2025-09-08T13:58:18,994 Created temporary directory: /tmp/pip-build-tracker-nrsrgppu
2025-09-08T13:58:18,995 Initialized build tracking at /tmp/pip-build-tracker-nrsrgppu
2025-09-08T13:58:18,995 Created build tracker: /tmp/pip-build-tracker-nrsrgppu
2025-09-08T13:58:18,995 Entered build tracker: /tmp/pip-build-tracker-nrsrgppu
2025-09-08T13:58:18,995 Created temporary directory: /tmp/pip-wheel-t6jso99w
2025-09-08T13:58:18,999 Created temporary directory: /tmp/pip-ephem-wheel-cache-ope36zih
2025-09-08T13:58:19,053 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-08T13:58:19,055 2 location(s) to search for versions of pyxmolpp2:
2025-09-08T13:58:19,055 * https://pypi.org/simple/pyxmolpp2/
2025-09-08T13:58:19,055 * https://www.piwheels.org/simple/pyxmolpp2/
2025-09-08T13:58:19,056 Fetching project page and analyzing links: https://pypi.org/simple/pyxmolpp2/
2025-09-08T13:58:19,056 Getting page https://pypi.org/simple/pyxmolpp2/
2025-09-08T13:58:19,057 Found index url https://pypi.org/simple/
2025-09-08T13:58:19,129 Fetched page https://pypi.org/simple/pyxmolpp2/ as application/vnd.pypi.simple.v1+json
2025-09-08T13:58:19,133   Found link https://files.pythonhosted.org/packages/41/1d/65a5e96d7d0c86d687b4e7e8d10ac232f573e14b9d1884111ebd1a477502/pyxmolpp2-0.0.1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.0.1
2025-09-08T13:58:19,134   Found link https://files.pythonhosted.org/packages/e2/27/027a784be451eb7fe624a90523f4f289d6814db90adddbf09318ae136e4e/pyxmolpp2-0.1.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.1.0
2025-09-08T13:58:19,134   Found link https://files.pythonhosted.org/packages/49/94/6e7b42f4898aff76225a6e7ac3148dd53fd871a8cf1fa87876b5e5661fe4/pyxmolpp2-0.1.1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.1.1
2025-09-08T13:58:19,134   Found link https://files.pythonhosted.org/packages/d9/89/7e348a861f1cbf78307f4617881c0996e74b38ab6f1d5d927b5be3c8b934/pyxmolpp2-0.2.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.2.0
2025-09-08T13:58:19,134   Found link https://files.pythonhosted.org/packages/8c/89/16cf719b01cb66c3f62f5540abeca7bc26a1dbe7cd83c048d94dd4c60c37/pyxmolpp2-0.3.0.dev0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.3.0.dev0
2025-09-08T13:58:19,135   Found link https://files.pythonhosted.org/packages/32/94/5d324e82f3785ea81d6913a781e674f95995cbaa54ec32171d0da3056f1c/pyxmolpp2-0.3.0.dev1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.3.0.dev1
2025-09-08T13:58:19,135   Found link https://files.pythonhosted.org/packages/66/fa/f3e3cd5cdf297b37e10a8131075358a3e663831b965ce71900122e765d06/pyxmolpp2-0.3.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.3.0
2025-09-08T13:58:19,135   Found link https://files.pythonhosted.org/packages/db/70/90e7913b6629f135ab3f8dcfae9c428aaf311e981db0caada01f51c8751a/pyxmolpp2-0.4.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.4.0
2025-09-08T13:58:19,135   Found link https://files.pythonhosted.org/packages/ea/1d/22d1b9eff0ed0b73bb8ba213c459a8818103847199add714dec7c0862c9b/pyxmolpp2-0.6.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.6.0
2025-09-08T13:58:19,135   Found link https://files.pythonhosted.org/packages/fb/26/6420cdf2349c7bbdf98f58cdb260e1ed0dee55d290cdab6b79d99b457ef9/pyxmolpp2-0.6.1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.6.1
2025-09-08T13:58:19,136   Found link https://files.pythonhosted.org/packages/27/33/21c7acd6275667d94465436e150f6f3724935c4fd171dd51db516d5a3495/pyxmolpp2-0.7.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.7.0
2025-09-08T13:58:19,136   Found link https://files.pythonhosted.org/packages/7b/36/aac554b63b1e7fd94ead8a17af4a3d968b9ebab94c905369d5ec20a140f0/pyxmolpp2-0.7.1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.7.1
2025-09-08T13:58:19,136   Found link https://files.pythonhosted.org/packages/e0/ad/0e16148eed09fc4190458935fbbf948aaa2794d1620842f0e3fc3aaa7f14/pyxmolpp2-0.8.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.8.0
2025-09-08T13:58:19,136   Found link https://files.pythonhosted.org/packages/1a/97/f5a5894f690501edb1f32ce0373f364abd70a55293b4222a2e8fd2b62b08/pyxmolpp2-0.8.1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.8.1
2025-09-08T13:58:19,137   Found link https://files.pythonhosted.org/packages/c7/ed/0784103f8a79a3c24b71e560ef517c623b029a04c2c4f67820a70bc68f27/pyxmolpp2-0.8.2.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.8.2
2025-09-08T13:58:19,137   Found link https://files.pythonhosted.org/packages/85/17/8ab6537831012139ee04eaba92e3eb2b1724a81c3ed27f191b3d28f6789c/pyxmolpp2-0.9.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.9.0
2025-09-08T13:58:19,137   Found link https://files.pythonhosted.org/packages/55/4b/d6906a0c33681b8f03fa9497cd40a74b069c7393351927dd772503d0ecfb/pyxmolpp2-0.9.0.post1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.9.0.post1
2025-09-08T13:58:19,137   Found link https://files.pythonhosted.org/packages/b7/9b/fb4bb3e07ea292b34f258da0a9f08ae96f18a990477d2f7714319dc11bb1/pyxmolpp2-0.10.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.10.0
2025-09-08T13:58:19,137   Found link https://files.pythonhosted.org/packages/50/38/47ab868258a00a5d017424f8d5456a3718a475f1a854bdc999df7f116075/pyxmolpp2-0.10.1.post1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.10.1.post1
2025-09-08T13:58:19,138   Found link https://files.pythonhosted.org/packages/26/fc/9e70d088b5e6fd688e01c0f13ac748d813f813b8a358bacb8eb66d1971fb/pyxmolpp2-0.10.1.post2.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.10.1.post2
2025-09-08T13:58:19,138   Found link https://files.pythonhosted.org/packages/64/1e/ab2524f122b9966e8c51e2228fdde7f00d7475eec722a27b80aa3e26bfad/pyxmolpp2-0.10.2.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.10.2
2025-09-08T13:58:19,138   Found link https://files.pythonhosted.org/packages/ac/ac/417e76e0eb127e941fb6599915dd543a50e115925180fe97c83a6947ef5d/pyxmolpp2-0.10.3.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.10.3
2025-09-08T13:58:19,138   Found link https://files.pythonhosted.org/packages/60/57/46db548b97f72c8ce5fbdc48392cf8870cff33afb5e95d24d78dec9c23c4/pyxmolpp2-0.10.4.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 0.10.4
2025-09-08T13:58:19,138   Found link https://files.pythonhosted.org/packages/3a/2c/8275c969590e230dd2c56daab6e40d236df9736f268aa121ea426c97f819/pyxmolpp2-1.0.0.dev1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.0.0.dev1
2025-09-08T13:58:19,139   Found link https://files.pythonhosted.org/packages/78/a7/ea6c951361316cf343a0f16da27f031ab2cfb16c90159ac52691540873fe/pyxmolpp2-1.0.0.dev3.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.0.0.dev3
2025-09-08T13:58:19,139   Found link https://files.pythonhosted.org/packages/dd/96/b6aa5603b5f40b892572e42338b23a75a78c162ec958f75f429cc4d05f34/pyxmolpp2-1.0.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.0.0
2025-09-08T13:58:19,139   Found link https://files.pythonhosted.org/packages/b6/4f/9e63388cb7670452069a038097371bd5c87ea665ea9f9cd2b3009498ab0f/pyxmolpp2-1.1.0.dev0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.1.0.dev0
2025-09-08T13:58:19,139   Found link https://files.pythonhosted.org/packages/07/ef/f93acfeedd3cfd180366afa66c555ef0ad5f59daa22a023f7d56a37b3774/pyxmolpp2-1.1.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.1.0
2025-09-08T13:58:19,140   Found link https://files.pythonhosted.org/packages/40/25/974e02ffd74a29b48d37f7ead5988c4fc31554ab2439361dbe6ade50df5c/pyxmolpp2-1.1.0.post1.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.1.0.post1
2025-09-08T13:58:19,140   Found link https://files.pythonhosted.org/packages/94/eb/8b82d34f5f0fff1ae0ee57db7bc01d5c582896a21aa6c23a0691f8dd2cef/pyxmolpp2-1.2.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.2.0
2025-09-08T13:58:19,140   Found link https://files.pythonhosted.org/packages/8e/37/8e017030208308e0c9b96ab4799e06229a1bc3e30eb5931aa65d7bd44fc6/pyxmolpp2-1.3.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.3.0
2025-09-08T13:58:19,140   Found link https://files.pythonhosted.org/packages/69/d9/818b1d2533d74bbc1b571061bc6eadb3e8179ad45f98b996e2e752bbb8d7/pyxmolpp2-1.4.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.4.0
2025-09-08T13:58:19,140   Found link https://files.pythonhosted.org/packages/4b/7d/3a0beee575fc48b90d6685200925e081c9f00a80785f6c3399460f7a3a36/pyxmolpp2-1.5.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.5.0
2025-09-08T13:58:19,141   Found link https://files.pythonhosted.org/packages/5b/2a/67fff35be6b97a56c5c21823a7e98765379b83dfc6f1875e5282cbd85267/pyxmolpp2-1.5.2.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.5.2
2025-09-08T13:58:19,141   Found link https://files.pythonhosted.org/packages/ea/be/6ff70c774714c681459f089f77e92bbc13fb9bd068727404f525e4a3dbbb/pyxmolpp2-1.5.3.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.5.3
2025-09-08T13:58:19,141   Found link https://files.pythonhosted.org/packages/13/09/0b0c1f7ed58aa7605854268f7eaeadafed70cded0855d450b93fbe278cc0/pyxmolpp2-1.6.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 1.6.0
2025-09-08T13:58:19,141   Found link https://files.pythonhosted.org/packages/43/af/adb175fd4c9a52ddfd9e943962e1da8810579bc4a0643db7bfff99b8f8cb/pyxmolpp2-2.0a0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 2.0a0
2025-09-08T13:58:19,142   Found link https://files.pythonhosted.org/packages/bd/65/7f96775c57a613b95a7abae1956572a570e9e488d9bb0b05241338a72774/pyxmolpp2-2.0.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 2.0
2025-09-08T13:58:19,142   Found link https://files.pythonhosted.org/packages/5a/bc/01f71b18a8713194f43920fb0d89e7ae3c219abeb0efc734f0bf3303c86f/pyxmolpp2-2.0.2.tar.gz (from https://pypi.org/simple/pyxmolpp2/), version: 2.0.2
2025-09-08T13:58:19,142 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyxmolpp2/
2025-09-08T13:58:19,142 Getting page https://www.piwheels.org/simple/pyxmolpp2/
2025-09-08T13:58:19,143 Found index url https://www.piwheels.org/simple/
2025-09-08T13:58:19,227 Fetched page https://www.piwheels.org/simple/pyxmolpp2/ as text/html
2025-09-08T13:58:19,229   Skipping link: No binaries permitted for pyxmolpp2: https://archive1.piwheels.org/simple/pyxmolpp2/pyxmolpp2-0.0.1-cp34-cp34m-linux_armv7l.whl#sha256=176920d3ec472d788331912a641cf8eb70e3eb87aac83c1e527ef33cdc152da6 (from https://www.piwheels.org/simple/pyxmolpp2/)
2025-09-08T13:58:19,229   Skipping link: No binaries permitted for pyxmolpp2: https://archive1.piwheels.org/simple/pyxmolpp2/pyxmolpp2-0.0.1-cp34-cp34m-linux_armv6l.whl#sha256=176920d3ec472d788331912a641cf8eb70e3eb87aac83c1e527ef33cdc152da6 (from https://www.piwheels.org/simple/pyxmolpp2/)
2025-09-08T13:58:19,229   Skipping link: No binaries permitted for pyxmolpp2: https://archive1.piwheels.org/simple/pyxmolpp2/pyxmolpp2-0.0.1-cp35-cp35m-linux_armv7l.whl#sha256=7f7fc7bce046e180693cc029132c8ab2ee085fd82c822f949a0e7852b96e50e0 (from https://www.piwheels.org/simple/pyxmolpp2/)
2025-09-08T13:58:19,229   Skipping link: No binaries permitted for pyxmolpp2: https://archive1.piwheels.org/simple/pyxmolpp2/pyxmolpp2-0.0.1-cp35-cp35m-linux_armv6l.whl#sha256=7f7fc7bce046e180693cc029132c8ab2ee085fd82c822f949a0e7852b96e50e0 (from https://www.piwheels.org/simple/pyxmolpp2/)
2025-09-08T13:58:19,229 Skipping link: not a file: https://www.piwheels.org/simple/pyxmolpp2/
2025-09-08T13:58:19,229 Skipping link: not a file: https://pypi.org/simple/pyxmolpp2/
2025-09-08T13:58:19,261 Given no hashes to check 1 links for project 'pyxmolpp2': discarding no candidates
2025-09-08T13:58:19,262 Collecting pyxmolpp2==0.3.0.dev0
2025-09-08T13:58:19,263   Created temporary directory: /tmp/pip-unpack-1cgnm1qg
2025-09-08T13:58:19,906   Downloading pyxmolpp2-0.3.0.dev0.tar.gz (70 kB)
2025-09-08T13:58:20,017   Added pyxmolpp2==0.3.0.dev0 from https://files.pythonhosted.org/packages/8c/89/16cf719b01cb66c3f62f5540abeca7bc26a1dbe7cd83c048d94dd4c60c37/pyxmolpp2-0.3.0.dev0.tar.gz to build tracker '/tmp/pip-build-tracker-nrsrgppu'
2025-09-08T13:58:20,018   Running setup.py (path:/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py) egg_info for package pyxmolpp2
2025-09-08T13:58:20,019   Created temporary directory: /tmp/pip-pip-egg-info-1d5gma6_
2025-09-08T13:58:20,019   Preparing metadata (setup.py): started
2025-09-08T13:58:20,020   Running command python setup.py egg_info
2025-09-08T13:58:20,734   fatal: not a git repository (or any parent up to mount point /)
2025-09-08T13:58:20,734   Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
2025-09-08T13:58:21,108   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:332: InformationOnly: Normalizing '0.3.0.dev.0' to '0.3.0.dev0'
2025-09-08T13:58:21,108     self.metadata.version = self._normalize_version(self.metadata.version)
2025-09-08T13:58:21,185   running egg_info
2025-09-08T13:58:21,262   creating /tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info
2025-09-08T13:58:21,262   writing /tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info/PKG-INFO
2025-09-08T13:58:21,264   writing dependency_links to /tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info/dependency_links.txt
2025-09-08T13:58:21,264   writing top-level names to /tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info/top_level.txt
2025-09-08T13:58:21,265   writing manifest file '/tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info/SOURCES.txt'
2025-09-08T13:58:21,413   reading manifest file '/tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info/SOURCES.txt'
2025-09-08T13:58:21,414   reading manifest template 'MANIFEST.in'
2025-09-08T13:58:21,423   warning: no files found matching '*' under directory 'external'
2025-09-08T13:58:21,423   warning: no files found matching '.'
2025-09-08T13:58:21,424   warning: no files found matching '.'
2025-09-08T13:58:21,424   warning: no files found matching '.'
2025-09-08T13:58:21,425   warning: no previously-included files matching '.git' found anywhere in distribution
2025-09-08T13:58:21,426   warning: no previously-included files matching '.js' found anywhere in distribution
2025-09-08T13:58:21,426   warning: no previously-included files matching '.html' found anywhere in distribution
2025-09-08T13:58:21,426   warning: no previously-included files matching '.png' found anywhere in distribution
2025-09-08T13:58:21,427   warning: no previously-included files matching '.dox' found anywhere in distribution
2025-09-08T13:58:21,437   writing manifest file '/tmp/pip-pip-egg-info-1d5gma6_/pyxmolpp2.egg-info/SOURCES.txt'
2025-09-08T13:58:21,550   Preparing metadata (setup.py): finished with status 'done'
2025-09-08T13:58:21,555   Source in /tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e has version 0.3.0.dev0, which satisfies requirement pyxmolpp2==0.3.0.dev0 from https://files.pythonhosted.org/packages/8c/89/16cf719b01cb66c3f62f5540abeca7bc26a1dbe7cd83c048d94dd4c60c37/pyxmolpp2-0.3.0.dev0.tar.gz
2025-09-08T13:58:21,555   Removed pyxmolpp2==0.3.0.dev0 from https://files.pythonhosted.org/packages/8c/89/16cf719b01cb66c3f62f5540abeca7bc26a1dbe7cd83c048d94dd4c60c37/pyxmolpp2-0.3.0.dev0.tar.gz from build tracker '/tmp/pip-build-tracker-nrsrgppu'
2025-09-08T13:58:21,558 Created temporary directory: /tmp/pip-unpack-byledqvz
2025-09-08T13:58:21,558 Created temporary directory: /tmp/pip-unpack-s9tseo7v
2025-09-08T13:58:21,559 Building wheels for collected packages: pyxmolpp2
2025-09-08T13:58:21,560   Created temporary directory: /tmp/pip-wheel-2qajgd82
2025-09-08T13:58:21,560   DEPRECATION: Building 'pyxmolpp2' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'pyxmolpp2'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-09-08T13:58:21,561   Building wheel for pyxmolpp2 (setup.py): started
2025-09-08T13:58:21,562   Destination directory: /tmp/pip-wheel-2qajgd82
2025-09-08T13:58:21,562   Running command python setup.py bdist_wheel
2025-09-08T13:58:22,276   fatal: not a git repository (or any parent up to mount point /)
2025-09-08T13:58:22,276   Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
2025-09-08T13:58:22,655   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:332: InformationOnly: Normalizing '0.3.0.dev.0' to '0.3.0.dev0'
2025-09-08T13:58:22,655     self.metadata.version = self._normalize_version(self.metadata.version)
2025-09-08T13:58:22,658   running bdist_wheel
2025-09-08T13:58:22,957   running build
2025-09-08T13:58:22,957   running build_ext
2025-09-08T13:58:23,007   /tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py:27: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
2025-09-08T13:58:23,007     cmake_version = LooseVersion(re.search(r'version\s*([\d.]+)', out.decode()).group(1))
2025-09-08T13:58:23,008   /tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py:28: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
2025-09-08T13:58:23,008     if cmake_version < LooseVersion('3.5.0'):
2025-09-08T13:58:23,057   CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
2025-09-08T13:58:23,057     Compatibility with CMake < 3.10 will be removed from a future version of
2025-09-08T13:58:23,058     CMake.

2025-09-08T13:58:23,058     Update the VERSION argument <min> value.  Or, use the <min>...<max> syntax
2025-09-08T13:58:23,058     to tell CMake that the project requires at least <min> but has been updated
2025-09-08T13:58:23,058     to work with policies introduced by <max> or earlier.


2025-09-08T13:58:23,322   -- The C compiler identification is GNU 14.2.0
2025-09-08T13:58:23,638   -- The CXX compiler identification is GNU 14.2.0
2025-09-08T13:58:23,685   -- Detecting C compiler ABI info
2025-09-08T13:58:24,114   -- Detecting C compiler ABI info - done
2025-09-08T13:58:24,185   -- Check for working C compiler: /usr/bin/cc - skipped
2025-09-08T13:58:24,187   -- Detecting C compile features
2025-09-08T13:58:24,189   -- Detecting C compile features - done
2025-09-08T13:58:24,260   -- Detecting CXX compiler ABI info
2025-09-08T13:58:24,743   -- Detecting CXX compiler ABI info - done
2025-09-08T13:58:24,822   -- Check for working CXX compiler: /usr/bin/c++ - skipped
2025-09-08T13:58:24,824   -- Detecting CXX compile features
2025-09-08T13:58:24,827   -- Detecting CXX compile features - done
2025-09-08T13:58:24,863   CMake Warning (dev) at CMakeLists.txt:8 (find_package):
2025-09-08T13:58:24,863     Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
2025-09-08T13:58:24,863     are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
2025-09-08T13:58:24,863     the cmake_policy command to set the policy and suppress this warning.

2025-09-08T13:58:24,863   This warning is for project developers.  Use -Wno-dev to suppress it.

2025-09-08T13:58:24,936   -- Found PythonInterp: /usr/bin/python3 (found version "3.13.5")
2025-09-08T13:58:24,937   CMake Warning (dev) at CMakeLists.txt:9 (find_package):
2025-09-08T13:58:24,937     Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
2025-09-08T13:58:24,937     are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
2025-09-08T13:58:24,937     the cmake_policy command to set the policy and suppress this warning.

2025-09-08T13:58:24,938   This warning is for project developers.  Use -Wno-dev to suppress it.

2025-09-08T13:58:24,968   -- Found PythonLibs: /usr/lib/arm-linux-gnueabihf/libpython3.13.so (found suitable version "3.13.5", minimum required is "3.13")
2025-09-08T13:58:24,968   Using default python version: 3.13.5
2025-09-08T13:58:24,969   DONT USE COVERAGE PROFILE
2025-09-08T13:58:24,969   CMake Error at CMakeLists.txt:40 (add_subdirectory):
2025-09-08T13:58:24,969     add_subdirectory given source "external/googletest" which is not an
2025-09-08T13:58:24,969     existing directory.


2025-09-08T13:58:24,970   CMake Error at CMakeLists.txt:45 (add_subdirectory):
2025-09-08T13:58:24,970     add_subdirectory given source "external/pybind11" which is not an existing
2025-09-08T13:58:24,970     directory.


2025-09-08T13:58:24,973   selectionTestsSources
2025-09-08T13:58:24,974   polymerTestsSources
2025-09-08T13:58:24,975   pdbTestsSources
2025-09-08T13:58:24,976   trjtoolTestsSources
2025-09-08T13:58:24,978   geometryTestsSources
2025-09-08T13:58:24,979   crystalTestsSources
2025-09-08T13:58:24,986   CMake Error at WriteVersionInfo.cmake:15 (message):
2025-09-08T13:58:24,986     message called with incorrect number of arguments
2025-09-08T13:58:24,986   Call Stack (most recent call first):
2025-09-08T13:58:24,987     CMakeLists.txt:53 (include)


2025-09-08T13:58:24,994   CMake Error at CMakeLists.txt:82 (pybind11_add_module):
2025-09-08T13:58:24,994     Unknown CMake command "pybind11_add_module".


2025-09-08T13:58:24,995   -- Configuring incomplete, errors occurred!
2025-09-08T13:58:25,019   Traceback (most recent call last):
2025-09-08T13:58:25,027     File "<string>", line 2, in <module>
2025-09-08T13:58:25,027       exec(compile('''
2025-09-08T13:58:25,027       ~~~~^^^^^^^^^^^^
2025-09-08T13:58:25,027       # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2025-09-08T13:58:25,027       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T13:58:25,028       ...<32 lines>...
2025-09-08T13:58:25,028       exec(compile(setup_py_code, filename, "exec"))
2025-09-08T13:58:25,028       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T13:58:25,028       ''' % ('/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py',), "<pip-setuptools-caller>", "exec"))
2025-09-08T13:58:25,028       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T13:58:25,028     File "<pip-setuptools-caller>", line 35, in <module>
2025-09-08T13:58:25,029     File "/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py", line 67, in <module>
2025-09-08T13:58:25,029       setup(
2025-09-08T13:58:25,029       ~~~~~^
2025-09-08T13:58:25,029           name='pyxmolpp2',
2025-09-08T13:58:25,029           ^^^^^^^^^^^^^^^^^
2025-09-08T13:58:25,029       ...<9 lines>...
2025-09-08T13:58:25,029           zip_safe=False,
2025-09-08T13:58:25,029           ^^^^^^^^^^^^^^^
2025-09-08T13:58:25,030       )
2025-09-08T13:58:25,030       ^
2025-09-08T13:58:25,030     File "/usr/local/lib/python3.13/dist-packages/setuptools/__init__.py", line 115, in setup
2025-09-08T13:58:25,030       return distutils.core.setup(**attrs)
2025-09-08T13:58:25,030              ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,030     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 186, in setup
2025-09-08T13:58:25,031       return run_commands(dist)
2025-09-08T13:58:25,031     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/core.py", line 202, in run_commands
2025-09-08T13:58:25,031       dist.run_commands()
2025-09-08T13:58:25,031       ~~~~~~~~~~~~~~~~~^^
2025-09-08T13:58:25,031     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
2025-09-08T13:58:25,031       self.run_command(cmd)
2025-09-08T13:58:25,031       ~~~~~~~~~~~~~~~~^^^^^
2025-09-08T13:58:25,032     File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command
2025-09-08T13:58:25,032       super().run_command(command)
2025-09-08T13:58:25,032       ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,032     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command
2025-09-08T13:58:25,032       cmd_obj.run()
2025-09-08T13:58:25,032       ~~~~~~~~~~~^^
2025-09-08T13:58:25,032     File "/usr/local/lib/python3.13/dist-packages/setuptools/command/bdist_wheel.py", line 370, in run
2025-09-08T13:58:25,032       self.run_command("build")
2025-09-08T13:58:25,033       ~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,033     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command
2025-09-08T13:58:25,033       self.distribution.run_command(command)
2025-09-08T13:58:25,033       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,033     File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command
2025-09-08T13:58:25,033       super().run_command(command)
2025-09-08T13:58:25,034       ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,034     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command
2025-09-08T13:58:25,034       cmd_obj.run()
2025-09-08T13:58:25,034       ~~~~~~~~~~~^^
2025-09-08T13:58:25,034     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/command/build.py", line 135, in run
2025-09-08T13:58:25,034       self.run_command(cmd_name)
2025-09-08T13:58:25,034       ~~~~~~~~~~~~~~~~^^^^^^^^^^
2025-09-08T13:58:25,035     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/cmd.py", line 357, in run_command
2025-09-08T13:58:25,035       self.distribution.run_command(command)
2025-09-08T13:58:25,035       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,035     File "/usr/local/lib/python3.13/dist-packages/setuptools/dist.py", line 1102, in run_command
2025-09-08T13:58:25,035       super().run_command(command)
2025-09-08T13:58:25,035       ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
2025-09-08T13:58:25,035     File "/usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py", line 1021, in run_command
2025-09-08T13:58:25,036       cmd_obj.run()
2025-09-08T13:58:25,036       ~~~~~~~~~~~^^
2025-09-08T13:58:25,036     File "/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py", line 32, in run
2025-09-08T13:58:25,036       self.build_extension(ext)
2025-09-08T13:58:25,036       ~~~~~~~~~~~~~~~~~~~~^^^^^
2025-09-08T13:58:25,036     File "/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py", line 60, in build_extension
2025-09-08T13:58:25,036       subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
2025-09-08T13:58:25,037       ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T13:58:25,037     File "/usr/lib/python3.13/subprocess.py", line 419, in check_call
2025-09-08T13:58:25,037       raise CalledProcessError(retcode, cmd)
2025-09-08T13:58:25,037   subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/build/lib.linux-armv7l-cpython-313', '-DPYTHON_EXECUTABLE=/usr/bin/python3', '-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE', '-DCMAKE_INSTALL_RPATH=$ORIGIN', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
2025-09-08T13:58:25,144   ERROR: python setup.py bdist_wheel exited with 1
2025-09-08T13:58:25,157   [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c '
2025-09-08T13:58:25,157   exec(compile('"'"''"'"''"'"'
2025-09-08T13:58:25,157   # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
2025-09-08T13:58:25,157   #
2025-09-08T13:58:25,157   # - It imports setuptools before invoking setup.py, to enable projects that directly
2025-09-08T13:58:25,157   #   import from `distutils.core` to work with newer packaging standards.
2025-09-08T13:58:25,157   # - It provides a clear error message when setuptools is not installed.
2025-09-08T13:58:25,157   # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2025-09-08T13:58:25,157   #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2025-09-08T13:58:25,157   #     manifest_maker: standard file '"'"'-c'"'"' not found".
2025-09-08T13:58:25,157   # - It generates a shim setup.py, for handling setup.cfg-only projects.
2025-09-08T13:58:25,157   import os, sys, tokenize, traceback
2025-09-08T13:58:25,157   
2025-09-08T13:58:25,157   try:
2025-09-08T13:58:25,157       import setuptools
2025-09-08T13:58:25,157   except ImportError:
2025-09-08T13:58:25,157       print(
2025-09-08T13:58:25,157           "ERROR: Can not execute `setup.py` since setuptools failed to import in "
2025-09-08T13:58:25,157           "the build environment with exception:",
2025-09-08T13:58:25,157           file=sys.stderr,
2025-09-08T13:58:25,157       )
2025-09-08T13:58:25,157       traceback.print_exc()
2025-09-08T13:58:25,157       sys.exit(1)
2025-09-08T13:58:25,157   
2025-09-08T13:58:25,157   __file__ = %r
2025-09-08T13:58:25,157   sys.argv[0] = __file__
2025-09-08T13:58:25,157   
2025-09-08T13:58:25,157   if os.path.exists(__file__):
2025-09-08T13:58:25,157       filename = __file__
2025-09-08T13:58:25,157       with tokenize.open(__file__) as f:
2025-09-08T13:58:25,157           setup_py_code = f.read()
2025-09-08T13:58:25,157   else:
2025-09-08T13:58:25,157       filename = "<auto-generated setuptools caller>"
2025-09-08T13:58:25,157       setup_py_code = "from setuptools import setup; setup()"
2025-09-08T13:58:25,157   
2025-09-08T13:58:25,157   exec(compile(setup_py_code, filename, "exec"))
2025-09-08T13:58:25,157   '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' bdist_wheel -d /tmp/pip-wheel-2qajgd82[/]
2025-09-08T13:58:25,157   [bold magenta]cwd[/]: /tmp/pip-wheel-t6jso99w/pyxmolpp2_78aa63f9cf934ef8a2b5bdb66f5a913e/
2025-09-08T13:58:25,157   Building wheel for pyxmolpp2 (setup.py): finished with status 'error'
2025-09-08T13:58:25,158   ERROR: Failed building wheel for pyxmolpp2
2025-09-08T13:58:25,159   Running setup.py clean for pyxmolpp2
2025-09-08T13:58:25,160   Running command python setup.py clean
2025-09-08T13:58:25,871   fatal: not a git repository (or any parent up to mount point /)
2025-09-08T13:58:25,871   Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).
2025-09-08T13:58:26,247   /usr/local/lib/python3.13/dist-packages/setuptools/dist.py:332: InformationOnly: Normalizing '0.3.0.dev.0' to '0.3.0.dev0'
2025-09-08T13:58:26,247     self.metadata.version = self._normalize_version(self.metadata.version)
2025-09-08T13:58:26,324   running clean
2025-09-08T13:58:26,467   removing 'build/temp.linux-armv7l-cpython-313' (and everything under it)
2025-09-08T13:58:26,469   'build/lib.linux-armv7l-cpython-313' does not exist -- can't clean it
2025-09-08T13:58:26,469   'build/bdist.linux-armv7l' does not exist -- can't clean it
2025-09-08T13:58:26,469   'build/scripts-3.13' does not exist -- can't clean it
2025-09-08T13:58:26,469   removing 'build'
2025-09-08T13:58:26,582 Failed to build pyxmolpp2
2025-09-08T13:58:26,583 ERROR: Failed to build one or more wheels
2025-09-08T13:58:26,584 Exception information:
2025-09-08T13:58:26,584 Traceback (most recent call last):
2025-09-08T13:58:26,584   File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
2025-09-08T13:58:26,584     status = _inner_run()
2025-09-08T13:58:26,584   File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
2025-09-08T13:58:26,584     return self.run(options, args)
2025-09-08T13:58:26,584            ~~~~~~~~^^^^^^^^^^^^^^^
2025-09-08T13:58:26,584   File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper
2025-09-08T13:58:26,584     return func(self, options, args)
2025-09-08T13:58:26,584   File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run
2025-09-08T13:58:26,584     raise CommandError("Failed to build one or more wheels")
2025-09-08T13:58:26,584 pip._internal.exceptions.CommandError: Failed to build one or more wheels
2025-09-08T13:58:26,588 Removed build tracker: '/tmp/pip-build-tracker-nrsrgppu'