2023-09-19T10:38:36,265 Created temporary directory: /tmp/pip-build-tracker-n91_9ba2 2023-09-19T10:38:36,266 Initialized build tracking at /tmp/pip-build-tracker-n91_9ba2 2023-09-19T10:38:36,267 Created build tracker: /tmp/pip-build-tracker-n91_9ba2 2023-09-19T10:38:36,267 Entered build tracker: /tmp/pip-build-tracker-n91_9ba2 2023-09-19T10:38:36,268 Created temporary directory: /tmp/pip-wheel-uwl9trpe 2023-09-19T10:38:36,272 Created temporary directory: /tmp/pip-ephem-wheel-cache-khv3vka9 2023-09-19T10:38:36,296 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-19T10:38:36,300 2 location(s) to search for versions of anagenex-mdtraj: 2023-09-19T10:38:36,300 * https://pypi.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,300 * https://www.piwheels.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,301 Fetching project page and analyzing links: https://pypi.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,301 Getting page https://pypi.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,303 Found index url https://pypi.org/simple/ 2023-09-19T10:38:36,557 Fetched page https://pypi.org/simple/anagenex-mdtraj/ as application/vnd.pypi.simple.v1+json 2023-09-19T10:38:36,558 Found link https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz (from https://pypi.org/simple/anagenex-mdtraj/), version: 1.9.8.dev0 2023-09-19T10:38:36,559 Skipping link: No binaries permitted for anagenex-mdtraj: https://files.pythonhosted.org/packages/9a/4f/049a6cbd218ae2fffe1d49c08621b441e955eb54ee6ea4262cda8a8f0488/anagenex_mdtraj-1.9.8.dev0-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,560 Skipping link: No binaries permitted for anagenex-mdtraj: https://files.pythonhosted.org/packages/69/29/844b7e93b675d6aac44675c0b220a2cbc744daffe6e25943fc14c036014d/anagenex_mdtraj-1.9.8.dev0-cp310-cp310-macosx_11_0_arm64.whl (from https://pypi.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,560 Skipping link: No binaries permitted for anagenex-mdtraj: https://files.pythonhosted.org/packages/06/84/e1f2ab8a2ef56a8f272f8ea2ebff8e0c0d89334bde155510004361e72ccc/anagenex_mdtraj-1.9.8.dev0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,561 Fetching project page and analyzing links: https://www.piwheels.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,562 Getting page https://www.piwheels.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,563 Found index url https://www.piwheels.org/simple/ 2023-09-19T10:38:36,833 Fetched page https://www.piwheels.org/simple/anagenex-mdtraj/ as text/html 2023-09-19T10:38:36,835 Skipping link: No binaries permitted for anagenex-mdtraj: https://www.piwheels.org/simple/anagenex-mdtraj/anagenex_mdtraj-1.9.8.dev0-cp39-cp39-linux_armv7l.whl#sha256=00c759fc5a471a013bb75798993f0b783fa4e860d20b3297f588e8252daaf42d (from https://www.piwheels.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,836 Skipping link: No binaries permitted for anagenex-mdtraj: https://www.piwheels.org/simple/anagenex-mdtraj/anagenex_mdtraj-1.9.8.dev0-cp39-cp39-linux_armv6l.whl#sha256=00c759fc5a471a013bb75798993f0b783fa4e860d20b3297f588e8252daaf42d (from https://www.piwheels.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,837 Skipping link: No binaries permitted for anagenex-mdtraj: https://www.piwheels.org/simple/anagenex-mdtraj/anagenex_mdtraj-1.9.8.dev0-cp37-cp37m-linux_armv7l.whl#sha256=3294a802a4106ad821f88efe3c291dd1671b0eb6151ee56ac4fabd7b50ab9250 (from https://www.piwheels.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,837 Skipping link: No binaries permitted for anagenex-mdtraj: https://www.piwheels.org/simple/anagenex-mdtraj/anagenex_mdtraj-1.9.8.dev0-cp37-cp37m-linux_armv6l.whl#sha256=3294a802a4106ad821f88efe3c291dd1671b0eb6151ee56ac4fabd7b50ab9250 (from https://www.piwheels.org/simple/anagenex-mdtraj/) 2023-09-19T10:38:36,838 Skipping link: not a file: https://www.piwheels.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,838 Skipping link: not a file: https://pypi.org/simple/anagenex-mdtraj/ 2023-09-19T10:38:36,857 Given no hashes to check 1 links for project 'anagenex-mdtraj': discarding no candidates 2023-09-19T10:38:36,875 Collecting anagenex-mdtraj==1.9.8.dev0 2023-09-19T10:38:36,877 Created temporary directory: /tmp/pip-unpack-4cd89j7y 2023-09-19T10:38:37,617 Downloading anagenex-mdtraj-1.9.8.dev0.tar.gz (2.2 MB) 2023-09-19T10:38:38,973 Added anagenex-mdtraj==1.9.8.dev0 from https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz to build tracker '/tmp/pip-build-tracker-n91_9ba2' 2023-09-19T10:38:38,979 Created temporary directory: /tmp/pip-build-env-_75xxcbd 2023-09-19T10:38:38,983 Installing build dependencies: started 2023-09-19T10:38:38,985 Running command pip subprocess to install build dependencies 2023-09-19T10:38:40,218 Using pip 23.2.1 from /usr/local/lib/python3.11/dist-packages/pip (python 3.11) 2023-09-19T10:38:40,963 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-19T10:38:42,635 Collecting setuptools 2023-09-19T10:38:42,636 Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/bb/26/7945080113158354380a12ce26873dd6c1ebd88d47f5bc24e2c5bb38c16a/setuptools-68.2.2-py3-none-any.whl.metadata 2023-09-19T10:38:42,642 Using cached setuptools-68.2.2-py3-none-any.whl.metadata (6.3 kB) 2023-09-19T10:38:42,850 Collecting wheel 2023-09-19T10:38:42,866 Using cached https://www.piwheels.org/simple/wheel/wheel-0.41.2-py3-none-any.whl (64 kB) 2023-09-19T10:38:42,978 Collecting oldest-supported-numpy 2023-09-19T10:38:42,995 Using cached https://www.piwheels.org/simple/oldest-supported-numpy/oldest_supported_numpy-2023.8.3-py3-none-any.whl (4.8 kB) 2023-09-19T10:38:44,361 Collecting Cython>0.28 2023-09-19T10:38:44,363 Obtaining dependency information for Cython>0.28 from https://files.pythonhosted.org/packages/03/e9/9cc0c4f0d8a566089d096254cd25168a0db02dd047863a7f995d8d3eefa7/Cython-3.0.2-py2.py3-none-any.whl.metadata 2023-09-19T10:38:44,368 Using cached Cython-3.0.2-py2.py3-none-any.whl.metadata (3.1 kB) 2023-09-19T10:38:45,408 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/3a/be/650f9c091ef71cb01d735775d554e068752d3ff63d7943b26316dc401749/numpy-1.21.2.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-09-19T10:38:45,416 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/5f/d6/ad58ded26556eaeaa8c971e08b6466f17c4ac4d786cd3d800e26ce59cc01/numpy-1.21.3.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-09-19T10:38:45,423 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/fb/48/b0708ebd7718a8933f0d3937513ef8ef2f4f04529f1f66ca86d873043921/numpy-1.21.4.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-09-19T10:38:45,431 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/c2/a8/a924a09492bdfee8c2ec3094d0a13f2799800b4fdc9c890738aeeb12c72e/numpy-1.21.5.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-09-19T10:38:45,438 Link requires a different Python (3.11.2 not in: '>=3.7,<3.11'): https://files.pythonhosted.org/packages/45/b7/de7b8e67f2232c26af57c205aaad29fe17754f793404f59c8a730c7a191a/numpy-1.21.6.zip (from https://pypi.org/simple/numpy/) (requires-python:>=3.7,<3.11) 2023-09-19T10:38:45,805 Collecting numpy==1.23.2 (from oldest-supported-numpy) 2023-09-19T10:38:45,815 Downloading https://www.piwheels.org/simple/numpy/numpy-1.23.2-cp311-cp311-linux_armv7l.whl (12.4 MB) 2023-09-19T10:38:46,797 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.4/12.4 MB 11.8 MB/s eta 0:00:00 2023-09-19T10:38:47,117 Using cached setuptools-68.2.2-py3-none-any.whl (807 kB) 2023-09-19T10:38:47,155 Using cached Cython-3.0.2-py2.py3-none-any.whl (1.2 MB) 2023-09-19T10:38:49,813 Installing collected packages: wheel, setuptools, numpy, Cython, oldest-supported-numpy 2023-09-19T10:38:50,033 Creating /tmp/pip-build-env-_75xxcbd/overlay/local/bin 2023-09-19T10:38:50,035 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/wheel to 755 2023-09-19T10:39:01,082 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/f2py to 755 2023-09-19T10:39:01,084 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/f2py3 to 755 2023-09-19T10:39:01,086 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/f2py3.11 to 755 2023-09-19T10:39:04,654 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/cygdb to 755 2023-09-19T10:39:04,657 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/cython to 755 2023-09-19T10:39:04,659 changing mode of /tmp/pip-build-env-_75xxcbd/overlay/local/bin/cythonize to 755 2023-09-19T10:39:04,716 Successfully installed Cython-3.0.2 numpy-1.23.2 oldest-supported-numpy-2023.8.3 setuptools-68.2.2 wheel-0.41.2 2023-09-19T10:39:05,363 Installing build dependencies: finished with status 'done' 2023-09-19T10:39:05,375 Getting requirements to build wheel: started 2023-09-19T10:39:05,376 Running command Getting requirements to build wheel 2023-09-19T10:39:06,529 Using built-in specs. 2023-09-19T10:39:06,529 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-19T10:39:06,530 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2023-09-19T10:39:06,530 Target: arm-linux-gnueabihf 2023-09-19T10:39:06,531 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-19T10:39:06,531 Thread model: posix 2023-09-19T10:39:06,532 Supported LTO compression algorithms: zlib zstd 2023-09-19T10:39:06,533 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-19T10:39:10,447 C compiler: 2023-09-19T10:39:10,448 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-09-19T10:39:10,448 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-09-19T10:39:10,449 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-09-19T10:39:10,449 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-09-19T10:39:10,450 Attempting to autodetect NEON support... Did not detect NEON support 2023-09-19T10:39:10,451 running egg_info 2023-09-19T10:39:10,454 writing anagenex_mdtraj.egg-info/PKG-INFO 2023-09-19T10:39:10,457 writing dependency_links to anagenex_mdtraj.egg-info/dependency_links.txt 2023-09-19T10:39:10,458 writing entry points to anagenex_mdtraj.egg-info/entry_points.txt 2023-09-19T10:39:10,460 writing requirements to anagenex_mdtraj.egg-info/requires.txt 2023-09-19T10:39:10,461 writing top-level names to anagenex_mdtraj.egg-info/top_level.txt 2023-09-19T10:39:10,492 reading manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2023-09-19T10:39:10,523 reading manifest template 'MANIFEST.in' 2023-09-19T10:39:11,333 no previously-included directories found matching '__pycache__' 2023-09-19T10:39:11,335 no previously-included directories found matching '*.pyc' 2023-09-19T10:39:11,335 adding license file 'LICENSE' 2023-09-19T10:39:11,347 writing manifest file 'anagenex_mdtraj.egg-info/SOURCES.txt' 2023-09-19T10:39:11,438 Getting requirements to build wheel: finished with status 'done' 2023-09-19T10:39:11,451 Created temporary directory: /tmp/pip-modern-metadata-o3y3fy0i 2023-09-19T10:39:11,453 Preparing metadata (pyproject.toml): started 2023-09-19T10:39:11,454 Running command Preparing metadata (pyproject.toml) 2023-09-19T10:39:12,074 Using built-in specs. 2023-09-19T10:39:12,075 COLLECT_GCC=/usr/bin/arm-linux-gnueabihf-gcc 2023-09-19T10:39:12,076 COLLECT_LTO_WRAPPER=/usr/lib/gcc/arm-linux-gnueabihf/12/lto-wrapper 2023-09-19T10:39:12,076 Target: arm-linux-gnueabihf 2023-09-19T10:39:12,077 Configured with: ../src/configure -v --with-pkgversion='Raspbian 12.2.0-14+rpi1' --with-bugurl=file:///usr/share/doc/gcc-12/README.Bugs --enable-languages=c,ada,c++,go,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-12 --program-prefix=arm-linux-gnueabihf- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-libitm --disable-libquadmath --disable-libquadmath-support --enable-plugin --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-sjlj-exceptions --with-arch=armv6+fp --with-float=hard --disable-werror --enable-checking=release --build=arm-linux-gnueabihf --host=arm-linux-gnueabihf --target=arm-linux-gnueabihf 2023-09-19T10:39:12,077 Thread model: posix 2023-09-19T10:39:12,077 Supported LTO compression algorithms: zlib zstd 2023-09-19T10:39:12,078 gcc version 12.2.0 (Raspbian 12.2.0-14+rpi1) 2023-09-19T10:39:15,935 /tmp/pip-wheel-uwl9trpe/anagenex-mdtraj_a9ee4bef9c294466af7a7e1586706f2f/basesetup.py:451: UserWarning: Unrecognized setuptools command ('dist_info --output-dir /tmp/pip-modern-metadata-o3y3fy0i --keep-egg-info'), proceeding with generating Cython sources and expanding templates 2023-09-19T10:39:15,935 warnings.warn("Unrecognized setuptools command ('{}'), proceeding with " 2023-09-19T10:39:21,834 warning: mdtraj/formats/dcd/dcdlib.pxd:12:12: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-19T10:39:21,835 warning: mdtraj/formats/dcd/dcdlib.pxd:12:16: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-19T10:39:21,836 warning: mdtraj/formats/dcd/dcdlib.pxd:12:20: Non-trivial type declarators in shared declaration (e.g. mix of pointers and values). Each pointer declaration should be on its own line. 2023-09-19T10:39:43,173 Error compiling Cython file: 2023-09-19T10:39:43,174 ------------------------------------------------------------ 2023-09-19T10:39:43,174 ... 2023-09-19T10:39:43,175 offset[k] += frame_unitcell_vectors[0, k]*roundf((delta[0]-offset[0])/frame_unitcell_vectors[0,0]) 2023-09-19T10:39:43,175 frame_positions[atom2, k] = frame_positions[atom2, k] - offset[k] 2023-09-19T10:39:43,177 cdef void anchor_dists(float[:,::1] frame_positions, 2023-09-19T10:39:43,177 float[:,::1] frame_unitcell_vectors, 2023-09-19T10:39:43,178 vector[int[:]] anchor_molecules, 2023-09-19T10:39:43,179 ^ 2023-09-19T10:39:43,179 ------------------------------------------------------------ 2023-09-19T10:39:43,180 mdtraj/geometry/src/image_molecules.pxi:33:24: Reference-counted type 'int[:]' cannot be used as a template argument 2023-09-19T10:39:43,182 Error compiling Cython file: 2023-09-19T10:39:43,182 ------------------------------------------------------------ 2023-09-19T10:39:43,183 ... 2023-09-19T10:39:43,184 anchor_nearest_atoms[mol2, mol1, 1] = ca2 2023-09-19T10:39:43,185 cdef void wrap_mols(float[:,::1] frame_positions, 2023-09-19T10:39:43,185 float[:,::1] frame_unitcell_vectors, 2023-09-19T10:39:43,186 float[:] center, 2023-09-19T10:39:43,186 vector[int[:]] other_molecules) nogil: 2023-09-19T10:39:43,187 ^ 2023-09-19T10:39:43,187 ------------------------------------------------------------ 2023-09-19T10:39:43,189 mdtraj/geometry/src/image_molecules.pxi:55:26: Reference-counted type 'int[:]' cannot be used as a template argument 2023-09-19T10:39:43,190 Error compiling Cython file: 2023-09-19T10:39:43,190 ------------------------------------------------------------ 2023-09-19T10:39:43,191 ... 2023-09-19T10:39:43,192 cdef void image_frame(frame_positions, 2023-09-19T10:39:43,193 frame_unitcell_vectors, 2023-09-19T10:39:43,193 anchor_molecules, 2023-09-19T10:39:43,194 vector[int[:]] other_molecules, 2023-09-19T10:39:43,194 ^ 2023-09-19T10:39:43,195 ------------------------------------------------------------ 2023-09-19T10:39:43,196 mdtraj/geometry/src/image_molecules.pxi:96:23: Reference-counted type 'int[:]' cannot be used as a template argument 2023-09-19T10:39:43,215 Error compiling Cython file: 2023-09-19T10:39:43,216 ------------------------------------------------------------ 2023-09-19T10:39:43,216 ... 2023-09-19T10:39:43,217 anchor_atom_indices = np.concatenate(anchor_molecules) 2023-09-19T10:39:43,217 center = np.mean(frame_positions[anchor_atom_indices], axis=0) 2023-09-19T10:39:43,218 wrap_mols(frame_positions, frame_unitcell_vectors, center, other_molecules) 2023-09-19T10:39:43,219 def image_molecules(xyz, box, anchor_molecules, other_molecules, sorted_bonds): 2023-09-19T10:39:43,219 cdef vector[int[:]] omol = other_molecules 2023-09-19T10:39:43,220 ^ 2023-09-19T10:39:43,220 ------------------------------------------------------------ 2023-09-19T10:39:43,221 mdtraj/geometry/src/image_molecules.pxi:144:15: Reference-counted type 'int[:]' cannot be used as a template argument 2023-09-19T10:39:43,566 Error compiling Cython file: 2023-09-19T10:39:43,566 ------------------------------------------------------------ 2023-09-19T10:39:43,567 ... 2023-09-19T10:39:43,568 cdef int[:] mol 2023-09-19T10:39:43,568 cdef float mol_center[3] 2023-09-19T10:39:43,569 cdef float mol_offset[3] 2023-09-19T10:39:43,570 cdef int n 2023-09-19T10:39:43,570 for i in range(other_molecules.size()): 2023-09-19T10:39:43,571 ^ 2023-09-19T10:39:43,571 ------------------------------------------------------------ 2023-09-19T10:39:43,572 mdtraj/geometry/src/image_molecules.pxi:72:39: Coercion from Python not allowed without the GIL 2023-09-19T10:39:43,573 Error compiling Cython file: 2023-09-19T10:39:43,574 ------------------------------------------------------------ 2023-09-19T10:39:43,574 ... 2023-09-19T10:39:43,575 cdef int[:] mol 2023-09-19T10:39:43,575 cdef float mol_center[3] 2023-09-19T10:39:43,576 cdef float mol_offset[3] 2023-09-19T10:39:43,577 cdef int n 2023-09-19T10:39:43,577 for i in range(other_molecules.size()): 2023-09-19T10:39:43,578 ^ 2023-09-19T10:39:43,578 ------------------------------------------------------------ 2023-09-19T10:39:43,580 mdtraj/geometry/src/image_molecules.pxi:72:39: Calling gil-requiring function not allowed without gil 2023-09-19T10:39:43,581 Error compiling Cython file: 2023-09-19T10:39:43,581 ------------------------------------------------------------ 2023-09-19T10:39:43,582 ... 2023-09-19T10:39:43,583 cdef int[:] mol 2023-09-19T10:39:43,583 cdef float mol_center[3] 2023-09-19T10:39:43,584 cdef float mol_offset[3] 2023-09-19T10:39:43,585 cdef int n 2023-09-19T10:39:43,585 for i in range(other_molecules.size()): 2023-09-19T10:39:43,586 ^ 2023-09-19T10:39:43,586 ------------------------------------------------------------ 2023-09-19T10:39:43,587 mdtraj/geometry/src/image_molecules.pxi:72:34: Accessing Python attribute not allowed without gil 2023-09-19T10:39:43,588 Error compiling Cython file: 2023-09-19T10:39:43,588 ------------------------------------------------------------ 2023-09-19T10:39:43,588 ... 2023-09-19T10:39:43,589 cdef int[:] mol 2023-09-19T10:39:43,589 cdef float mol_center[3] 2023-09-19T10:39:43,590 cdef float mol_offset[3] 2023-09-19T10:39:43,590 cdef int n 2023-09-19T10:39:43,591 for i in range(other_molecules.size()): 2023-09-19T10:39:43,591 ^ 2023-09-19T10:39:43,592 ------------------------------------------------------------ 2023-09-19T10:39:43,593 mdtraj/geometry/src/image_molecules.pxi:72:39: Constructing Python tuple not allowed without gil 2023-09-19T10:39:45,133 C compiler: 2023-09-19T10:39:45,134 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-09-19T10:39:45,134 Attempting to autodetect SSE2 support... Did not detect SSE2 support 2023-09-19T10:39:45,135 Attempting to autodetect SSE3 support... Did not detect SSE3 support 2023-09-19T10:39:45,135 Attempting to autodetect SSE4.1 support... Did not detect SSE4.1 support 2023-09-19T10:39:45,136 Attempting to autodetect NEON support... Did not detect NEON support 2023-09-19T10:39:45,137 Compiling mdtraj/formats/xtc/xtc.pyx because it changed. 2023-09-19T10:39:45,137 Compiling mdtraj/formats/xtc/trr.pyx because it changed. 2023-09-19T10:39:45,138 Compiling mdtraj/formats/tng/tng.pyx because it changed. 2023-09-19T10:39:45,139 Compiling mdtraj/formats/dcd/dcd.pyx because it changed. 2023-09-19T10:39:45,139 Compiling mdtraj/formats/binpos/binpos.pyx because it changed. 2023-09-19T10:39:45,140 Compiling mdtraj/formats/dtr/dtr.pyx because it changed. 2023-09-19T10:39:45,140 Compiling mdtraj/rmsd/_rmsd.pyx because it changed. 2023-09-19T10:39:45,141 Compiling mdtraj/rmsd/_lprmsd.pyx because it changed. 2023-09-19T10:39:45,142 Compiling mdtraj/geometry/src/_geometry.pyx because it changed. 2023-09-19T10:39:45,142 Compiling mdtraj/geometry/drid.pyx because it changed. 2023-09-19T10:39:45,143 Compiling mdtraj/geometry/neighbors.pyx because it changed. 2023-09-19T10:39:45,143 Compiling mdtraj/geometry/neighborlist.pyx because it changed. 2023-09-19T10:39:45,144 [ 1/12] Cythonizing mdtraj/formats/binpos/binpos.pyx 2023-09-19T10:39:45,145 [ 2/12] Cythonizing mdtraj/formats/dcd/dcd.pyx 2023-09-19T10:39:45,145 [ 3/12] Cythonizing mdtraj/formats/dtr/dtr.pyx 2023-09-19T10:39:45,146 [ 4/12] Cythonizing mdtraj/formats/tng/tng.pyx 2023-09-19T10:39:45,146 [ 5/12] Cythonizing mdtraj/formats/xtc/trr.pyx 2023-09-19T10:39:45,147 [ 6/12] Cythonizing mdtraj/formats/xtc/xtc.pyx 2023-09-19T10:39:45,147 [ 7/12] Cythonizing mdtraj/geometry/drid.pyx 2023-09-19T10:39:45,148 [ 8/12] Cythonizing mdtraj/geometry/neighborlist.pyx 2023-09-19T10:39:45,149 [ 9/12] Cythonizing mdtraj/geometry/neighbors.pyx 2023-09-19T10:39:45,149 [10/12] Cythonizing mdtraj/geometry/src/_geometry.pyx 2023-09-19T10:39:45,150 Traceback (most recent call last): 2023-09-19T10:39:45,151 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in 2023-09-19T10:39:45,152 main() 2023-09-19T10:39:45,153 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main 2023-09-19T10:39:45,153 json_out['return_val'] = hook(**hook_input['kwargs']) 2023-09-19T10:39:45,154 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,155 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel 2023-09-19T10:39:45,155 return hook(metadata_directory, config_settings) 2023-09-19T10:39:45,156 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,157 File "/tmp/pip-build-env-_75xxcbd/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 396, in prepare_metadata_for_build_wheel 2023-09-19T10:39:45,157 self.run_setup() 2023-09-19T10:39:45,158 File "/tmp/pip-build-env-_75xxcbd/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 507, in run_setup 2023-09-19T10:39:45,158 super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script) 2023-09-19T10:39:45,159 File "/tmp/pip-build-env-_75xxcbd/overlay/local/lib/python3.11/dist-packages/setuptools/build_meta.py", line 341, in run_setup 2023-09-19T10:39:45,159 exec(code, locals()) 2023-09-19T10:39:45,160 File "", line 307, in 2023-09-19T10:39:45,161 File "/tmp/pip-build-env-_75xxcbd/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1134, in cythonize 2023-09-19T10:39:45,161 cythonize_one(*args) 2023-09-19T10:39:45,162 File "/tmp/pip-build-env-_75xxcbd/overlay/local/lib/python3.11/dist-packages/Cython/Build/Dependencies.py", line 1301, in cythonize_one 2023-09-19T10:39:45,162 raise CompileError(None, pyx_file) 2023-09-19T10:39:45,163 Cython.Compiler.Errors.CompileError: mdtraj/geometry/src/_geometry.pyx 2023-09-19T10:39:45,689 ERROR: [present-rich] Preparing metadata (pyproject.toml) exited with 1 2023-09-19T10:39:45,703 [bold magenta]full command[/]: [blue]/usr/bin/python3 /usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /tmp/tmpdm7g2962[/] 2023-09-19T10:39:45,703 [bold magenta]cwd[/]: /tmp/pip-wheel-uwl9trpe/anagenex-mdtraj_a9ee4bef9c294466af7a7e1586706f2f 2023-09-19T10:39:45,704 Preparing metadata (pyproject.toml): finished with status 'error' 2023-09-19T10:39:45,706 ERROR: [present-rich] metadata generation failed 2023-09-19T10:39:45,712 Exception information: 2023-09-19T10:39:45,712 Traceback (most recent call last): 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/build/metadata.py", line 35, in generate_metadata 2023-09-19T10:39:45,712 distinfo_dir = backend.prepare_metadata_for_build_wheel(metadata_dir) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/misc.py", line 718, in prepare_metadata_for_build_wheel 2023-09-19T10:39:45,712 return super().prepare_metadata_for_build_wheel( 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 186, in prepare_metadata_for_build_wheel 2023-09-19T10:39:45,712 return self._call_hook('prepare_metadata_for_build_wheel', { 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/pyproject_hooks/_impl.py", line 311, in _call_hook 2023-09-19T10:39:45,712 self._subprocess_runner( 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 252, in runner 2023-09-19T10:39:45,712 call_subprocess( 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess 2023-09-19T10:39:45,712 raise error 2023-09-19T10:39:45,712 pip._internal.exceptions.InstallationSubprocessError: Preparing metadata (pyproject.toml) exited with 1 2023-09-19T10:39:45,712 2023-09-19T10:39:45,712 The above exception was the direct cause of the following exception: 2023-09-19T10:39:45,712 2023-09-19T10:39:45,712 Traceback (most recent call last): 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-19T10:39:45,712 status = run_func(*args) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-19T10:39:45,712 return func(self, options, args) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2023-09-19T10:39:45,712 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve 2023-09-19T10:39:45,712 result = self._result = resolver.resolve( 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve 2023-09-19T10:39:45,712 state = resolution.resolve(requirements, max_rounds=max_rounds) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve 2023-09-19T10:39:45,712 self._add_to_criteria(self.state.criteria, r, parent=None) 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria 2023-09-19T10:39:45,712 if not criterion.candidates: 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__ 2023-09-19T10:39:45,712 return bool(self._sequence) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__ 2023-09-19T10:39:45,712 return any(self) 2023-09-19T10:39:45,712 ^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in 2023-09-19T10:39:45,712 return (c for c in iterator if id(c) not in self._incompatible_ids) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built 2023-09-19T10:39:45,712 candidate = func() 2023-09-19T10:39:45,712 ^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link 2023-09-19T10:39:45,712 self._link_candidate_cache[link] = LinkCandidate( 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ 2023-09-19T10:39:45,712 super().__init__( 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ 2023-09-19T10:39:45,712 self.dist = self._prepare() 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare 2023-09-19T10:39:45,712 dist = self._prepare_distribution() 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution 2023-09-19T10:39:45,712 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 538, in prepare_linked_requirement 2023-09-19T10:39:45,712 return self._prepare_linked_requirement(req, parallel_builds) 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 653, in _prepare_linked_requirement 2023-09-19T10:39:45,712 dist = _get_prepared_distribution( 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution 2023-09-19T10:39:45,712 abstract_dist.prepare_distribution_metadata( 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata 2023-09-19T10:39:45,712 self.req.prepare_metadata() 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/req/req_install.py", line 562, in prepare_metadata 2023-09-19T10:39:45,712 self.metadata_directory = generate_metadata( 2023-09-19T10:39:45,712 ^^^^^^^^^^^^^^^^^^ 2023-09-19T10:39:45,712 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/build/metadata.py", line 37, in generate_metadata 2023-09-19T10:39:45,712 raise MetadataGenerationFailed(package_details=details) from error 2023-09-19T10:39:45,712 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2023-09-19T10:39:45,729 Removed anagenex-mdtraj==1.9.8.dev0 from https://files.pythonhosted.org/packages/6d/b0/fd322f30cc3e01045259805ba97313b6de4cb905f7067d5082c5dedb45e7/anagenex-mdtraj-1.9.8.dev0.tar.gz from build tracker '/tmp/pip-build-tracker-n91_9ba2' 2023-09-19T10:39:45,730 Removed build tracker: '/tmp/pip-build-tracker-n91_9ba2'