2025-09-08T14:32:26,314 Created temporary directory: /tmp/pip-build-tracker-q0xngsry 2025-09-08T14:32:26,315 Initialized build tracking at /tmp/pip-build-tracker-q0xngsry 2025-09-08T14:32:26,315 Created build tracker: /tmp/pip-build-tracker-q0xngsry 2025-09-08T14:32:26,315 Entered build tracker: /tmp/pip-build-tracker-q0xngsry 2025-09-08T14:32:26,315 Created temporary directory: /tmp/pip-wheel-k2725oei 2025-09-08T14:32:26,319 Created temporary directory: /tmp/pip-ephem-wheel-cache-tgxk54fo 2025-09-08T14:32:26,377 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T14:32:26,379 2 location(s) to search for versions of hmm-kit: 2025-09-08T14:32:26,379 * https://pypi.org/simple/hmm-kit/ 2025-09-08T14:32:26,379 * https://www.piwheels.org/simple/hmm-kit/ 2025-09-08T14:32:26,380 Fetching project page and analyzing links: https://pypi.org/simple/hmm-kit/ 2025-09-08T14:32:26,380 Getting page https://pypi.org/simple/hmm-kit/ 2025-09-08T14:32:26,381 Found index url https://pypi.org/simple/ 2025-09-08T14:32:26,454 Fetched page https://pypi.org/simple/hmm-kit/ as application/vnd.pypi.simple.v1+json 2025-09-08T14:32:26,455 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/c7/9a/8c0ce2dbd213f7170b4c788050d2a41b1732bca1178586bc9720619231e6/hmm_kit-0.1-py2.7-linux-x86_64.egg (from https://pypi.org/simple/hmm-kit/) 2025-09-08T14:32:26,456 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/02/27/2cc4cbbdb9e565d604a8d55ede5497cc65c0a5f0275a59c214e8983626e1/hmm_kit-0.1-py3.6-linux-x86_64.egg (from https://pypi.org/simple/hmm-kit/) 2025-09-08T14:32:26,456 Found link https://files.pythonhosted.org/packages/2c/9d/be59085bdca5bee636c73e181f59f8028907610c42fc9df24f2f2e51f930/hmm_kit-0.1.tar.gz (from https://pypi.org/simple/hmm-kit/), version: 0.1 2025-09-08T14:32:26,456 Found link https://files.pythonhosted.org/packages/ea/95/33cbefe7eb18093ff50a57904533fb1803cf6e67f3ead128a87d3ede14a4/hmm_kit-0.1.1.tar.gz (from https://pypi.org/simple/hmm-kit/), version: 0.1.1 2025-09-08T14:32:26,456 Found link https://files.pythonhosted.org/packages/58/98/19298072ec14929245012098ca657aedff1210e6445cd630b9be46c6e59f/hmm_kit-0.2.0.tar.gz (from https://pypi.org/simple/hmm-kit/), version: 0.2.0 2025-09-08T14:32:26,457 Found link https://files.pythonhosted.org/packages/0c/97/cb151084e460a53ae2e1f1a1e1735ee0aa22e88b555bdd2bd258e8466fef/hmm_kit-0.3.0.tar.gz (from https://pypi.org/simple/hmm-kit/), version: 0.3.0 2025-09-08T14:32:26,457 Fetching project page and analyzing links: https://www.piwheels.org/simple/hmm-kit/ 2025-09-08T14:32:26,457 Getting page https://www.piwheels.org/simple/hmm-kit/ 2025-09-08T14:32:26,458 Found index url https://www.piwheels.org/simple/ 2025-09-08T14:32:26,554 Fetched page https://www.piwheels.org/simple/hmm-kit/ as text/html 2025-09-08T14:32:26,555 Skipping link: not a file: https://www.piwheels.org/simple/hmm-kit/ 2025-09-08T14:32:26,555 Skipping link: not a file: https://pypi.org/simple/hmm-kit/ 2025-09-08T14:32:26,582 Given no hashes to check 1 links for project 'hmm-kit': discarding no candidates 2025-09-08T14:32:26,583 Collecting hmm-kit==0.1.1 2025-09-08T14:32:26,585 Created temporary directory: /tmp/pip-unpack-pzo50yai 2025-09-08T14:32:26,722 Downloading hmm_kit-0.1.1.tar.gz (83 kB) 2025-09-08T14:32:26,773 Added hmm-kit==0.1.1 from https://files.pythonhosted.org/packages/ea/95/33cbefe7eb18093ff50a57904533fb1803cf6e67f3ead128a87d3ede14a4/hmm_kit-0.1.1.tar.gz to build tracker '/tmp/pip-build-tracker-q0xngsry' 2025-09-08T14:32:26,774 Running setup.py (path:/tmp/pip-wheel-k2725oei/hmm-kit_bc6d948532c541ed91e7b31646758cbd/setup.py) egg_info for package hmm-kit 2025-09-08T14:32:26,774 Created temporary directory: /tmp/pip-pip-egg-info-ugnfnh39 2025-09-08T14:32:26,775 Preparing metadata (setup.py): started 2025-09-08T14:32:26,775 Running command python setup.py egg_info 2025-09-08T14:32:27,771 Traceback (most recent call last): 2025-09-08T14:32:27,774 File "", line 2, in 2025-09-08T14:32:27,774 exec(compile(''' 2025-09-08T14:32:27,774 ~~~~^^^^^^^^^^^^ 2025-09-08T14:32:27,774 # This is -- a caller that pip uses to run setup.py 2025-09-08T14:32:27,774 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,775 ...<32 lines>... 2025-09-08T14:32:27,775 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T14:32:27,775 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,775 ''' % ('/tmp/pip-wheel-k2725oei/hmm-kit_bc6d948532c541ed91e7b31646758cbd/setup.py',), "", "exec")) 2025-09-08T14:32:27,775 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,775 File "", line 35, in 2025-09-08T14:32:27,775 File "/tmp/pip-wheel-k2725oei/hmm-kit_bc6d948532c541ed91e7b31646758cbd/setup.py", line 12, in 2025-09-08T14:32:27,775 ext_modules = cythonize(['hmm_kit/_hmmc.pyx']) 2025-09-08T14:32:27,776 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 978, in cythonize 2025-09-08T14:32:27,776 module_list, module_metadata = create_extension_list( 2025-09-08T14:32:27,776 ~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,776 module_list, 2025-09-08T14:32:27,776 ^^^^^^^^^^^^ 2025-09-08T14:32:27,776 ...<4 lines>... 2025-09-08T14:32:27,776 language=language, 2025-09-08T14:32:27,776 ^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,776 aliases=aliases) 2025-09-08T14:32:27,777 ^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,777 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 809, in create_extension_list 2025-09-08T14:32:27,777 for file in nonempty(sorted(extended_iglob(filepattern)), "'%s' doesn't match any files" % filepattern): 2025-09-08T14:32:27,777 ~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,777 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 80, in nonempty 2025-09-08T14:32:27,777 raise ValueError(error_msg) 2025-09-08T14:32:27,777 ValueError: 'hmm_kit/_hmmc.pyx' doesn't match any files 2025-09-08T14:32:27,907 ERROR: python setup.py egg_info exited with 1 2025-09-08T14:32:27,920 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2025-09-08T14:32:27,920 exec(compile('"'"''"'"''"'"' 2025-09-08T14:32:27,920 # This is -- a caller that pip uses to run setup.py 2025-09-08T14:32:27,920 # 2025-09-08T14:32:27,920 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T14:32:27,920 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T14:32:27,920 # - It provides a clear error message when setuptools is not installed. 2025-09-08T14:32:27,920 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T14:32:27,920 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T14:32:27,920 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T14:32:27,920 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T14:32:27,920 import os, sys, tokenize, traceback 2025-09-08T14:32:27,920 2025-09-08T14:32:27,920 try: 2025-09-08T14:32:27,920 import setuptools 2025-09-08T14:32:27,920 except ImportError: 2025-09-08T14:32:27,920 print( 2025-09-08T14:32:27,920 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T14:32:27,920 "the build environment with exception:", 2025-09-08T14:32:27,920 file=sys.stderr, 2025-09-08T14:32:27,920 ) 2025-09-08T14:32:27,920 traceback.print_exc() 2025-09-08T14:32:27,920 sys.exit(1) 2025-09-08T14:32:27,920 2025-09-08T14:32:27,920 __file__ = %r 2025-09-08T14:32:27,920 sys.argv[0] = __file__ 2025-09-08T14:32:27,920 2025-09-08T14:32:27,920 if os.path.exists(__file__): 2025-09-08T14:32:27,920 filename = __file__ 2025-09-08T14:32:27,920 with tokenize.open(__file__) as f: 2025-09-08T14:32:27,920 setup_py_code = f.read() 2025-09-08T14:32:27,920 else: 2025-09-08T14:32:27,920 filename = "" 2025-09-08T14:32:27,920 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T14:32:27,920 2025-09-08T14:32:27,920 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T14:32:27,920 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-k2725oei/hmm-kit_bc6d948532c541ed91e7b31646758cbd/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-ugnfnh39[/] 2025-09-08T14:32:27,920 [bold magenta]cwd[/]: /tmp/pip-wheel-k2725oei/hmm-kit_bc6d948532c541ed91e7b31646758cbd/ 2025-09-08T14:32:27,921 Preparing metadata (setup.py): finished with status 'error' 2025-09-08T14:32:27,922 ERROR: metadata generation failed 2025-09-08T14:32:27,927 Exception information: 2025-09-08T14:32:27,927 Traceback (most recent call last): 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 63, in generate_metadata 2025-09-08T14:32:27,927 call_subprocess( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 args, 2025-09-08T14:32:27,927 ^^^^^ 2025-09-08T14:32:27,927 ...<2 lines>... 2025-09-08T14:32:27,927 spinner=spinner, 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess 2025-09-08T14:32:27,927 raise error 2025-09-08T14:32:27,927 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2025-09-08T14:32:27,927 2025-09-08T14:32:27,927 The above exception was the direct cause of the following exception: 2025-09-08T14:32:27,927 2025-09-08T14:32:27,927 Traceback (most recent call last): 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T14:32:27,927 status = _inner_run() 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T14:32:27,927 return self.run(options, args) 2025-09-08T14:32:27,927 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T14:32:27,927 return func(self, options, args) 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2025-09-08T14:32:27,927 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve 2025-09-08T14:32:27,927 result = self._result = resolver.resolve( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 collected.requirements, max_rounds=limit_how_complex_resolution_can_be 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve 2025-09-08T14:32:27,927 state = resolution.resolve(requirements, max_rounds=max_rounds) 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve 2025-09-08T14:32:27,927 self._add_to_criteria(self.state.criteria, r, parent=None) 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria 2025-09-08T14:32:27,927 if not criterion.candidates: 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__ 2025-09-08T14:32:27,927 return bool(self._sequence) 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__ 2025-09-08T14:32:27,927 self._bool = any(self) 2025-09-08T14:32:27,927 ~~~^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in 2025-09-08T14:32:27,927 return (c for c in iterator if id(c) not in self._incompatible_ids) 2025-09-08T14:32:27,927 ^^^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built 2025-09-08T14:32:27,927 candidate = func() 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link 2025-09-08T14:32:27,927 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 link, template, name, version 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link 2025-09-08T14:32:27,927 self._link_candidate_cache[link] = LinkCandidate( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 link, 2025-09-08T14:32:27,927 ^^^^^ 2025-09-08T14:32:27,927 ...<3 lines>... 2025-09-08T14:32:27,927 version=version, 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__ 2025-09-08T14:32:27,927 super().__init__( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 link=link, 2025-09-08T14:32:27,927 ^^^^^^^^^^ 2025-09-08T14:32:27,927 ...<4 lines>... 2025-09-08T14:32:27,927 version=version, 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ 2025-09-08T14:32:27,927 self.dist = self._prepare() 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare 2025-09-08T14:32:27,927 dist = self._prepare_distribution() 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution 2025-09-08T14:32:27,927 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement 2025-09-08T14:32:27,927 return self._prepare_linked_requirement(req, parallel_builds) 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement 2025-09-08T14:32:27,927 dist = _get_prepared_distribution( 2025-09-08T14:32:27,927 req, 2025-09-08T14:32:27,927 ...<3 lines>... 2025-09-08T14:32:27,927 self.check_build_deps, 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2025-09-08T14:32:27,927 abstract_dist.prepare_distribution_metadata( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 finder, build_isolation, check_build_deps 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata 2025-09-08T14:32:27,927 self.req.prepare_metadata() 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata 2025-09-08T14:32:27,927 self.metadata_directory = generate_metadata_legacy( 2025-09-08T14:32:27,927 ~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T14:32:27,927 build_env=self.build_env, 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ...<3 lines>... 2025-09-08T14:32:27,927 details=details, 2025-09-08T14:32:27,927 ^^^^^^^^^^^^^^^^ 2025-09-08T14:32:27,927 ) 2025-09-08T14:32:27,927 ^ 2025-09-08T14:32:27,927 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 70, in generate_metadata 2025-09-08T14:32:27,927 raise MetadataGenerationFailed(package_details=details) from error 2025-09-08T14:32:27,927 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2025-09-08T14:32:27,948 Removed hmm-kit==0.1.1 from https://files.pythonhosted.org/packages/ea/95/33cbefe7eb18093ff50a57904533fb1803cf6e67f3ead128a87d3ede14a4/hmm_kit-0.1.1.tar.gz from build tracker '/tmp/pip-build-tracker-q0xngsry' 2025-09-08T14:32:27,949 Removed build tracker: '/tmp/pip-build-tracker-q0xngsry'