cp39-cp39-linux_armv7l.whl (19.3 MB) 2023-12-05T17:32:36,541 Installing collected packages: ninja, cmake, wheel, setuptools 2023-12-05T17:32:36,595 Creating /tmp/pip-build-env-35wn5dwo/overlay/bin 2023-12-05T17:32:36,597 changing mode of /tmp/pip-build-env-35wn5dwo/overlay/bin/ninja to 755 2023-12-05T17:32:42,743 changing mode of /tmp/pip-build-env-35wn5dwo/overlay/bin/cmake to 755 2023-12-05T17:32:42,745 changing mode of /tmp/pip-build-env-35wn5dwo/overlay/bin/cpack to 755 2023-12-05T17:32:42,748 changing mode of /tmp/pip-build-env-35wn5dwo/overlay/bin/ctest to 755 2023-12-05T17:32:43,032 changing mode of /tmp/pip-build-env-35wn5dwo/overlay/bin/wheel to 755 2023-12-05T17:32:45,132 Successfully installed cmake-3.27.9 ninja-1.11.1.1 setuptools-69.0.2 wheel-0.42.0 2023-12-05T17:32:45,635 Installing build dependencies: finished with status 'done' 2023-12-05T17:32:45,640 Getting requirements to build wheel: started 2023-12-05T17:32:45,641 Running command Getting requirements to build wheel 2023-12-05T17:32:46,189 running egg_info 2023-12-05T17:32:46,194 writing AmberMDrun.egg-info/PKG-INFO 2023-12-05T17:32:46,197 writing dependency_links to AmberMDrun.egg-info/dependency_links.txt 2023-12-05T17:32:46,199 writing entry points to AmberMDrun.egg-info/entry_points.txt 2023-12-05T17:32:46,200 writing requirements to AmberMDrun.egg-info/requires.txt 2023-12-05T17:32:46,201 writing top-level names to AmberMDrun.egg-info/top_level.txt 2023-12-05T17:32:46,226 reading manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2023-12-05T17:32:46,274 reading manifest template 'MANIFEST.in' 2023-12-05T17:32:46,303 adding license file 'LICENSE' 2023-12-05T17:32:46,321 writing manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2023-12-05T17:32:46,384 Getting requirements to build wheel: finished with status 'done' 2023-12-05T17:32:46,393 Created temporary directory: /tmp/pip-modern-metadata-9dhpnvil 2023-12-05T17:32:46,396 Preparing metadata (pyproject.toml): started 2023-12-05T17:32:46,397 Running command Preparing metadata (pyproject.toml) 2023-12-05T17:32:46,902 running dist_info 2023-12-05T17:32:46,921 creating /tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info 2023-12-05T17:32:46,927 writing /tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/PKG-INFO 2023-12-05T17:32:46,930 writing dependency_links to /tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/dependency_links.txt 2023-12-05T17:32:46,932 writing entry points to /tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/entry_points.txt 2023-12-05T17:32:46,933 writing requirements to /tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/requires.txt 2023-12-05T17:32:46,934 writing top-level names to /tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/top_level.txt 2023-12-05T17:32:46,936 writing manifest file '/tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/SOURCES.txt' 2023-12-05T17:32:46,958 reading manifest file '/tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/SOURCES.txt' 2023-12-05T17:32:46,960 reading manifest template 'MANIFEST.in' 2023-12-05T17:32:46,980 adding license file 'LICENSE' 2023-12-05T17:32:46,993 writing manifest file '/tmp/pip-modern-metadata-9dhpnvil/AmberMDrun.egg-info/SOURCES.txt' 2023-12-05T17:32:46,994 creating '/tmp/pip-modern-metadata-9dhpnvil/AmberMDrun-0.0.6.dist-info' 2023-12-05T17:32:47,162 Preparing metadata (pyproject.toml): finished with status 'done' 2023-12-05T17:32:47,168 Source in /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162 has version 0.0.6, which satisfies requirement ambermdrun==0.0.6 from https://files.pythonhosted.org/packages/59/b5/852f6b3877971d39fe9f07b6606d1de1128c1fe478801d96a315f0830d05/AmberMDrun-0.0.6.tar.gz 2023-12-05T17:32:47,169 Removed ambermdrun==0.0.6 from https://files.pythonhosted.org/packages/59/b5/852f6b3877971d39fe9f07b6606d1de1128c1fe478801d96a315f0830d05/AmberMDrun-0.0.6.tar.gz from build tracker '/tmp/pip-build-tracker-ra52w089' 2023-12-05T17:32:47,175 Created temporary directory: /tmp/pip-unpack-97maz_er 2023-12-05T17:32:47,176 Created temporary directory: /tmp/pip-unpack-w8dx696a 2023-12-05T17:32:47,180 Building wheels for collected packages: ambermdrun 2023-12-05T17:32:47,185 Created temporary directory: /tmp/pip-wheel-08d8adgi 2023-12-05T17:32:47,185 Destination directory: /tmp/pip-wheel-08d8adgi 2023-12-05T17:32:47,187 Building wheel for ambermdrun (pyproject.toml): started 2023-12-05T17:32:47,188 Running command Building wheel for ambermdrun (pyproject.toml) 2023-12-05T17:32:47,966 running bdist_wheel 2023-12-05T17:32:48,008 running build 2023-12-05T17:32:48,009 running build_py 2023-12-05T17:32:48,017 creating build 2023-12-05T17:32:48,017 creating build/lib.linux-armv7l-cpython-39 2023-12-05T17:32:48,018 creating build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,019 copying AmberMDrun/version.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,021 copying AmberMDrun/mmpbsa.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,023 copying AmberMDrun/__init__.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,024 copying AmberMDrun/equil.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,026 copying AmberMDrun/pyamber.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,028 copying AmberMDrun/main.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:48,031 running build_ext 2023-12-05T17:32:48,502 -- The CXX compiler identification is GNU 10.2.1 2023-12-05T17:32:48,589 -- Detecting CXX compiler ABI info 2023-12-05T17:32:48,927 -- Detecting CXX compiler ABI info - done 2023-12-05T17:32:48,968 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-12-05T17:32:48,970 -- Detecting CXX compile features 2023-12-05T17:32:48,973 -- Detecting CXX compile features - done 2023-12-05T17:32:48,990 -- Performing Test COMPILER_SUPPORTS_CXX23 2023-12-05T17:32:49,117 -- Performing Test COMPILER_SUPPORTS_CXX23 - Failed 2023-12-05T17:32:49,123 -- Performing Test COMPILER_SUPPORTS_CXX20 2023-12-05T17:32:49,498 -- Performing Test COMPILER_SUPPORTS_CXX20 - Success 2023-12-05T17:32:49,502 -- Performing Test COMPILER_SUPPORTS_CXX17 2023-12-05T17:32:49,810 -- Performing Test COMPILER_SUPPORTS_CXX17 - Success 2023-12-05T17:32:49,810 -- current platform: Linux 2023-12-05T17:32:49,815 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2023-12-05T17:32:50,118 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed 2023-12-05T17:32:50,119 -- Looking for pthread_create in pthreads 2023-12-05T17:32:50,350 -- Looking for pthread_create in pthreads - not found 2023-12-05T17:32:50,350 -- Looking for pthread_create in pthread 2023-12-05T17:32:50,602 -- Looking for pthread_create in pthread - found 2023-12-05T17:32:50,606 -- Found Threads: TRUE 2023-12-05T17:32:50,612 CMake Deprecation Warning at AmberMDrun/extern/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2023-12-05T17:32:50,612 Compatibility with CMake < 3.5 will be removed from a future version of 2023-12-05T17:32:50,612 CMake. 2023-12-05T17:32:50,613 Update the VERSION argument value or use a ... suffix to tell 2023-12-05T17:32:50,613 CMake that the project does not need compatibility with older versions. 2023-12-05T17:32:50,628 -- pybind11 v2.10.4 2023-12-05T17:32:50,636 CMake Warning (dev) at AmberMDrun/extern/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package): 2023-12-05T17:32:50,636 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2023-12-05T17:32:50,636 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2023-12-05T17:32:50,636 the cmake_policy command to set the policy and suppress this warning. 2023-12-05T17:32:50,637 Call Stack (most recent call first): 2023-12-05T17:32:50,637 AmberMDrun/extern/pybind11/tools/pybind11Tools.cmake:50 (find_package) 2023-12-05T17:32:50,637 AmberMDrun/extern/pybind11/tools/pybind11Common.cmake:180 (include) 2023-12-05T17:32:50,637 AmberMDrun/extern/pybind11/CMakeLists.txt:208 (include) 2023-12-05T17:32:50,637 This warning is for project developers. Use -Wno-dev to suppress it. 2023-12-05T17:32:50,693 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-12-05T17:32:51,202 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-12-05T17:32:51,207 -- Performing Test HAS_FLTO 2023-12-05T17:32:51,568 -- Performing Test HAS_FLTO - Success 2023-12-05T17:32:51,575 -- Configuring done (3.4s) 2023-12-05T17:32:51,611 -- Generating done (0.0s) 2023-12-05T17:32:51,636 -- Build files have been written to: /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/build/temp.linux-armv7l-cpython-39/AmberMDrun 2023-12-05T17:32:55,208 [1/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/fswatch.cpp.o 2023-12-05T17:33:04,440 [2/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o 2023-12-05T17:33:04,440 FAILED: AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o 2023-12-05T17:33:04,441 /usr/bin/c++ -I/tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include -I/tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/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-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp 2023-12-05T17:33:04,441 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp: In function ‘std::string executeCMD2(const std::vector >&, bool)’: 2023-12-05T17:33:04,441 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:51:5: error: ‘pipe’ was not declared in this scope 2023-12-05T17:33:04,442 51 | pipe(stdout_fds); 2023-12-05T17:33:04,442 | ^~~~ 2023-12-05T17:33:04,442 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:59:23: error: ‘fork’ was not declared in this scope 2023-12-05T17:33:04,443 59 | const pid_t pid = fork(); 2023-12-05T17:33:04,443 | ^~~~ 2023-12-05T17:33:04,443 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:62:9: error: ‘close’ was not declared in this scope; did you mean ‘pclose’? 2023-12-05T17:33:04,444 62 | close(stdout_fds[0]); 2023-12-05T17:33:04,444 | ^~~~~ 2023-12-05T17:33:04,444 | pclose 2023-12-05T17:33:04,444 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:63:9: error: ‘dup2’ was not declared in this scope 2023-12-05T17:33:04,445 63 | dup2(stdout_fds[1], 1); 2023-12-05T17:33:04,445 | ^~~~ 2023-12-05T17:33:04,445 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:84:9: error: ‘execvp’ was not declared in this scope 2023-12-05T17:33:04,446 84 | execvp(vc[0], &vc[0]); 2023-12-05T17:33:04,446 | ^~~~~~ 2023-12-05T17:33:04,446 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:88:5: error: ‘close’ was not declared in this scope; did you mean ‘pclose’? 2023-12-05T17:33:04,447 88 | close(stdout_fds[1]); 2023-12-05T17:33:04,447 | ^~~~~ 2023-12-05T17:33:04,447 | pclose 2023-12-05T17:33:04,448 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:94:27: error: ‘read’ was not declared in this scope; did you mean ‘fread’? 2023-12-05T17:33:04,448 94 | const ssize_t r = read(stdout_fds[0], buffer, buf_size); 2023-12-05T17:33:04,448 | ^~~~ 2023-12-05T17:33:04,449 | fread 2023-12-05T17:33:04,449 /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/common.cpp:112:31: error: ‘read’ was not declared in this scope; did you mean ‘fread’? 2023-12-05T17:33:04,449 112 | const ssize_t r = read(stderr_fds[0], buffer, buf_size); 2023-12-05T17:33:04,449 | ^~~~ 2023-12-05T17:33:04,450 | fread 2023-12-05T17:33:11,406 [3/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/SystemInfo.cpp.o 2023-12-05T17:33:18,284 [4/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/format.cc.o 2023-12-05T17:33:18,868 [5/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/gamd.cpp.o 2023-12-05T17:33:20,322 [6/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/base.cpp.o 2023-12-05T17:33:20,322 In file included from /usr/include/c++/10/vector:72, 2023-12-05T17:33:20,322 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/SystemInfo.hpp:12, 2023-12-05T17:33:20,322 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/base.hpp:17, 2023-12-05T17:33:20,322 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/base.cpp:4: 2023-12-05T17:33:20,323 /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]’: 2023-12-05T17:33:20,323 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-12-05T17:33:20,323 426 | vector<_Tp, _Alloc>:: 2023-12-05T17:33:20,323 | ^~~~~~~~~~~~~~~~~~~ 2023-12-05T17:33:20,323 In file included from /usr/include/c++/10/vector:67, 2023-12-05T17:33:20,323 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/SystemInfo.hpp:12, 2023-12-05T17:33:20,323 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/base.hpp:17, 2023-12-05T17:33:20,323 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/base.cpp:4: 2023-12-05T17:33:20,324 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void tqdm::progress(int, int)’: 2023-12-05T17:33:20,324 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-12-05T17:33:20,324 1198 | _M_realloc_insert(end(), __x); 2023-12-05T17:33:20,324 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-12-05T17:33:23,177 [7/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/md.cpp.o 2023-12-05T17:33:23,178 In file included from /usr/include/c++/10/vector:72, 2023-12-05T17:33:23,178 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/SystemInfo.hpp:12, 2023-12-05T17:33:23,178 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/base.hpp:17, 2023-12-05T17:33:23,178 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/md.hpp:8, 2023-12-05T17:33:23,178 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/md.cpp:4: 2023-12-05T17:33:23,178 /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]’: 2023-12-05T17:33:23,178 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-12-05T17:33:23,178 426 | vector<_Tp, _Alloc>:: 2023-12-05T17:33:23,179 | ^~~~~~~~~~~~~~~~~~~ 2023-12-05T17:33:23,179 In file included from /usr/include/c++/10/vector:67, 2023-12-05T17:33:23,179 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/SystemInfo.hpp:12, 2023-12-05T17:33:23,179 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/base.hpp:17, 2023-12-05T17:33:23,179 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/include/md.hpp:8, 2023-12-05T17:33:23,179 from /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162/AmberMDrun/src/md.cpp:4: 2023-12-05T17:33:23,179 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void tqdm::progress(int, int)’: 2023-12-05T17:33:23,179 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-12-05T17:33:23,179 1198 | _M_realloc_insert(end(), __x); 2023-12-05T17:33:23,180 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-12-05T17:33:23,180 ninja: build stopped: subcommand failed. 2023-12-05T17:33:23,197 Traceback (most recent call last): 2023-12-05T17:33:23,199 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in 2023-12-05T17:33:23,199 main() 2023-12-05T17:33:23,199 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main 2023-12-05T17:33:23,201 json_out['return_val'] = hook(**hook_input['kwargs']) 2023-12-05T17:33:23,202 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel 2023-12-05T17:33:23,204 return _build_backend().build_wheel(wheel_directory, config_settings, 2023-12-05T17:33:23,205 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 404, in build_wheel 2023-12-05T17:33:23,205 return self._build_with_temp_dir( 2023-12-05T17:33:23,205 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 389, in _build_with_temp_dir 2023-12-05T17:33:23,205 self.run_setup() 2023-12-05T17:33:23,205 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 311, in run_setup 2023-12-05T17:33:23,205 exec(code, locals()) 2023-12-05T17:33:23,205 File "", line 126, in 2023-12-05T17:33:23,206 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 103, in setup 2023-12-05T17:33:23,206 return distutils.core.setup(**attrs) 2023-12-05T17:33:23,206 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup 2023-12-05T17:33:23,206 return run_commands(dist) 2023-12-05T17:33:23,206 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands 2023-12-05T17:33:23,206 dist.run_commands() 2023-12-05T17:33:23,206 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands 2023-12-05T17:33:23,206 self.run_command(cmd) 2023-12-05T17:33:23,206 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command 2023-12-05T17:33:23,208 super().run_command(command) 2023-12-05T17:33:23,209 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-12-05T17:33:23,209 cmd_obj.run() 2023-12-05T17:33:23,210 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 368, in run 2023-12-05T17:33:23,210 self.run_command("build") 2023-12-05T17:33:23,210 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-12-05T17:33:23,210 self.distribution.run_command(command) 2023-12-05T17:33:23,212 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command 2023-12-05T17:33:23,212 super().run_command(command) 2023-12-05T17:33:23,212 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-12-05T17:33:23,213 cmd_obj.run() 2023-12-05T17:33:23,213 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run 2023-12-05T17:33:23,214 self.run_command(cmd_name) 2023-12-05T17:33:23,214 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-12-05T17:33:23,215 self.distribution.run_command(command) 2023-12-05T17:33:23,215 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 963, in run_command 2023-12-05T17:33:23,216 super().run_command(command) 2023-12-05T17:33:23,216 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-12-05T17:33:23,217 cmd_obj.run() 2023-12-05T17:33:23,218 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 88, in run 2023-12-05T17:33:23,218 _build_ext.run(self) 2023-12-05T17:33:23,218 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run 2023-12-05T17:33:23,219 self.build_extensions() 2023-12-05T17:33:23,219 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions 2023-12-05T17:33:23,220 self._build_extensions_serial() 2023-12-05T17:33:23,220 File "/tmp/pip-build-env-35wn5dwo/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial 2023-12-05T17:33:23,221 self.build_extension(ext) 2023-12-05T17:33:23,222 File "", line 119, in build_extension 2023-12-05T17:33:23,222 File "/usr/lib/python3.9/subprocess.py", line 528, in run 2023-12-05T17:33:23,231 raise CalledProcessError(retcode, process.args, 2023-12-05T17:33:23,231 subprocess.CalledProcessError: Command '['cmake', '--build', '.']' returned non-zero exit status 1. 2023-12-05T17:33:23,299 ERROR: Building wheel for ambermdrun (pyproject.toml) exited with 1 2023-12-05T17:33:23,317 [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/tmpovrdelcl[/] 2023-12-05T17:33:23,317 [bold magenta]cwd[/]: /tmp/pip-wheel-w4n0vemf/ambermdrun_fac8101a99c0405a8a873a4b5f13a162 2023-12-05T17:33:23,317 Building wheel for ambermdrun (pyproject.toml): finished with status 'error' 2023-12-05T17:33:23,319 ERROR: Failed building wheel for ambermdrun 2023-12-05T17:33:23,322 Failed to build ambermdrun 2023-12-05T17:33:23,323 ERROR: Failed to build one or more wheels 2023-12-05T17:33:23,324 Exception information: 2023-12-05T17:33:23,324 Traceback (most recent call last): 2023-12-05T17:33:23,324 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-12-05T17:33:23,324 status = run_func(*args) 2023-12-05T17:33:23,324 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper 2023-12-05T17:33:23,324 return func(self, options, args) 2023-12-05T17:33:23,324 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-12-05T17:33:23,324 raise CommandError("Failed to build one or more wheels") 2023-12-05T17:33:23,324 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-12-05T17:33:23,326 Removed build tracker: '/tmp/pip-build-tracker-ra52w089'