2023-06-10T12:52:39,105 Created temporary directory: /tmp/pip-build-tracker-wn8qp5ss 2023-06-10T12:52:39,106 Initialized build tracking at /tmp/pip-build-tracker-wn8qp5ss 2023-06-10T12:52:39,106 Created build tracker: /tmp/pip-build-tracker-wn8qp5ss 2023-06-10T12:52:39,106 Entered build tracker: /tmp/pip-build-tracker-wn8qp5ss 2023-06-10T12:52:39,107 Created temporary directory: /tmp/pip-wheel-mnm9bmfy 2023-06-10T12:52:39,110 Created temporary directory: /tmp/pip-ephem-wheel-cache-opsd4sp9 2023-06-10T12:52:39,136 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-06-10T12:52:39,139 2 location(s) to search for versions of ambermdrun: 2023-06-10T12:52:39,139 * https://pypi.org/simple/ambermdrun/ 2023-06-10T12:52:39,139 * https://www.piwheels.org/simple/ambermdrun/ 2023-06-10T12:52:39,139 Fetching project page and analyzing links: https://pypi.org/simple/ambermdrun/ 2023-06-10T12:52:39,140 Getting page https://pypi.org/simple/ambermdrun/ 2023-06-10T12:52:39,142 Found index url https://pypi.org/simple/ 2023-06-10T12:52:39,201 Fetched page https://pypi.org/simple/ambermdrun/ as application/vnd.pypi.simple.v1+json 2023-06-10T12:52:39,203 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 2023-06-10T12:52:39,203 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 2023-06-10T12:52:39,204 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 2023-06-10T12:52:39,205 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 2023-06-10T12:52:39,205 Fetching project page and analyzing links: https://www.piwheels.org/simple/ambermdrun/ 2023-06-10T12:52:39,205 Getting page https://www.piwheels.org/simple/ambermdrun/ 2023-06-10T12:52:39,206 Found index url https://www.piwheels.org/simple/ 2023-06-10T12:52:39,371 Fetched page https://www.piwheels.org/simple/ambermdrun/ as text/html 2023-06-10T12:52:39,374 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) 2023-06-10T12:52:39,374 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) 2023-06-10T12:52:39,374 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) 2023-06-10T12:52:39,375 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) 2023-06-10T12:52:39,375 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) 2023-06-10T12:52:39,375 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) 2023-06-10T12:52:39,375 Skipping link: not a file: https://www.piwheels.org/simple/ambermdrun/ 2023-06-10T12:52:39,375 Skipping link: not a file: https://pypi.org/simple/ambermdrun/ 2023-06-10T12:52:39,393 Given no hashes to check 1 links for project 'ambermdrun': discarding no candidates 2023-06-10T12:52:39,410 Collecting ambermdrun==0.0.4 2023-06-10T12:52:39,412 Created temporary directory: /tmp/pip-unpack-0ml93ghm 2023-06-10T12:52:39,475 Downloading AmberMDrun-0.0.4.zip (1.1 MB) 2023-06-10T12:52:40,109 Added ambermdrun==0.0.4 from https://files.pythonhosted.org/packages/ed/d0/cf9b1bd460d898e4f264c3d2af7ef5838fa6c67044a2a798d4c1bf33bd96/AmberMDrun-0.0.4.zip to build tracker '/tmp/pip-build-tracker-wn8qp5ss' 2023-06-10T12:52:40,116 Created temporary directory: /tmp/pip-build-env-i0g15jbq 2023-06-10T12:52:40,126 Installing build dependencies: started 2023-06-10T12:52:40,127 Running command pip subprocess to install build dependencies 2023-06-10T12:52:41,312 Using pip 23.1.2 from /home/piwheels/.local/lib/python3.9/site-packages/pip (python 3.9) 2023-06-10T12:52:41,679 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-06-10T12:52:43,380 Collecting setuptools>=42 2023-06-10T12:52:43,471 Using cached https://www.piwheels.org/simple/setuptools/setuptools-67.8.0-py3-none-any.whl (1.1 MB) 2023-06-10T12:52:43,739 Collecting wheel 2023-06-10T12:52:43,758 Using cached https://www.piwheels.org/simple/wheel/wheel-0.40.0-py3-none-any.whl (64 kB) 2023-06-10T12:52:44,028 Collecting ninja 2023-06-10T12:52:44,053 Using cached https://www.piwheels.org/simple/ninja/ninja-1.11.1-cp39-cp39-linux_armv7l.whl (132 kB) 2023-06-10T12:52:44,893 Collecting cmake>=3.12 2023-06-10T12:52:46,362 Using cached https://www.piwheels.org/simple/cmake/cmake-3.26.4-cp39-cp39-linux_armv7l.whl (17.6 MB) 2023-06-10T12:52:48,875 Installing collected packages: ninja, cmake, wheel, setuptools 2023-06-10T12:52:48,933 Creating /tmp/pip-build-env-i0g15jbq/overlay/bin 2023-06-10T12:52:48,935 changing mode of /tmp/pip-build-env-i0g15jbq/overlay/bin/ninja to 755 2023-06-10T12:52:55,083 changing mode of /tmp/pip-build-env-i0g15jbq/overlay/bin/cmake to 755 2023-06-10T12:52:55,085 changing mode of /tmp/pip-build-env-i0g15jbq/overlay/bin/cpack to 755 2023-06-10T12:52:55,087 changing mode of /tmp/pip-build-env-i0g15jbq/overlay/bin/ctest to 755 2023-06-10T12:52:55,385 changing mode of /tmp/pip-build-env-i0g15jbq/overlay/bin/wheel to 755 2023-06-10T12:52:57,755 Successfully installed cmake-3.26.4 ninja-1.11.1 setuptools-67.8.0 wheel-0.40.0 2023-06-10T12:52:58,065 Installing build dependencies: finished with status 'done' 2023-06-10T12:52:58,069 Getting requirements to build wheel: started 2023-06-10T12:52:58,070 Running command Getting requirements to build wheel 2023-06-10T12:52:58,631 running egg_info 2023-06-10T12:52:58,636 writing AmberMDrun.egg-info/PKG-INFO 2023-06-10T12:52:58,638 writing dependency_links to AmberMDrun.egg-info/dependency_links.txt 2023-06-10T12:52:58,640 writing entry points to AmberMDrun.egg-info/entry_points.txt 2023-06-10T12:52:58,642 writing requirements to AmberMDrun.egg-info/requires.txt 2023-06-10T12:52:58,643 writing top-level names to AmberMDrun.egg-info/top_level.txt 2023-06-10T12:52:58,668 reading manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2023-06-10T12:52:58,713 reading manifest template 'MANIFEST.in' 2023-06-10T12:52:58,742 adding license file 'LICENSE' 2023-06-10T12:52:58,760 writing manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2023-06-10T12:52:58,826 Getting requirements to build wheel: finished with status 'done' 2023-06-10T12:52:58,836 Created temporary directory: /tmp/pip-modern-metadata-cjod2wpk 2023-06-10T12:52:58,838 Preparing metadata (pyproject.toml): started 2023-06-10T12:52:58,839 Running command Preparing metadata (pyproject.toml) 2023-06-10T12:52:59,356 running dist_info 2023-06-10T12:52:59,375 creating /tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info 2023-06-10T12:52:59,381 writing /tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/PKG-INFO 2023-06-10T12:52:59,384 writing dependency_links to /tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/dependency_links.txt 2023-06-10T12:52:59,386 writing entry points to /tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/entry_points.txt 2023-06-10T12:52:59,387 writing requirements to /tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/requires.txt 2023-06-10T12:52:59,388 writing top-level names to /tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/top_level.txt 2023-06-10T12:52:59,390 writing manifest file '/tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/SOURCES.txt' 2023-06-10T12:52:59,412 reading manifest file '/tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/SOURCES.txt' 2023-06-10T12:52:59,415 reading manifest template 'MANIFEST.in' 2023-06-10T12:52:59,435 adding license file 'LICENSE' 2023-06-10T12:52:59,448 writing manifest file '/tmp/pip-modern-metadata-cjod2wpk/AmberMDrun.egg-info/SOURCES.txt' 2023-06-10T12:52:59,449 creating '/tmp/pip-modern-metadata-cjod2wpk/AmberMDrun-0.0.4.dist-info' 2023-06-10T12:52:59,616 Preparing metadata (pyproject.toml): finished with status 'done' 2023-06-10T12:52:59,622 Source in /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310 has version 0.0.4, which satisfies requirement ambermdrun==0.0.4 from https://files.pythonhosted.org/packages/ed/d0/cf9b1bd460d898e4f264c3d2af7ef5838fa6c67044a2a798d4c1bf33bd96/AmberMDrun-0.0.4.zip 2023-06-10T12:52:59,623 Removed ambermdrun==0.0.4 from https://files.pythonhosted.org/packages/ed/d0/cf9b1bd460d898e4f264c3d2af7ef5838fa6c67044a2a798d4c1bf33bd96/AmberMDrun-0.0.4.zip from build tracker '/tmp/pip-build-tracker-wn8qp5ss' 2023-06-10T12:52:59,628 Created temporary directory: /tmp/pip-unpack-lmjz4wjs 2023-06-10T12:52:59,629 Building wheels for collected packages: ambermdrun 2023-06-10T12:52:59,633 Created temporary directory: /tmp/pip-wheel-it3l2wlf 2023-06-10T12:52:59,633 Destination directory: /tmp/pip-wheel-it3l2wlf 2023-06-10T12:52:59,635 Building wheel for ambermdrun (pyproject.toml): started 2023-06-10T12:52:59,637 Running command Building wheel for ambermdrun (pyproject.toml) 2023-06-10T12:53:00,202 running bdist_wheel 2023-06-10T12:53:00,220 running build 2023-06-10T12:53:00,220 running build_py 2023-06-10T12:53:00,229 creating build 2023-06-10T12:53:00,229 creating build/lib.linux-armv7l-cpython-39 2023-06-10T12:53:00,230 creating build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,231 copying AmberMDrun/main.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,233 copying AmberMDrun/mmpbsa.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,235 copying AmberMDrun/__init__.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,237 copying AmberMDrun/equil.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,238 copying AmberMDrun/pyamber.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,240 copying AmberMDrun/version.py -> build/lib.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:00,243 running build_ext 2023-06-10T12:53:00,708 -- The CXX compiler identification is GNU 10.2.1 2023-06-10T12:53:00,760 -- Detecting CXX compiler ABI info 2023-06-10T12:53:01,133 -- Detecting CXX compiler ABI info - done 2023-06-10T12:53:01,173 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2023-06-10T12:53:01,175 -- Detecting CXX compile features 2023-06-10T12:53:01,178 -- Detecting CXX compile features - done 2023-06-10T12:53:01,198 -- Performing Test COMPILER_SUPPORTS_CXX23 2023-06-10T12:53:01,303 -- Performing Test COMPILER_SUPPORTS_CXX23 - Failed 2023-06-10T12:53:01,307 -- Performing Test COMPILER_SUPPORTS_CXX20 2023-06-10T12:53:01,608 -- Performing Test COMPILER_SUPPORTS_CXX20 - Success 2023-06-10T12:53:01,612 -- Performing Test COMPILER_SUPPORTS_CXX17 2023-06-10T12:53:01,940 -- Performing Test COMPILER_SUPPORTS_CXX17 - Success 2023-06-10T12:53:01,941 -- current platform: Linux 2023-06-10T12:53:01,946 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2023-06-10T12:53:02,229 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed 2023-06-10T12:53:02,229 -- Looking for pthread_create in pthreads 2023-06-10T12:53:02,448 -- Looking for pthread_create in pthreads - not found 2023-06-10T12:53:02,448 -- Looking for pthread_create in pthread 2023-06-10T12:53:02,782 -- Looking for pthread_create in pthread - found 2023-06-10T12:53:02,788 -- Found Threads: TRUE 2023-06-10T12:53:02,811 -- pybind11 v2.10.4 2023-06-10T12:53:02,876 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.9.2", minimum required is "3.6") 2023-06-10T12:53:03,372 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.9.so 2023-06-10T12:53:03,378 -- Performing Test HAS_FLTO 2023-06-10T12:53:03,738 -- Performing Test HAS_FLTO - Success 2023-06-10T12:53:03,745 -- Configuring done (3.4s) 2023-06-10T12:53:03,783 -- Generating done (0.0s) 2023-06-10T12:53:03,809 -- Build files have been written to: /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/build/temp.linux-armv7l-cpython-39/AmberMDrun 2023-06-10T12:53:07,484 [1/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/fswatch.cpp.o 2023-06-10T12:53:14,898 [2/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o 2023-06-10T12:53:14,899 FAILED: AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o 2023-06-10T12:53:14,899 /usr/bin/c++ -I/tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include -I/tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/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-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp 2023-06-10T12:53:14,900 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp: In function ‘std::string executeCMD2(const std::vector >&, bool)’: 2023-06-10T12:53:14,900 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:51:5: error: ‘pipe’ was not declared in this scope 2023-06-10T12:53:14,900 51 | pipe(stdout_fds); 2023-06-10T12:53:14,900 | ^~~~ 2023-06-10T12:53:14,901 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:59:23: error: ‘fork’ was not declared in this scope 2023-06-10T12:53:14,901 59 | const pid_t pid = fork(); 2023-06-10T12:53:14,901 | ^~~~ 2023-06-10T12:53:14,902 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:62:9: error: ‘close’ was not declared in this scope; did you mean ‘pclose’? 2023-06-10T12:53:14,902 62 | close(stdout_fds[0]); 2023-06-10T12:53:14,902 | ^~~~~ 2023-06-10T12:53:14,903 | pclose 2023-06-10T12:53:14,903 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:63:9: error: ‘dup2’ was not declared in this scope 2023-06-10T12:53:14,903 63 | dup2(stdout_fds[1], 1); 2023-06-10T12:53:14,903 | ^~~~ 2023-06-10T12:53:14,904 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:84:9: error: ‘execvp’ was not declared in this scope 2023-06-10T12:53:14,904 84 | execvp(vc[0], &vc[0]); 2023-06-10T12:53:14,904 | ^~~~~~ 2023-06-10T12:53:14,905 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:88:5: error: ‘close’ was not declared in this scope; did you mean ‘pclose’? 2023-06-10T12:53:14,905 88 | close(stdout_fds[1]); 2023-06-10T12:53:14,905 | ^~~~~ 2023-06-10T12:53:14,905 | pclose 2023-06-10T12:53:14,906 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:94:27: error: ‘read’ was not declared in this scope; did you mean ‘fread’? 2023-06-10T12:53:14,906 94 | const ssize_t r = read(stdout_fds[0], buffer, buf_size); 2023-06-10T12:53:14,906 | ^~~~ 2023-06-10T12:53:14,907 | fread 2023-06-10T12:53:14,907 /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/common.cpp:112:31: error: ‘read’ was not declared in this scope; did you mean ‘fread’? 2023-06-10T12:53:14,907 112 | const ssize_t r = read(stderr_fds[0], buffer, buf_size); 2023-06-10T12:53:14,908 | ^~~~ 2023-06-10T12:53:14,908 | fread 2023-06-10T12:53:21,019 [3/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/SystemInfo.cpp.o 2023-06-10T12:53:30,918 [4/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/format.cc.o 2023-06-10T12:53:31,231 [5/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/gamd.cpp.o 2023-06-10T12:53:32,763 [6/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/base.cpp.o 2023-06-10T12:53:32,763 In file included from /usr/include/c++/10/vector:72, 2023-06-10T12:53:32,763 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/SystemInfo.hpp:12, 2023-06-10T12:53:32,763 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/base.hpp:17, 2023-06-10T12:53:32,763 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/base.cpp:4: 2023-06-10T12:53:32,764 /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]’: 2023-06-10T12:53:32,764 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-06-10T12:53:32,764 426 | vector<_Tp, _Alloc>:: 2023-06-10T12:53:32,764 | ^~~~~~~~~~~~~~~~~~~ 2023-06-10T12:53:32,764 In file included from /usr/include/c++/10/vector:67, 2023-06-10T12:53:32,764 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/SystemInfo.hpp:12, 2023-06-10T12:53:32,765 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/base.hpp:17, 2023-06-10T12:53:32,765 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/base.cpp:4: 2023-06-10T12:53:32,765 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void tqdm::progress(int, int)’: 2023-06-10T12:53:32,765 /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 2023-06-10T12:53:32,765 1198 | _M_realloc_insert(end(), __x); 2023-06-10T12:53:32,765 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-06-10T12:53:34,855 [7/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/md.cpp.o 2023-06-10T12:53:34,855 In file included from /usr/include/c++/10/vector:72, 2023-06-10T12:53:34,855 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/SystemInfo.hpp:12, 2023-06-10T12:53:34,856 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/base.hpp:17, 2023-06-10T12:53:34,856 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/md.hpp:8, 2023-06-10T12:53:34,856 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/md.cpp:4: 2023-06-10T12:53:34,856 /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]’: 2023-06-10T12:53:34,856 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-06-10T12:53:34,856 426 | vector<_Tp, _Alloc>:: 2023-06-10T12:53:34,857 | ^~~~~~~~~~~~~~~~~~~ 2023-06-10T12:53:34,857 In file included from /usr/include/c++/10/vector:67, 2023-06-10T12:53:34,857 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/SystemInfo.hpp:12, 2023-06-10T12:53:34,857 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/base.hpp:17, 2023-06-10T12:53:34,857 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/include/md.hpp:8, 2023-06-10T12:53:34,857 from /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310/AmberMDrun/src/md.cpp:4: 2023-06-10T12:53:34,858 /usr/include/c++/10/bits/stl_vector.h: In member function ‘void tqdm::progress(int, int)’: 2023-06-10T12:53:34,858 /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 2023-06-10T12:53:34,858 1198 | _M_realloc_insert(end(), __x); 2023-06-10T12:53:34,858 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-06-10T12:53:34,858 ninja: build stopped: subcommand failed. 2023-06-10T12:53:34,873 Traceback (most recent call last): 2023-06-10T12:53:34,873 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in 2023-06-10T12:53:34,874 main() 2023-06-10T12:53:34,874 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main 2023-06-10T12:53:34,875 json_out['return_val'] = hook(**hook_input['kwargs']) 2023-06-10T12:53:34,875 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel 2023-06-10T12:53:34,876 return _build_backend().build_wheel(wheel_directory, config_settings, 2023-06-10T12:53:34,876 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 416, in build_wheel 2023-06-10T12:53:34,877 return self._build_with_temp_dir(['bdist_wheel'], '.whl', 2023-06-10T12:53:34,877 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 401, in _build_with_temp_dir 2023-06-10T12:53:34,878 self.run_setup() 2023-06-10T12:53:34,878 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 338, in run_setup 2023-06-10T12:53:34,879 exec(code, locals()) 2023-06-10T12:53:34,879 File "", line 126, in 2023-06-10T12:53:34,880 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/__init__.py", line 107, in setup 2023-06-10T12:53:34,881 return distutils.core.setup(**attrs) 2023-06-10T12:53:34,881 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 185, in setup 2023-06-10T12:53:34,881 return run_commands(dist) 2023-06-10T12:53:34,882 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/core.py", line 201, in run_commands 2023-06-10T12:53:34,882 dist.run_commands() 2023-06-10T12:53:34,882 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands 2023-06-10T12:53:34,884 self.run_command(cmd) 2023-06-10T12:53:34,884 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1244, in run_command 2023-06-10T12:53:34,885 super().run_command(command) 2023-06-10T12:53:34,885 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-06-10T12:53:34,886 cmd_obj.run() 2023-06-10T12:53:34,886 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/wheel/bdist_wheel.py", line 343, in run 2023-06-10T12:53:34,887 self.run_command("build") 2023-06-10T12:53:34,888 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-06-10T12:53:34,889 self.distribution.run_command(command) 2023-06-10T12:53:34,889 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1244, in run_command 2023-06-10T12:53:34,890 super().run_command(command) 2023-06-10T12:53:34,890 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-06-10T12:53:34,892 cmd_obj.run() 2023-06-10T12:53:34,892 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build.py", line 131, in run 2023-06-10T12:53:34,893 self.run_command(cmd_name) 2023-06-10T12:53:34,893 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/cmd.py", line 318, in run_command 2023-06-10T12:53:34,893 self.distribution.run_command(command) 2023-06-10T12:53:34,894 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/dist.py", line 1244, in run_command 2023-06-10T12:53:34,895 super().run_command(command) 2023-06-10T12:53:34,895 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/dist.py", line 988, in run_command 2023-06-10T12:53:34,897 cmd_obj.run() 2023-06-10T12:53:34,897 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/command/build_ext.py", line 84, in run 2023-06-10T12:53:34,898 _build_ext.run(self) 2023-06-10T12:53:34,898 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run 2023-06-10T12:53:34,899 self.build_extensions() 2023-06-10T12:53:34,899 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions 2023-06-10T12:53:34,900 self._build_extensions_serial() 2023-06-10T12:53:34,901 File "/tmp/pip-build-env-i0g15jbq/overlay/lib/python3.9/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial 2023-06-10T12:53:34,901 self.build_extension(ext) 2023-06-10T12:53:34,902 File "", line 119, in build_extension 2023-06-10T12:53:34,902 File "/usr/lib/python3.9/subprocess.py", line 528, in run 2023-06-10T12:53:34,903 raise CalledProcessError(retcode, process.args, 2023-06-10T12:53:34,903 subprocess.CalledProcessError: Command '['cmake', '--build', '.']' returned non-zero exit status 1. 2023-06-10T12:53:34,979 ERROR: [present-rich] Building wheel for ambermdrun (pyproject.toml) exited with 1 2023-06-10T12:53:34,996 [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/tmpdgcqrdq2[/] 2023-06-10T12:53:34,996 [bold magenta]cwd[/]: /tmp/pip-wheel-mnm9bmfy/ambermdrun_32357abd45d649ffa11b5767b4879310 2023-06-10T12:53:34,996 Building wheel for ambermdrun (pyproject.toml): finished with status 'error' 2023-06-10T12:53:34,999 ERROR: Failed building wheel for ambermdrun 2023-06-10T12:53:35,001 Failed to build ambermdrun 2023-06-10T12:53:35,002 ERROR: Failed to build one or more wheels 2023-06-10T12:53:35,003 Exception information: 2023-06-10T12:53:35,003 Traceback (most recent call last): 2023-06-10T12:53:35,003 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/base_command.py", line 169, in exc_logging_wrapper 2023-06-10T12:53:35,003 status = run_func(*args) 2023-06-10T12:53:35,003 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-06-10T12:53:35,003 return func(self, options, args) 2023-06-10T12:53:35,003 File "/home/piwheels/.local/lib/python3.9/site-packages/pip/_internal/commands/wheel.py", line 178, in run 2023-06-10T12:53:35,003 raise CommandError("Failed to build one or more wheels") 2023-06-10T12:53:35,003 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-06-10T12:53:35,006 Removed build tracker: '/tmp/pip-build-tracker-wn8qp5ss'