2026-06-27T16:25:41,855 Created temporary directory: /tmp/pip-ephem-wheel-cache-bqgt9ggi 2026-06-27T16:25:41,857 Created temporary directory: /tmp/pip-build-tracker-qaibiy1z 2026-06-27T16:25:41,858 Initialized build tracking at /tmp/pip-build-tracker-qaibiy1z 2026-06-27T16:25:41,858 Created build tracker: /tmp/pip-build-tracker-qaibiy1z 2026-06-27T16:25:41,859 Entered build tracker: /tmp/pip-build-tracker-qaibiy1z 2026-06-27T16:25:41,860 Created temporary directory: /tmp/pip-wheel-ryyem5jd 2026-06-27T16:25:41,863 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-06-27T16:25:41,865 Created temporary directory: /tmp/pip-ephem-wheel-cache-qfd5hmha 2026-06-27T16:25:41,887 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-06-27T16:25:41,890 2 location(s) to search for versions of ambermdrun: 2026-06-27T16:25:41,890 * https://pypi.org/simple/ambermdrun/ 2026-06-27T16:25:41,890 * https://www.piwheels.org/simple/ambermdrun/ 2026-06-27T16:25:41,891 Fetching project page and analyzing links: https://pypi.org/simple/ambermdrun/ 2026-06-27T16:25:41,892 Getting page https://pypi.org/simple/ambermdrun/ 2026-06-27T16:25:41,893 Found index url https://pypi.org/simple 2026-06-27T16:25:42,045 Fetched page https://pypi.org/simple/ambermdrun/ as application/vnd.pypi.simple.v1+json 2026-06-27T16:25:42,051 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 2026-06-27T16:25:42,052 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 2026-06-27T16:25:42,053 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 2026-06-27T16:25:42,054 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 2026-06-27T16:25:42,055 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 2026-06-27T16:25:42,056 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 2026-06-27T16:25:42,057 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/2a/aa/7f76eb296323a2e3b279bf0faffd830f28bbd8a4c380e84fa9a2b998d8ce/ambermdrun-0.0.8-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,057 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/af/50/052cc602d85f863400e47ce949e98bce7a3d304d79cdc593321a25b76e70/ambermdrun-0.0.8-cp310-cp310-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,058 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/c1/2c/070907112138eda7cd2d33730ec00f5182b7557e34fa2d96ba2ef127563d/ambermdrun-0.0.8-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,059 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/26/af/558f6e7e61a92516345e6506ca6dc9c68db12354a6ff056c64119ea0b0b8/ambermdrun-0.0.8-cp311-cp311-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,059 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/23/dd/b38e40f3f136f871c9984844813833f7133dbfb3b08cc0e3d23b226cb40d/ambermdrun-0.0.8-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,060 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/17/f6/2e313d9de916552feccc0c1ea4863d4ba24c6354810f2c8c3f623279db54/ambermdrun-0.0.8-cp312-cp312-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,060 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/31/34/6481c939444165b4d2be4ee2681d00ee3c9538215f3ce47ca806ea27b65b/ambermdrun-0.0.8-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,061 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/6b/ce/10fe7570c15bc63ca0f8764b410a6ff34c1f4bcebed49154cd930c1c2cd5/ambermdrun-0.0.8-cp313-cp313-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,061 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/3f/19/4d44439094bab2ba9293363f280943e009ce6f27717d4dce2bab57db35cb/ambermdrun-0.0.8-cp38-cp38-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,062 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/45/22/3bc1e89636204f24f00da8164f4e2adf3f079ab2567a3357af575b0c900e/ambermdrun-0.0.8-cp38-cp38-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,062 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/ee/f5/78d0e07dd2eb4a245b32d2c63ad809b49f5da9e2757a790b7e6c335c2df3/ambermdrun-0.0.8-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,063 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/71/1a/3b230245873b9328f2d73d9edb14d9de98c92e7853471e178726655d77d9/ambermdrun-0.0.8-cp39-cp39-musllinux_1_2_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8) 2026-06-27T16:25:42,064 Found link https://files.pythonhosted.org/packages/da/8f/82fd35f3b34573576acb0058d1fb3f2b819418e4851f8f3aad2c9102d0af/ambermdrun-0.0.8.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:>=3.8), version: 0.0.8 2026-06-27T16:25:42,065 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/e5/f3/843b208e53b784d1fcbd909c2cc5320e16af0773438b6de4ea0e9d3b6a12/ambermdrun-0.0.9-cp310-cp310-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9) 2026-06-27T16:25:42,065 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/80/86/3d68fd8df42d66eaeb870b8f04359d9a8687c43aae6e7039b9eef7dfb117/ambermdrun-0.0.9-cp311-cp311-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9) 2026-06-27T16:25:42,066 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/79/93/5d72d77e0304c53a631ac14e3ce1fde9c65f48a1cda116e3f3e937908e61/ambermdrun-0.0.9-cp312-cp312-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9) 2026-06-27T16:25:42,066 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/81/bf/a930c03931f71ca6d4c2f9e876d8c427c82925d7fd2d37c330cab356cfea/ambermdrun-0.0.9-cp313-cp313-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9) 2026-06-27T16:25:42,067 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/76/8d/3a195825759d210c3c898b92a4127e4b2e44fdb77f6ecc19956694bd2ea4/ambermdrun-0.0.9-cp314-cp314-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9) 2026-06-27T16:25:42,068 Skipping link: No binaries permitted for ambermdrun: https://files.pythonhosted.org/packages/d0/51/a61fdd09a5179260d26d27b561462e28c127b17eb417fdd46bb9fa276a68/ambermdrun-0.0.9-cp39-cp39-manylinux_2_26_x86_64.manylinux_2_28_x86_64.whl (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9) 2026-06-27T16:25:42,069 Found link https://files.pythonhosted.org/packages/22/df/230c510d424fe874d40b8c248f50a69d8347259b1b4a488bf13c08394d74/ambermdrun-0.0.9.tar.gz (from https://pypi.org/simple/ambermdrun/) (requires-python:<3.15,>=3.9), version: 0.0.9 2026-06-27T16:25:42,069 Fetching project page and analyzing links: https://www.piwheels.org/simple/ambermdrun/ 2026-06-27T16:25:42,070 Getting page https://www.piwheels.org/simple/ambermdrun/ 2026-06-27T16:25:42,071 Found index url https://www.piwheels.org/simple 2026-06-27T16:25:42,424 Fetched page https://www.piwheels.org/simple/ambermdrun/ as text/html 2026-06-27T16:25:42,429 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,429 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,430 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,430 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,431 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,431 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,432 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,433 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,433 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,434 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,435 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,435 Skipping link: No binaries permitted for ambermdrun: https://archive1.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) 2026-06-27T16:25:42,436 Skipping link: not a file: https://www.piwheels.org/simple/ambermdrun/ 2026-06-27T16:25:42,436 Skipping link: not a file: https://pypi.org/simple/ambermdrun/ 2026-06-27T16:25:42,456 Given no hashes to check 1 links for project 'ambermdrun': discarding no candidates 2026-06-27T16:25:42,474 Collecting ambermdrun==0.0.8 2026-06-27T16:25:42,477 Created temporary directory: /tmp/pip-unpack-fq1fgttg 2026-06-27T16:25:42,707 Downloading ambermdrun-0.0.8.tar.gz (400 kB) 2026-06-27T16:25:43,109 Added ambermdrun==0.0.8 from https://files.pythonhosted.org/packages/da/8f/82fd35f3b34573576acb0058d1fb3f2b819418e4851f8f3aad2c9102d0af/ambermdrun-0.0.8.tar.gz to build tracker '/tmp/pip-build-tracker-qaibiy1z' 2026-06-27T16:25:43,115 Created temporary directory: /tmp/pip-build-env-bdw95tf2 2026-06-27T16:25:43,119 Installing build dependencies: started 2026-06-27T16:25:43,120 Running command pip subprocess to install build dependencies 2026-06-27T16:25:44,262 Using pip 23.0.1 from /usr/lib/python3/dist-packages/pip (python 3.11) 2026-06-27T16:25:44,729 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2026-06-27T16:25:44,752 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2026-06-27T16:25:46,673 Collecting setuptools<77,>=42 2026-06-27T16:25:46,674 Obtaining dependency information for setuptools<77,>=42 from https://www.piwheels.org/simple/setuptools/setuptools-76.1.0-py3-none-any.whl.metadata 2026-06-27T16:25:46,692 Using cached https://www.piwheels.org/simple/setuptools/setuptools-76.1.0-py3-none-any.whl.metadata (6.7 kB) 2026-06-27T16:25:46,926 Collecting wheel 2026-06-27T16:25:46,927 Obtaining dependency information for wheel from https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata 2026-06-27T16:25:46,942 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB) 2026-06-27T16:25:47,207 Collecting ninja 2026-06-27T16:25:47,218 Using cached ninja-1.13.0-py3-none-manylinux_2_28_armv7l.manylinux_2_31_armv7l.whl (146 kB) 2026-06-27T16:25:48,295 Collecting cmake>=3.12 2026-06-27T16:25:48,662 Using cached cmake-4.3.4-py3-none-manylinux_2_31_armv7l.whl (26.6 MB) 2026-06-27T16:25:50,959 Collecting packaging>=24.0 2026-06-27T16:25:50,960 Obtaining dependency information for packaging>=24.0 from https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata 2026-06-27T16:25:50,974 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl.metadata (3.5 kB) 2026-06-27T16:25:51,238 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-06-27T16:25:51,259 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-06-27T16:25:51,370 Using cached https://www.piwheels.org/simple/setuptools/setuptools-76.1.0-py3-none-any.whl (1.2 MB) 2026-06-27T16:25:51,408 Using cached https://www.piwheels.org/simple/wheel/wheel-0.47.0-py3-none-any.whl (32 kB) 2026-06-27T16:25:51,431 Using cached https://www.piwheels.org/simple/packaging/packaging-26.2-py3-none-any.whl (100 kB) 2026-06-27T16:25:51,534 Using cached https://www.piwheels.org/simple/setuptools/setuptools-76.1.0-py3-none-any.whl (1.2 MB) 2026-06-27T16:25:54,404 Installing collected packages: setuptools, packaging, ninja, cmake, wheel 2026-06-27T16:26:07,032 changing mode of /tmp/pip-build-env-bdw95tf2/overlay/local/bin/ccmake to 755 2026-06-27T16:26:07,034 changing mode of /tmp/pip-build-env-bdw95tf2/overlay/local/bin/cmake to 755 2026-06-27T16:26:07,036 changing mode of /tmp/pip-build-env-bdw95tf2/overlay/local/bin/cpack to 755 2026-06-27T16:26:07,038 changing mode of /tmp/pip-build-env-bdw95tf2/overlay/local/bin/ctest to 755 2026-06-27T16:26:07,245 changing mode of /tmp/pip-build-env-bdw95tf2/overlay/local/bin/wheel to 755 2026-06-27T16:26:07,281 Successfully installed cmake-4.3.4 ninja-1.13.0 packaging-26.2 setuptools-76.1.0 wheel-0.47.0 2026-06-27T16:26:07,635 Installing build dependencies: finished with status 'done' 2026-06-27T16:26:07,642 Getting requirements to build wheel: started 2026-06-27T16:26:07,643 Running command Getting requirements to build wheel 2026-06-27T16:26:08,313 running egg_info 2026-06-27T16:26:08,320 writing AmberMDrun.egg-info/PKG-INFO 2026-06-27T16:26:08,323 writing dependency_links to AmberMDrun.egg-info/dependency_links.txt 2026-06-27T16:26:08,325 writing entry points to AmberMDrun.egg-info/entry_points.txt 2026-06-27T16:26:08,326 writing requirements to AmberMDrun.egg-info/requires.txt 2026-06-27T16:26:08,327 writing top-level names to AmberMDrun.egg-info/top_level.txt 2026-06-27T16:26:08,355 reading manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:26:08,377 reading manifest template 'MANIFEST.in' 2026-06-27T16:26:08,389 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2026-06-27T16:26:08,390 warning: no previously-included files matching '__pycache__/*' found anywhere in distribution 2026-06-27T16:26:08,391 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.git' 2026-06-27T16:26:08,392 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.appveyor.yml' 2026-06-27T16:26:08,393 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.clang-format' 2026-06-27T16:26:08,394 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.clang-tidy' 2026-06-27T16:26:08,395 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.cmake-format.yaml' 2026-06-27T16:26:08,396 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.codespell-ignore-lines' 2026-06-27T16:26:08,396 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.gitattributes' 2026-06-27T16:26:08,397 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.gitignore' 2026-06-27T16:26:08,398 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.pre-commit-config.yaml' 2026-06-27T16:26:08,399 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.readthedocs.yml' 2026-06-27T16:26:08,400 no previously-included directories found matching 'AmberMDrun/extern/pybind11/.github' 2026-06-27T16:26:08,400 no previously-included directories found matching 'AmberMDrun/extern/pybind11/docs' 2026-06-27T16:26:08,402 no previously-included directories found matching 'AmberMDrun/extern/pybind11/tests' 2026-06-27T16:26:08,402 adding license file 'LICENSE' 2026-06-27T16:26:08,409 writing manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:26:08,501 Getting requirements to build wheel: finished with status 'done' 2026-06-27T16:26:08,504 Created temporary directory: /tmp/pip-modern-metadata-nsu_y120 2026-06-27T16:26:08,506 Preparing metadata (pyproject.toml): started 2026-06-27T16:26:08,507 Running command Preparing metadata (pyproject.toml) 2026-06-27T16:26:09,074 running dist_info 2026-06-27T16:26:09,087 creating /tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info 2026-06-27T16:26:09,088 writing /tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/PKG-INFO 2026-06-27T16:26:09,092 writing dependency_links to /tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/dependency_links.txt 2026-06-27T16:26:09,094 writing entry points to /tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/entry_points.txt 2026-06-27T16:26:09,095 writing requirements to /tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/requires.txt 2026-06-27T16:26:09,096 writing top-level names to /tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/top_level.txt 2026-06-27T16:26:09,097 writing manifest file '/tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:26:09,122 reading manifest file '/tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:26:09,124 reading manifest template 'MANIFEST.in' 2026-06-27T16:26:09,133 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2026-06-27T16:26:09,133 warning: no previously-included files matching '__pycache__/*' found anywhere in distribution 2026-06-27T16:26:09,134 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.git' 2026-06-27T16:26:09,135 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.appveyor.yml' 2026-06-27T16:26:09,136 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.clang-format' 2026-06-27T16:26:09,136 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.clang-tidy' 2026-06-27T16:26:09,137 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.cmake-format.yaml' 2026-06-27T16:26:09,138 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.codespell-ignore-lines' 2026-06-27T16:26:09,139 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.gitattributes' 2026-06-27T16:26:09,139 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.gitignore' 2026-06-27T16:26:09,140 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.pre-commit-config.yaml' 2026-06-27T16:26:09,141 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.readthedocs.yml' 2026-06-27T16:26:09,142 no previously-included directories found matching 'AmberMDrun/extern/pybind11/.github' 2026-06-27T16:26:09,142 no previously-included directories found matching 'AmberMDrun/extern/pybind11/docs' 2026-06-27T16:26:09,143 no previously-included directories found matching 'AmberMDrun/extern/pybind11/tests' 2026-06-27T16:26:09,144 adding license file 'LICENSE' 2026-06-27T16:26:09,149 writing manifest file '/tmp/pip-modern-metadata-nsu_y120/AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:26:09,151 creating '/tmp/pip-modern-metadata-nsu_y120/ambermdrun-0.0.8.dist-info' 2026-06-27T16:26:09,280 Preparing metadata (pyproject.toml): finished with status 'done' 2026-06-27T16:26:09,285 Source in /tmp/pip-wheel-ryyem5jd/ambermdrun_fd1c23a9c82d4271a14ee9b3a218a3c2 has version 0.0.8, which satisfies requirement ambermdrun==0.0.8 from https://files.pythonhosted.org/packages/da/8f/82fd35f3b34573576acb0058d1fb3f2b819418e4851f8f3aad2c9102d0af/ambermdrun-0.0.8.tar.gz 2026-06-27T16:26:09,286 Removed ambermdrun==0.0.8 from https://files.pythonhosted.org/packages/da/8f/82fd35f3b34573576acb0058d1fb3f2b819418e4851f8f3aad2c9102d0af/ambermdrun-0.0.8.tar.gz from build tracker '/tmp/pip-build-tracker-qaibiy1z' 2026-06-27T16:26:09,292 Created temporary directory: /tmp/pip-unpack-t2fld4bo 2026-06-27T16:26:09,293 Building wheels for collected packages: ambermdrun 2026-06-27T16:26:09,297 Created temporary directory: /tmp/pip-wheel-cltl_2i3 2026-06-27T16:26:09,297 Destination directory: /tmp/pip-wheel-cltl_2i3 2026-06-27T16:26:09,299 Building wheel for ambermdrun (pyproject.toml): started 2026-06-27T16:26:09,301 Running command Building wheel for ambermdrun (pyproject.toml) 2026-06-27T16:26:09,860 running bdist_wheel 2026-06-27T16:26:09,879 running build 2026-06-27T16:26:09,879 running build_py 2026-06-27T16:26:09,890 creating build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,892 copying AmberMDrun/equil.py -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,894 copying AmberMDrun/__init__.py -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,896 copying AmberMDrun/pyamber.py -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,898 copying AmberMDrun/version.py -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,900 copying AmberMDrun/mmpbsa.py -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,903 copying AmberMDrun/main.py -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,905 copying AmberMDrun/_pyamber.pyi -> build/lib.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:09,909 running build_ext 2026-06-27T16:26:10,626 -- The CXX compiler identification is GNU 12.2.0 2026-06-27T16:26:10,674 -- Detecting CXX compiler ABI info 2026-06-27T16:26:11,002 -- Detecting CXX compiler ABI info - done 2026-06-27T16:26:11,086 -- Check for working CXX compiler: /usr/bin/c++ - skipped 2026-06-27T16:26:11,088 -- Detecting CXX compile features 2026-06-27T16:26:11,092 -- Detecting CXX compile features - done 2026-06-27T16:26:11,148 -- Performing Test COMPILER_SUPPORTS_CXX23 2026-06-27T16:26:11,451 -- Performing Test COMPILER_SUPPORTS_CXX23 - Success 2026-06-27T16:26:11,454 -- Performing Test COMPILER_SUPPORTS_CXX20 2026-06-27T16:26:11,760 -- Performing Test COMPILER_SUPPORTS_CXX20 - Success 2026-06-27T16:26:11,765 -- Performing Test COMPILER_SUPPORTS_CXX17 2026-06-27T16:26:12,099 -- Performing Test COMPILER_SUPPORTS_CXX17 - Success 2026-06-27T16:26:12,100 -- current platform: Linux 2026-06-27T16:26:12,104 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD 2026-06-27T16:26:12,409 -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success 2026-06-27T16:26:12,413 -- Found Threads: TRUE 2026-06-27T16:26:12,419 CMake Deprecation Warning at AmberMDrun/extern/pybind11/CMakeLists.txt:8 (cmake_minimum_required): 2026-06-27T16:26:12,420 Compatibility with CMake < 3.10 will be removed from a future version of 2026-06-27T16:26:12,421 CMake. 2026-06-27T16:26:12,421 Update the VERSION argument value. Or, use the ... syntax 2026-06-27T16:26:12,422 to tell CMake that the project requires at least but has been updated 2026-06-27T16:26:12,422 to work with policies introduced by or earlier. 2026-06-27T16:26:12,441 -- pybind11 v2.11.1 2026-06-27T16:26:12,449 CMake Warning (dev) at AmberMDrun/extern/pybind11/tools/FindPythonLibsNew.cmake:98 (find_package): 2026-06-27T16:26:12,449 Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules 2026-06-27T16:26:12,450 are removed. Run "cmake --help-policy CMP0148" for policy details. Use 2026-06-27T16:26:12,451 the cmake_policy command to set the policy and suppress this warning. 2026-06-27T16:26:12,452 Call Stack (most recent call first): 2026-06-27T16:26:12,453 AmberMDrun/extern/pybind11/tools/pybind11Tools.cmake:50 (find_package) 2026-06-27T16:26:12,453 AmberMDrun/extern/pybind11/tools/pybind11Common.cmake:188 (include) 2026-06-27T16:26:12,454 AmberMDrun/extern/pybind11/CMakeLists.txt:210 (include) 2026-06-27T16:26:12,455 This warning is for project developers. Use -Wno-dev to suppress it. 2026-06-27T16:26:12,529 -- Found PythonInterp: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") 2026-06-27T16:26:12,638 -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.11.so 2026-06-27T16:26:12,647 -- Performing Test HAS_FLTO 2026-06-27T16:26:13,017 -- Performing Test HAS_FLTO - Success 2026-06-27T16:26:13,043 -- Configuring done (2.8s) 2026-06-27T16:26:13,105 -- Generating done (0.1s) 2026-06-27T16:26:13,110 -- Build files have been written to: /tmp/pip-wheel-ryyem5jd/ambermdrun_fd1c23a9c82d4271a14ee9b3a218a3c2/build/temp.linux-armv7l-cpython-311/AmberMDrun 2026-06-27T16:26:18,905 [1/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/fswatch.cpp.o 2026-06-27T16:26:26,568 [2/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/common.cpp.o 2026-06-27T16:26:36,669 [3/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/SystemInfo.cpp.o 2026-06-27T16:26:52,421 [4/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/npt.cpp.o 2026-06-27T16:26:53,781 [5/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/base.cpp.o 2026-06-27T16:26:55,096 [6/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/format.cc.o 2026-06-27T16:26:57,331 [7/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/gamd.cpp.o 2026-06-27T16:27:01,341 [8/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/md.cpp.o 2026-06-27T16:27:02,108 [9/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/os.cc.o 2026-06-27T16:27:08,200 [10/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/nvt.cpp.o 2026-06-27T16:27:09,730 [11/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/min.cpp.o 2026-06-27T16:27:19,896 [12/17] Building CXX object AmberMDrun/CMakeFiles/amberMd.dir/main.cpp.o 2026-06-27T16:27:23,298 [13/17] Building CXX object AmberMDrun/CMakeFiles/ambermd.dir/src/smd.cpp.o 2026-06-27T16:27:23,670 [14/17] Linking CXX static library AmberMDrun/libambermd.a 2026-06-27T16:27:24,376 [15/17] Linking CXX executable AmberMDrun/amberMd 2026-06-27T16:27:32,073 [16/17] Building CXX object AmberMDrun/CMakeFiles/_pyamber.dir/pyamber.cpp.o 2026-06-27T16:27:54,400 [17/17] Linking CXX shared module /tmp/pip-wheel-ryyem5jd/ambermdrun_fd1c23a9c82d4271a14ee9b3a218a3c2/build/lib.linux-armv7l-cpython-311/AmberMDrun/_pyamber.cpython-311-arm-linux-gnueabihf.so 2026-06-27T16:27:54,401 lto-wrapper: warning: using serial compilation of 5 LTRANS jobs 2026-06-27T16:27:54,401 lto-wrapper: note: see the ‘-flto’ option documentation for more information 2026-06-27T16:27:54,425 installing to build/bdist.linux-armv7l/wheel 2026-06-27T16:27:54,425 running install 2026-06-27T16:27:54,450 running install_lib 2026-06-27T16:27:54,460 creating build/bdist.linux-armv7l/wheel 2026-06-27T16:27:54,462 creating build/bdist.linux-armv7l/wheel/AmberMDrun 2026-06-27T16:27:54,463 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/equil.py -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,465 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/_pyamber.cpython-311-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,495 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/_pyamber.pyi -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,497 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/__init__.py -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,499 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/pyamber.py -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,501 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/version.py -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,503 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/mmpbsa.py -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,505 copying build/lib.linux-armv7l-cpython-311/AmberMDrun/main.py -> build/bdist.linux-armv7l/wheel/./AmberMDrun 2026-06-27T16:27:54,507 running install_egg_info 2026-06-27T16:27:54,530 running egg_info 2026-06-27T16:27:54,537 writing AmberMDrun.egg-info/PKG-INFO 2026-06-27T16:27:54,541 writing dependency_links to AmberMDrun.egg-info/dependency_links.txt 2026-06-27T16:27:54,542 writing entry points to AmberMDrun.egg-info/entry_points.txt 2026-06-27T16:27:54,543 writing requirements to AmberMDrun.egg-info/requires.txt 2026-06-27T16:27:54,544 writing top-level names to AmberMDrun.egg-info/top_level.txt 2026-06-27T16:27:54,556 reading manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:27:54,578 reading manifest template 'MANIFEST.in' 2026-06-27T16:27:54,587 warning: no previously-included files matching '*.py[cod]' found anywhere in distribution 2026-06-27T16:27:54,588 warning: no previously-included files matching '__pycache__/*' found anywhere in distribution 2026-06-27T16:27:54,589 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.git' 2026-06-27T16:27:54,590 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.appveyor.yml' 2026-06-27T16:27:54,591 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.clang-format' 2026-06-27T16:27:54,592 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.clang-tidy' 2026-06-27T16:27:54,592 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.cmake-format.yaml' 2026-06-27T16:27:54,593 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.codespell-ignore-lines' 2026-06-27T16:27:54,594 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.gitattributes' 2026-06-27T16:27:54,595 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.gitignore' 2026-06-27T16:27:54,596 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.pre-commit-config.yaml' 2026-06-27T16:27:54,596 warning: no previously-included files found matching 'AmberMDrun/extern/pybind11/.readthedocs.yml' 2026-06-27T16:27:54,597 no previously-included directories found matching 'AmberMDrun/extern/pybind11/.github' 2026-06-27T16:27:54,598 no previously-included directories found matching 'AmberMDrun/extern/pybind11/docs' 2026-06-27T16:27:54,599 no previously-included directories found matching 'AmberMDrun/extern/pybind11/tests' 2026-06-27T16:27:54,600 adding license file 'LICENSE' 2026-06-27T16:27:54,607 writing manifest file 'AmberMDrun.egg-info/SOURCES.txt' 2026-06-27T16:27:54,608 Copying AmberMDrun.egg-info to build/bdist.linux-armv7l/wheel/./AmberMDrun-0.0.8-py3.11.egg-info 2026-06-27T16:27:54,622 running install_scripts 2026-06-27T16:27:54,665 creating build/bdist.linux-armv7l/wheel/ambermdrun-0.0.8.dist-info/WHEEL 2026-06-27T16:27:54,669 creating '/tmp/pip-wheel-cltl_2i3/.tmp-k0uq7br2/ambermdrun-0.0.8-cp311-cp311-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2026-06-27T16:27:54,672 adding 'AmberMDrun/__init__.py' 2026-06-27T16:27:54,959 adding 'AmberMDrun/_pyamber.cpython-311-arm-linux-gnueabihf.so' 2026-06-27T16:27:54,971 adding 'AmberMDrun/_pyamber.pyi' 2026-06-27T16:27:54,972 adding 'AmberMDrun/equil.py' 2026-06-27T16:27:54,974 adding 'AmberMDrun/main.py' 2026-06-27T16:27:54,975 adding 'AmberMDrun/mmpbsa.py' 2026-06-27T16:27:54,977 adding 'AmberMDrun/pyamber.py' 2026-06-27T16:27:54,978 adding 'AmberMDrun/version.py' 2026-06-27T16:27:54,980 adding 'ambermdrun-0.0.8.dist-info/LICENSE' 2026-06-27T16:27:54,982 adding 'ambermdrun-0.0.8.dist-info/METADATA' 2026-06-27T16:27:54,983 adding 'ambermdrun-0.0.8.dist-info/WHEEL' 2026-06-27T16:27:54,984 adding 'ambermdrun-0.0.8.dist-info/entry_points.txt' 2026-06-27T16:27:54,985 adding 'ambermdrun-0.0.8.dist-info/top_level.txt' 2026-06-27T16:27:54,986 adding 'ambermdrun-0.0.8.dist-info/RECORD' 2026-06-27T16:27:54,994 removing build/bdist.linux-armv7l/wheel 2026-06-27T16:27:55,095 Building wheel for ambermdrun (pyproject.toml): finished with status 'done' 2026-06-27T16:27:55,114 Created wheel for ambermdrun: filename=ambermdrun-0.0.8-cp311-cp311-linux_armv7l.whl size=596086 sha256=f19d3023b35d6f2d62252573858443dac56ea05fd6e5085ebb70b548b508c13a 2026-06-27T16:27:55,115 Stored in directory: /tmp/pip-ephem-wheel-cache-qfd5hmha/wheels/d0/c5/c1/2e4b15c9e1ad38344f0dab408483cb9e38212b7b6954e4257a 2026-06-27T16:27:55,126 Successfully built ambermdrun 2026-06-27T16:27:55,148 Removed build tracker: '/tmp/pip-build-tracker-qaibiy1z'