2023-09-08T16:39:26,221 Created temporary directory: /tmp/pip-build-tracker-_onunham 2023-09-08T16:39:26,222 Initialized build tracking at /tmp/pip-build-tracker-_onunham 2023-09-08T16:39:26,223 Created build tracker: /tmp/pip-build-tracker-_onunham 2023-09-08T16:39:26,223 Entered build tracker: /tmp/pip-build-tracker-_onunham 2023-09-08T16:39:26,225 Created temporary directory: /tmp/pip-wheel-mju34h1a 2023-09-08T16:39:26,227 Created temporary directory: /tmp/pip-ephem-wheel-cache-7lfxmgpd 2023-09-08T16:39:26,250 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T16:39:26,254 2 location(s) to search for versions of pyrmsd: 2023-09-08T16:39:26,254 * https://pypi.org/simple/pyrmsd/ 2023-09-08T16:39:26,254 * https://www.piwheels.org/simple/pyrmsd/ 2023-09-08T16:39:26,255 Fetching project page and analyzing links: https://pypi.org/simple/pyrmsd/ 2023-09-08T16:39:26,255 Getting page https://pypi.org/simple/pyrmsd/ 2023-09-08T16:39:26,257 Found index url https://pypi.org/simple/ 2023-09-08T16:39:26,398 Fetched page https://pypi.org/simple/pyrmsd/ as application/vnd.pypi.simple.v1+json 2023-09-08T16:39:26,400 Found link https://files.pythonhosted.org/packages/80/b5/1fd41c73d58d030d036ba78ed3a9291b1916e3975c071c521576715a41c8/pyRMSD-4.0.0.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.0.0 2023-09-08T16:39:26,401 Found link https://files.pythonhosted.org/packages/f3/30/bf5cc08908f79127fecd306e126be5984ccb30be76bcdb62a39c582975aa/pyRMSD-4.0.1.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.0.1 2023-09-08T16:39:26,402 Found link https://files.pythonhosted.org/packages/45/7e/ac00abc640a76116139741b73c6eadd1cae264bb324f62acdb43f7806847/pyRMSD-4.1.0.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.1.0 2023-09-08T16:39:26,402 Found link https://files.pythonhosted.org/packages/fb/17/cb4a46781fa84b8d974c1da54ace55674a1182c7bccd87047a8404971e41/pyRMSD-4.2.0.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.2.0 2023-09-08T16:39:26,403 Found link https://files.pythonhosted.org/packages/21/18/170ed35c7aaaae5bbb522b3c9a6bb1a7f4fd978702ea64e188975c2017aa/pyRMSD-4.2.1.tar.gz (from https://pypi.org/simple/pyrmsd/), version: 4.2.1 2023-09-08T16:39:26,404 Fetching project page and analyzing links: https://www.piwheels.org/simple/pyrmsd/ 2023-09-08T16:39:26,405 Getting page https://www.piwheels.org/simple/pyrmsd/ 2023-09-08T16:39:26,406 Found index url https://www.piwheels.org/simple/ 2023-09-08T16:39:26,730 Fetched page https://www.piwheels.org/simple/pyrmsd/ as text/html 2023-09-08T16:39:26,731 Skipping link: not a file: https://www.piwheels.org/simple/pyrmsd/ 2023-09-08T16:39:26,731 Skipping link: not a file: https://pypi.org/simple/pyrmsd/ 2023-09-08T16:39:26,751 Given no hashes to check 1 links for project 'pyrmsd': discarding no candidates 2023-09-08T16:39:26,769 Collecting pyrmsd==4.2.0 2023-09-08T16:39:26,772 Created temporary directory: /tmp/pip-unpack-eliwxih6 2023-09-08T16:39:27,269 Downloading pyRMSD-4.2.0.tar.gz (54 kB) 2023-09-08T16:39:27,447 Added pyrmsd==4.2.0 from https://files.pythonhosted.org/packages/fb/17/cb4a46781fa84b8d974c1da54ace55674a1182c7bccd87047a8404971e41/pyRMSD-4.2.0.tar.gz to build tracker '/tmp/pip-build-tracker-_onunham' 2023-09-08T16:39:27,449 Running setup.py (path:/tmp/pip-wheel-mju34h1a/pyrmsd_155f2fa7e67d4ed4911603458f54d8e3/setup.py) egg_info for package pyrmsd 2023-09-08T16:39:27,450 Created temporary directory: /tmp/pip-pip-egg-info-xqim0pur 2023-09-08T16:39:27,450 Preparing metadata (setup.py): started 2023-09-08T16:39:27,452 Running command python setup.py egg_info 2023-09-08T16:39:27,868 Traceback (most recent call last): 2023-09-08T16:39:27,868 File "/usr/local/lib/python3.11/dist-packages/numpy/core/__init__.py", line 23, in 2023-09-08T16:39:27,869 from . import multiarray 2023-09-08T16:39:27,870 File "/usr/local/lib/python3.11/dist-packages/numpy/core/multiarray.py", line 10, in 2023-09-08T16:39:27,871 from . import overrides 2023-09-08T16:39:27,871 File "/usr/local/lib/python3.11/dist-packages/numpy/core/overrides.py", line 8, in 2023-09-08T16:39:27,872 from numpy.core._multiarray_umath import ( 2023-09-08T16:39:27,873 ImportError: libopenblas.so.0: cannot open shared object file: No such file or directory 2023-09-08T16:39:27,875 During handling of the above exception, another exception occurred: 2023-09-08T16:39:27,876 Traceback (most recent call last): 2023-09-08T16:39:27,877 File "", line 2, in 2023-09-08T16:39:27,877 File "", line 34, in 2023-09-08T16:39:27,878 File "/tmp/pip-wheel-mju34h1a/pyrmsd_155f2fa7e67d4ed4911603458f54d8e3/setup.py", line 7, in 2023-09-08T16:39:27,879 import numpy 2023-09-08T16:39:27,879 File "/usr/local/lib/python3.11/dist-packages/numpy/__init__.py", line 139, in 2023-09-08T16:39:27,880 from . import core 2023-09-08T16:39:27,881 File "/usr/local/lib/python3.11/dist-packages/numpy/core/__init__.py", line 49, in 2023-09-08T16:39:27,882 raise ImportError(msg) 2023-09-08T16:39:27,882 ImportError: 2023-09-08T16:39:27,884 IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 2023-09-08T16:39:27,885 Importing the numpy C-extensions failed. This error can happen for 2023-09-08T16:39:27,886 many reasons, often due to issues with your setup or how NumPy was 2023-09-08T16:39:27,886 installed. 2023-09-08T16:39:27,888 We have compiled some common reasons and troubleshooting tips at: 2023-09-08T16:39:27,889 https://numpy.org/devdocs/user/troubleshooting-importerror.html 2023-09-08T16:39:27,891 Please note and check the following: 2023-09-08T16:39:27,893 * The Python version is: Python3.11 from "/usr/bin/python3" 2023-09-08T16:39:27,893 * The NumPy version is: "1.25.2" 2023-09-08T16:39:27,895 and make sure that they are the versions you expect. 2023-09-08T16:39:27,896 Please carefully study the documentation linked above for further help. 2023-09-08T16:39:27,897 Original error was: libopenblas.so.0: cannot open shared object file: No such file or directory 2023-09-08T16:39:27,947 ERROR: [present-rich] python setup.py egg_info exited with 1 2023-09-08T16:39:27,960 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2023-09-08T16:39:27,960 exec(compile('"'"''"'"''"'"' 2023-09-08T16:39:27,960 # This is -- a caller that pip uses to run setup.py 2023-09-08T16:39:27,960 # 2023-09-08T16:39:27,960 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T16:39:27,960 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T16:39:27,960 # - It provides a clear error message when setuptools is not installed. 2023-09-08T16:39:27,960 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T16:39:27,960 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T16:39:27,960 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T16:39:27,960 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T16:39:27,960 import os, sys, tokenize 2023-09-08T16:39:27,960 2023-09-08T16:39:27,960 try: 2023-09-08T16:39:27,960 import setuptools 2023-09-08T16:39:27,960 except ImportError as error: 2023-09-08T16:39:27,960 print( 2023-09-08T16:39:27,960 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T16:39:27,960 "the build environment.", 2023-09-08T16:39:27,960 file=sys.stderr, 2023-09-08T16:39:27,960 ) 2023-09-08T16:39:27,960 sys.exit(1) 2023-09-08T16:39:27,960 2023-09-08T16:39:27,960 __file__ = %r 2023-09-08T16:39:27,960 sys.argv[0] = __file__ 2023-09-08T16:39:27,960 2023-09-08T16:39:27,960 if os.path.exists(__file__): 2023-09-08T16:39:27,960 filename = __file__ 2023-09-08T16:39:27,960 with tokenize.open(__file__) as f: 2023-09-08T16:39:27,960 setup_py_code = f.read() 2023-09-08T16:39:27,960 else: 2023-09-08T16:39:27,960 filename = "" 2023-09-08T16:39:27,960 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T16:39:27,960 2023-09-08T16:39:27,960 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T16:39:27,960 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-mju34h1a/pyrmsd_155f2fa7e67d4ed4911603458f54d8e3/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-xqim0pur[/] 2023-09-08T16:39:27,961 [bold magenta]cwd[/]: /tmp/pip-wheel-mju34h1a/pyrmsd_155f2fa7e67d4ed4911603458f54d8e3/ 2023-09-08T16:39:27,962 Preparing metadata (setup.py): finished with status 'error' 2023-09-08T16:39:27,963 ERROR: [present-rich] metadata generation failed 2023-09-08T16:39:27,969 Exception information: 2023-09-08T16:39:27,969 Traceback (most recent call last): 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 64, in generate_metadata 2023-09-08T16:39:27,969 call_subprocess( 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/utils/subprocess.py", line 224, in call_subprocess 2023-09-08T16:39:27,969 raise error 2023-09-08T16:39:27,969 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2023-09-08T16:39:27,969 2023-09-08T16:39:27,969 The above exception was the direct cause of the following exception: 2023-09-08T16:39:27,969 2023-09-08T16:39:27,969 Traceback (most recent call last): 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T16:39:27,969 status = run_func(*args) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T16:39:27,969 return func(self, options, args) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2023-09-08T16:39:27,969 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 92, in resolve 2023-09-08T16:39:27,969 result = self._result = resolver.resolve( 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 546, in resolve 2023-09-08T16:39:27,969 state = resolution.resolve(requirements, max_rounds=max_rounds) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 397, in resolve 2023-09-08T16:39:27,969 self._add_to_criteria(self.state.criteria, r, parent=None) 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/resolvers.py", line 173, in _add_to_criteria 2023-09-08T16:39:27,969 if not criterion.candidates: 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_vendor/resolvelib/structs.py", line 156, in __bool__ 2023-09-08T16:39:27,969 return bool(self._sequence) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 155, in __bool__ 2023-09-08T16:39:27,969 return any(self) 2023-09-08T16:39:27,969 ^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 143, in 2023-09-08T16:39:27,969 return (c for c in iterator if id(c) not in self._incompatible_ids) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 47, in _iter_built 2023-09-08T16:39:27,969 candidate = func() 2023-09-08T16:39:27,969 ^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 206, in _make_candidate_from_link 2023-09-08T16:39:27,969 self._link_candidate_cache[link] = LinkCandidate( 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 293, in __init__ 2023-09-08T16:39:27,969 super().__init__( 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 156, in __init__ 2023-09-08T16:39:27,969 self.dist = self._prepare() 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 225, in _prepare 2023-09-08T16:39:27,969 dist = self._prepare_distribution() 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 304, in _prepare_distribution 2023-09-08T16:39:27,969 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 538, in prepare_linked_requirement 2023-09-08T16:39:27,969 return self._prepare_linked_requirement(req, parallel_builds) 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 653, in _prepare_linked_requirement 2023-09-08T16:39:27,969 dist = _get_prepared_distribution( 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/prepare.py", line 69, in _get_prepared_distribution 2023-09-08T16:39:27,969 abstract_dist.prepare_distribution_metadata( 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/distributions/sdist.py", line 61, in prepare_distribution_metadata 2023-09-08T16:39:27,969 self.req.prepare_metadata() 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/req/req_install.py", line 568, in prepare_metadata 2023-09-08T16:39:27,969 self.metadata_directory = generate_metadata_legacy( 2023-09-08T16:39:27,969 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T16:39:27,969 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 71, in generate_metadata 2023-09-08T16:39:27,969 raise MetadataGenerationFailed(package_details=details) from error 2023-09-08T16:39:27,969 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2023-09-08T16:39:27,981 Removed pyrmsd==4.2.0 from https://files.pythonhosted.org/packages/fb/17/cb4a46781fa84b8d974c1da54ace55674a1182c7bccd87047a8404971e41/pyRMSD-4.2.0.tar.gz from build tracker '/tmp/pip-build-tracker-_onunham' 2023-09-08T16:39:27,982 Removed build tracker: '/tmp/pip-build-tracker-_onunham'