2025-09-08T00:47:34,324 Created temporary directory: /tmp/pip-build-tracker-3nqzmf6_ 2025-09-08T00:47:34,325 Initialized build tracking at /tmp/pip-build-tracker-3nqzmf6_ 2025-09-08T00:47:34,325 Created build tracker: /tmp/pip-build-tracker-3nqzmf6_ 2025-09-08T00:47:34,325 Entered build tracker: /tmp/pip-build-tracker-3nqzmf6_ 2025-09-08T00:47:34,325 Created temporary directory: /tmp/pip-wheel-nfks36sp 2025-09-08T00:47:34,329 Created temporary directory: /tmp/pip-ephem-wheel-cache-jrv7ld9a 2025-09-08T00:47:34,390 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T00:47:34,392 2 location(s) to search for versions of gtf-to-genes: 2025-09-08T00:47:34,392 * https://pypi.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,392 * https://www.piwheels.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,392 Fetching project page and analyzing links: https://pypi.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,393 Getting page https://pypi.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,394 Found index url https://pypi.org/simple/ 2025-09-08T00:47:34,465 Fetched page https://pypi.org/simple/gtf-to-genes/ as application/vnd.pypi.simple.v1+json 2025-09-08T00:47:34,467 Found link https://files.pythonhosted.org/packages/db/b2/41b8f386273680549587f8e4ac52d402982bd8631a07f011d39c1c300e38/gtf_to_genes-1.0beta.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.0beta 2025-09-08T00:47:34,467 Found link https://files.pythonhosted.org/packages/d8/9b/dbb884d7ddba138899608665954b0da8a749127f9d800fb1b67c606acf67/gtf_to_genes-1.0beta2.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.0beta2 2025-09-08T00:47:34,467 Found link https://files.pythonhosted.org/packages/b7/54/25d3ea7d65001e6ca592abaee4f669c02fa80c10192726cb8edd08986074/gtf_to_genes-1.0.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.0 2025-09-08T00:47:34,468 Found link https://files.pythonhosted.org/packages/21/1b/9bd5233344406bbbdb6f3088607bfd84c0150fa727a96ecd072f2c7d9d71/gtf_to_genes-1.01.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.01 2025-09-08T00:47:34,468 Found link https://files.pythonhosted.org/packages/f7/e1/216e2667156d48e1ceb9a714bf8d3ce2ac9896e86674455d948889d21e8c/gtf_to_genes-1.02.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.02 2025-09-08T00:47:34,468 Found link https://files.pythonhosted.org/packages/b5/01/41b154744520ad0c057eca7aaecb8b0e67239a5c3adadf0a964b3127d9e5/gtf_to_genes-1.03.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.03 2025-09-08T00:47:34,468 Found link https://files.pythonhosted.org/packages/f7/a6/1d457574172d90bdf38697171dd322722ef1bb43c29cc49103acea1c4000/gtf_to_genes-1.04.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.04 2025-09-08T00:47:34,468 Found link https://files.pythonhosted.org/packages/ba/79/2b65639653283fe1f8b8adf147d73ab520f168fa421e97fdec046af585fe/gtf_to_genes-1.06.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.06 2025-09-08T00:47:34,469 Found link https://files.pythonhosted.org/packages/14/bb/5246c5971c7da8cdaf6581472056f0aaab49f3471d0f8fc6bbfb216b5ad5/gtf_to_genes-1.07.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.07 2025-09-08T00:47:34,469 Found link https://files.pythonhosted.org/packages/47/d4/9fbbc912b084790878b7c59f51771b213f9d6a169233f84c9951e41f9770/gtf_to_genes-1.09.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.09 2025-09-08T00:47:34,469 Found link https://files.pythonhosted.org/packages/88/e6/317daf167ba5e076c647ccc3efac284431d404817290e0e7cef2a3e07f6e/gtf_to_genes-1.30.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.30 2025-09-08T00:47:34,469 Found link https://files.pythonhosted.org/packages/91/23/83cc3417984c5ff31d5bebaaed70b054632af16af0274821ffe0146b378a/gtf_to_genes-1.31.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.31 2025-09-08T00:47:34,469 Found link https://files.pythonhosted.org/packages/35/1d/eb9f5d711ee1b9717f8cfc41eadd0086066a08b99e35da95a0a42a1ae266/gtf_to_genes-1.40.tar.gz (from https://pypi.org/simple/gtf-to-genes/), version: 1.40 2025-09-08T00:47:34,470 Fetching project page and analyzing links: https://www.piwheels.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,470 Getting page https://www.piwheels.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,471 Found index url https://www.piwheels.org/simple/ 2025-09-08T00:47:34,563 Fetched page https://www.piwheels.org/simple/gtf-to-genes/ as text/html 2025-09-08T00:47:34,564 Skipping link: not a file: https://www.piwheels.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,564 Skipping link: not a file: https://pypi.org/simple/gtf-to-genes/ 2025-09-08T00:47:34,591 Given no hashes to check 1 links for project 'gtf-to-genes': discarding no candidates 2025-09-08T00:47:34,592 Collecting gtf-to-genes==1.40 2025-09-08T00:47:34,593 Created temporary directory: /tmp/pip-unpack-0mvc99k7 2025-09-08T00:47:34,729 Downloading gtf_to_genes-1.40.tar.gz (35 kB) 2025-09-08T00:47:34,761 Added gtf-to-genes==1.40 from https://files.pythonhosted.org/packages/35/1d/eb9f5d711ee1b9717f8cfc41eadd0086066a08b99e35da95a0a42a1ae266/gtf_to_genes-1.40.tar.gz to build tracker '/tmp/pip-build-tracker-3nqzmf6_' 2025-09-08T00:47:34,762 Running setup.py (path:/tmp/pip-wheel-nfks36sp/gtf-to-genes_c22f5756cc7146b68022eb4f9ca9dc8b/setup.py) egg_info for package gtf-to-genes 2025-09-08T00:47:34,762 Created temporary directory: /tmp/pip-pip-egg-info-mqkhliux 2025-09-08T00:47:34,762 Preparing metadata (setup.py): started 2025-09-08T00:47:34,763 Running command python setup.py egg_info 2025-09-08T00:47:35,272 Traceback (most recent call last): 2025-09-08T00:47:35,273 File "", line 2, in 2025-09-08T00:47:35,273 exec(compile(''' 2025-09-08T00:47:35,274 ~~~~^^^^^^^^^^^^ 2025-09-08T00:47:35,274 # This is -- a caller that pip uses to run setup.py 2025-09-08T00:47:35,274 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,274 ...<32 lines>... 2025-09-08T00:47:35,274 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T00:47:35,274 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,274 ''' % ('/tmp/pip-wheel-nfks36sp/gtf-to-genes_c22f5756cc7146b68022eb4f9ca9dc8b/setup.py',), "", "exec")) 2025-09-08T00:47:35,274 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,275 File "", line 35, in 2025-09-08T00:47:35,275 File "/tmp/pip-wheel-nfks36sp/gtf-to-genes_c22f5756cc7146b68022eb4f9ca9dc8b/setup.py", line 12, in 2025-09-08T00:47:35,275 import gtf_to_genes.gtf_to_genes_version 2025-09-08T00:47:35,275 File "/tmp/pip-wheel-nfks36sp/gtf-to-genes_c22f5756cc7146b68022eb4f9ca9dc8b/gtf_to_genes/__init__.py", line 27, in 2025-09-08T00:47:35,275 from gene import t_parse_gtf, t_gene, t_transcript 2025-09-08T00:47:35,275 ModuleNotFoundError: No module named 'gene' 2025-09-08T00:47:35,359 ERROR: python setup.py egg_info exited with 1 2025-09-08T00:47:35,371 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2025-09-08T00:47:35,371 exec(compile('"'"''"'"''"'"' 2025-09-08T00:47:35,371 # This is -- a caller that pip uses to run setup.py 2025-09-08T00:47:35,371 # 2025-09-08T00:47:35,371 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T00:47:35,371 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T00:47:35,371 # - It provides a clear error message when setuptools is not installed. 2025-09-08T00:47:35,371 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T00:47:35,371 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T00:47:35,371 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T00:47:35,371 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T00:47:35,371 import os, sys, tokenize, traceback 2025-09-08T00:47:35,371 2025-09-08T00:47:35,371 try: 2025-09-08T00:47:35,371 import setuptools 2025-09-08T00:47:35,371 except ImportError: 2025-09-08T00:47:35,371 print( 2025-09-08T00:47:35,371 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T00:47:35,371 "the build environment with exception:", 2025-09-08T00:47:35,371 file=sys.stderr, 2025-09-08T00:47:35,371 ) 2025-09-08T00:47:35,371 traceback.print_exc() 2025-09-08T00:47:35,371 sys.exit(1) 2025-09-08T00:47:35,371 2025-09-08T00:47:35,371 __file__ = %r 2025-09-08T00:47:35,371 sys.argv[0] = __file__ 2025-09-08T00:47:35,371 2025-09-08T00:47:35,371 if os.path.exists(__file__): 2025-09-08T00:47:35,371 filename = __file__ 2025-09-08T00:47:35,371 with tokenize.open(__file__) as f: 2025-09-08T00:47:35,371 setup_py_code = f.read() 2025-09-08T00:47:35,371 else: 2025-09-08T00:47:35,371 filename = "" 2025-09-08T00:47:35,371 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T00:47:35,371 2025-09-08T00:47:35,371 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T00:47:35,371 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-nfks36sp/gtf-to-genes_c22f5756cc7146b68022eb4f9ca9dc8b/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-mqkhliux[/] 2025-09-08T00:47:35,371 [bold magenta]cwd[/]: /tmp/pip-wheel-nfks36sp/gtf-to-genes_c22f5756cc7146b68022eb4f9ca9dc8b/ 2025-09-08T00:47:35,372 Preparing metadata (setup.py): finished with status 'error' 2025-09-08T00:47:35,372 ERROR: metadata generation failed 2025-09-08T00:47:35,378 Exception information: 2025-09-08T00:47:35,378 Traceback (most recent call last): 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 63, in generate_metadata 2025-09-08T00:47:35,378 call_subprocess( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 args, 2025-09-08T00:47:35,378 ^^^^^ 2025-09-08T00:47:35,378 ...<2 lines>... 2025-09-08T00:47:35,378 spinner=spinner, 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess 2025-09-08T00:47:35,378 raise error 2025-09-08T00:47:35,378 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2025-09-08T00:47:35,378 2025-09-08T00:47:35,378 The above exception was the direct cause of the following exception: 2025-09-08T00:47:35,378 2025-09-08T00:47:35,378 Traceback (most recent call last): 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T00:47:35,378 status = _inner_run() 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T00:47:35,378 return self.run(options, args) 2025-09-08T00:47:35,378 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T00:47:35,378 return func(self, options, args) 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2025-09-08T00:47:35,378 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve 2025-09-08T00:47:35,378 result = self._result = resolver.resolve( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 collected.requirements, max_rounds=limit_how_complex_resolution_can_be 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve 2025-09-08T00:47:35,378 state = resolution.resolve(requirements, max_rounds=max_rounds) 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve 2025-09-08T00:47:35,378 self._add_to_criteria(self.state.criteria, r, parent=None) 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria 2025-09-08T00:47:35,378 if not criterion.candidates: 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__ 2025-09-08T00:47:35,378 return bool(self._sequence) 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__ 2025-09-08T00:47:35,378 self._bool = any(self) 2025-09-08T00:47:35,378 ~~~^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in 2025-09-08T00:47:35,378 return (c for c in iterator if id(c) not in self._incompatible_ids) 2025-09-08T00:47:35,378 ^^^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built 2025-09-08T00:47:35,378 candidate = func() 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link 2025-09-08T00:47:35,378 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 link, template, name, version 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link 2025-09-08T00:47:35,378 self._link_candidate_cache[link] = LinkCandidate( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 link, 2025-09-08T00:47:35,378 ^^^^^ 2025-09-08T00:47:35,378 ...<3 lines>... 2025-09-08T00:47:35,378 version=version, 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__ 2025-09-08T00:47:35,378 super().__init__( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 link=link, 2025-09-08T00:47:35,378 ^^^^^^^^^^ 2025-09-08T00:47:35,378 ...<4 lines>... 2025-09-08T00:47:35,378 version=version, 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ 2025-09-08T00:47:35,378 self.dist = self._prepare() 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare 2025-09-08T00:47:35,378 dist = self._prepare_distribution() 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution 2025-09-08T00:47:35,378 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement 2025-09-08T00:47:35,378 return self._prepare_linked_requirement(req, parallel_builds) 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement 2025-09-08T00:47:35,378 dist = _get_prepared_distribution( 2025-09-08T00:47:35,378 req, 2025-09-08T00:47:35,378 ...<3 lines>... 2025-09-08T00:47:35,378 self.check_build_deps, 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2025-09-08T00:47:35,378 abstract_dist.prepare_distribution_metadata( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 finder, build_isolation, check_build_deps 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata 2025-09-08T00:47:35,378 self.req.prepare_metadata() 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata 2025-09-08T00:47:35,378 self.metadata_directory = generate_metadata_legacy( 2025-09-08T00:47:35,378 ~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-08T00:47:35,378 build_env=self.build_env, 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ...<3 lines>... 2025-09-08T00:47:35,378 details=details, 2025-09-08T00:47:35,378 ^^^^^^^^^^^^^^^^ 2025-09-08T00:47:35,378 ) 2025-09-08T00:47:35,378 ^ 2025-09-08T00:47:35,378 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 70, in generate_metadata 2025-09-08T00:47:35,378 raise MetadataGenerationFailed(package_details=details) from error 2025-09-08T00:47:35,378 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2025-09-08T00:47:35,398 Removed gtf-to-genes==1.40 from https://files.pythonhosted.org/packages/35/1d/eb9f5d711ee1b9717f8cfc41eadd0086066a08b99e35da95a0a42a1ae266/gtf_to_genes-1.40.tar.gz from build tracker '/tmp/pip-build-tracker-3nqzmf6_' 2025-09-08T00:47:35,398 Removed build tracker: '/tmp/pip-build-tracker-3nqzmf6_'