2025-09-14T04:12:39,617 Created temporary directory: /tmp/pip-build-tracker-v9rmpghz 2025-09-14T04:12:39,618 Initialized build tracking at /tmp/pip-build-tracker-v9rmpghz 2025-09-14T04:12:39,618 Created build tracker: /tmp/pip-build-tracker-v9rmpghz 2025-09-14T04:12:39,618 Entered build tracker: /tmp/pip-build-tracker-v9rmpghz 2025-09-14T04:12:39,618 Created temporary directory: /tmp/pip-wheel-61o3iq2d 2025-09-14T04:12:39,622 Created temporary directory: /tmp/pip-ephem-wheel-cache-qt61v24r 2025-09-14T04:12:39,678 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-14T04:12:39,680 2 location(s) to search for versions of samtool: 2025-09-14T04:12:39,680 * https://pypi.org/simple/samtool/ 2025-09-14T04:12:39,680 * https://www.piwheels.org/simple/samtool/ 2025-09-14T04:12:39,681 Fetching project page and analyzing links: https://pypi.org/simple/samtool/ 2025-09-14T04:12:39,681 Getting page https://pypi.org/simple/samtool/ 2025-09-14T04:12:39,682 Found index url https://pypi.org/simple/ 2025-09-14T04:12:39,829 Fetched page https://pypi.org/simple/samtool/ as application/vnd.pypi.simple.v1+json 2025-09-14T04:12:39,831 Skipping link: No binaries permitted for samtool: https://files.pythonhosted.org/packages/4f/4e/feb147c89b7ffcbfc4bbae02f6922fec09460d0ce69a55652835b72a2977/samtool-0.0.1-py3-none-any.whl (from https://pypi.org/simple/samtool/) (requires-python:>=3.10) 2025-09-14T04:12:39,832 Found link https://files.pythonhosted.org/packages/1f/f3/49433523caff950b141ca9c8ffb8498efb85cf397a5fb1e4e6cf9ea82e72/samtool-0.0.1.tar.gz (from https://pypi.org/simple/samtool/) (requires-python:>=3.10), version: 0.0.1 2025-09-14T04:12:39,833 Skipping link: No binaries permitted for samtool: https://files.pythonhosted.org/packages/40/d0/b4f7ccceaef4d387cb537c7a4a306f9c0c1fb0d5d46ce862d9177a68a5c9/samtool-0.0.2-py3-none-any.whl (from https://pypi.org/simple/samtool/) (requires-python:>=3.10) 2025-09-14T04:12:39,833 Found link https://files.pythonhosted.org/packages/24/c4/f550cfa5962e0c54bcf8bb6f008d7883ba01ace9f9e0a001ab3615d7350c/samtool-0.0.2.tar.gz (from https://pypi.org/simple/samtool/) (requires-python:>=3.10), version: 0.0.2 2025-09-14T04:12:39,834 Fetching project page and analyzing links: https://www.piwheels.org/simple/samtool/ 2025-09-14T04:12:39,834 Getting page https://www.piwheels.org/simple/samtool/ 2025-09-14T04:12:39,835 Found index url https://www.piwheels.org/simple/ 2025-09-14T04:12:39,929 Fetched page https://www.piwheels.org/simple/samtool/ as text/html 2025-09-14T04:12:39,929 Skipping link: not a file: https://www.piwheels.org/simple/samtool/ 2025-09-14T04:12:39,930 Skipping link: not a file: https://pypi.org/simple/samtool/ 2025-09-14T04:12:39,954 Given no hashes to check 1 links for project 'samtool': discarding no candidates 2025-09-14T04:12:39,955 Collecting samtool==0.0.1 2025-09-14T04:12:39,957 Created temporary directory: /tmp/pip-unpack-2bgh9yev 2025-09-14T04:12:40,293 Downloading samtool-0.0.1.tar.gz (4.4 kB) 2025-09-14T04:12:40,318 Added samtool==0.0.1 from https://files.pythonhosted.org/packages/1f/f3/49433523caff950b141ca9c8ffb8498efb85cf397a5fb1e4e6cf9ea82e72/samtool-0.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-v9rmpghz' 2025-09-14T04:12:40,320 Running setup.py (path:/tmp/pip-wheel-61o3iq2d/samtool_2fa3497f0fb445d69455b9f367950365/setup.py) egg_info for package samtool 2025-09-14T04:12:40,320 Created temporary directory: /tmp/pip-pip-egg-info-38i1uhj4 2025-09-14T04:12:40,320 Preparing metadata (setup.py): started 2025-09-14T04:12:40,321 Running command python setup.py egg_info 2025-09-14T04:12:41,177 WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. 2025-09-14T04:12:41,177 Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. 2025-09-14T04:12:41,177 To avoid this problem you can invoke Python with '-m pip' instead of running pip directly. 2025-09-14T04:12:41,631 error: externally-managed-environment 2025-09-14T04:12:41,631 × This environment is externally managed 2025-09-14T04:12:41,632 ╰─> To install Python packages system-wide, try apt install 2025-09-14T04:12:41,632 python3-xyz, where xyz is the package you are trying to 2025-09-14T04:12:41,632 install. 2025-09-14T04:12:41,632 If you wish to install a non-Debian-packaged Python package, 2025-09-14T04:12:41,632 create a virtual environment using python3 -m venv path/to/venv. 2025-09-14T04:12:41,632 Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make 2025-09-14T04:12:41,632 sure you have python3-full installed. 2025-09-14T04:12:41,632 For more information visit http://rptl.io/venv 2025-09-14T04:12:41,633 note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages. 2025-09-14T04:12:41,633 hint: See PEP 668 for the detailed specification. 2025-09-14T04:12:41,633 WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip. 2025-09-14T04:12:41,633 Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue. 2025-09-14T04:12:41,633 To avoid this problem you can invoke Python with '-m pip' instead of running pip directly. 2025-09-14T04:12:41,648 error: externally-managed-environment 2025-09-14T04:12:41,648 × This environment is externally managed 2025-09-14T04:12:41,648 ╰─> To install Python packages system-wide, try apt install 2025-09-14T04:12:41,648 python3-xyz, where xyz is the package you are trying to 2025-09-14T04:12:41,648 install. 2025-09-14T04:12:41,649 If you wish to install a non-Debian-packaged Python package, 2025-09-14T04:12:41,649 create a virtual environment using python3 -m venv path/to/venv. 2025-09-14T04:12:41,649 Then use path/to/venv/bin/python and path/to/venv/bin/pip. Make 2025-09-14T04:12:41,649 sure you have python3-full installed. 2025-09-14T04:12:41,649 For more information visit http://rptl.io/venv 2025-09-14T04:12:41,649 note: If you believe this is a mistake, please contact your Python installation or OS distribution provider. You can override this, at the risk of breaking your Python installation or OS, by passing --break-system-packages. 2025-09-14T04:12:41,649 hint: See PEP 668 for the detailed specification. 2025-09-14T04:12:41,650 Traceback (most recent call last): 2025-09-14T04:12:41,650 File "/tmp/pip-wheel-61o3iq2d/samtool_2fa3497f0fb445d69455b9f367950365/setup.py", line 3, in 2025-09-14T04:12:41,650 from install_preserve import preserve 2025-09-14T04:12:41,650 ModuleNotFoundError: No module named 'install_preserve' 2025-09-14T04:12:41,651 During handling of the above exception, another exception occurred: 2025-09-14T04:12:41,651 Traceback (most recent call last): 2025-09-14T04:12:41,652 File "", line 2, in 2025-09-14T04:12:41,652 exec(compile(''' 2025-09-14T04:12:41,652 ~~~~^^^^^^^^^^^^ 2025-09-14T04:12:41,652 # This is -- a caller that pip uses to run setup.py 2025-09-14T04:12:41,652 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,652 ...<32 lines>... 2025-09-14T04:12:41,652 exec(compile(setup_py_code, filename, "exec")) 2025-09-14T04:12:41,652 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,652 ''' % ('/tmp/pip-wheel-61o3iq2d/samtool_2fa3497f0fb445d69455b9f367950365/setup.py',), "", "exec")) 2025-09-14T04:12:41,653 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,653 File "", line 35, in 2025-09-14T04:12:41,653 File "/tmp/pip-wheel-61o3iq2d/samtool_2fa3497f0fb445d69455b9f367950365/setup.py", line 8, in 2025-09-14T04:12:41,653 from install_preserve import preserve # noqa 2025-09-14T04:12:41,653 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,653 ModuleNotFoundError: No module named 'install_preserve' 2025-09-14T04:12:41,840 ERROR: python setup.py egg_info exited with 1 2025-09-14T04:12:41,852 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c ' 2025-09-14T04:12:41,852 exec(compile('"'"''"'"''"'"' 2025-09-14T04:12:41,852 # This is -- a caller that pip uses to run setup.py 2025-09-14T04:12:41,852 # 2025-09-14T04:12:41,852 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-14T04:12:41,852 # import from `distutils.core` to work with newer packaging standards. 2025-09-14T04:12:41,852 # - It provides a clear error message when setuptools is not installed. 2025-09-14T04:12:41,852 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-14T04:12:41,852 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-14T04:12:41,852 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-14T04:12:41,852 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-14T04:12:41,852 import os, sys, tokenize, traceback 2025-09-14T04:12:41,852 2025-09-14T04:12:41,852 try: 2025-09-14T04:12:41,852 import setuptools 2025-09-14T04:12:41,852 except ImportError: 2025-09-14T04:12:41,852 print( 2025-09-14T04:12:41,852 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-14T04:12:41,852 "the build environment with exception:", 2025-09-14T04:12:41,852 file=sys.stderr, 2025-09-14T04:12:41,852 ) 2025-09-14T04:12:41,852 traceback.print_exc() 2025-09-14T04:12:41,852 sys.exit(1) 2025-09-14T04:12:41,852 2025-09-14T04:12:41,852 __file__ = %r 2025-09-14T04:12:41,852 sys.argv[0] = __file__ 2025-09-14T04:12:41,852 2025-09-14T04:12:41,852 if os.path.exists(__file__): 2025-09-14T04:12:41,852 filename = __file__ 2025-09-14T04:12:41,852 with tokenize.open(__file__) as f: 2025-09-14T04:12:41,852 setup_py_code = f.read() 2025-09-14T04:12:41,852 else: 2025-09-14T04:12:41,852 filename = "" 2025-09-14T04:12:41,852 setup_py_code = "from setuptools import setup; setup()" 2025-09-14T04:12:41,852 2025-09-14T04:12:41,852 exec(compile(setup_py_code, filename, "exec")) 2025-09-14T04:12:41,852 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-61o3iq2d/samtool_2fa3497f0fb445d69455b9f367950365/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-38i1uhj4[/] 2025-09-14T04:12:41,852 [bold magenta]cwd[/]: /tmp/pip-wheel-61o3iq2d/samtool_2fa3497f0fb445d69455b9f367950365/ 2025-09-14T04:12:41,852 Preparing metadata (setup.py): finished with status 'error' 2025-09-14T04:12:41,853 ERROR: metadata generation failed 2025-09-14T04:12:41,858 Exception information: 2025-09-14T04:12:41,858 Traceback (most recent call last): 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 63, in generate_metadata 2025-09-14T04:12:41,858 call_subprocess( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 args, 2025-09-14T04:12:41,858 ^^^^^ 2025-09-14T04:12:41,858 ...<2 lines>... 2025-09-14T04:12:41,858 spinner=spinner, 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess 2025-09-14T04:12:41,858 raise error 2025-09-14T04:12:41,858 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1 2025-09-14T04:12:41,858 2025-09-14T04:12:41,858 The above exception was the direct cause of the following exception: 2025-09-14T04:12:41,858 2025-09-14T04:12:41,858 Traceback (most recent call last): 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-14T04:12:41,858 status = _inner_run() 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-14T04:12:41,858 return self.run(options, args) 2025-09-14T04:12:41,858 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-14T04:12:41,858 return func(self, options, args) 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run 2025-09-14T04:12:41,858 requirement_set = resolver.resolve(reqs, check_supported_wheels=True) 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve 2025-09-14T04:12:41,858 result = self._result = resolver.resolve( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 collected.requirements, max_rounds=limit_how_complex_resolution_can_be 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve 2025-09-14T04:12:41,858 state = resolution.resolve(requirements, max_rounds=max_rounds) 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve 2025-09-14T04:12:41,858 self._add_to_criteria(self.state.criteria, r, parent=None) 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria 2025-09-14T04:12:41,858 if not criterion.candidates: 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__ 2025-09-14T04:12:41,858 return bool(self._sequence) 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__ 2025-09-14T04:12:41,858 self._bool = any(self) 2025-09-14T04:12:41,858 ~~~^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in 2025-09-14T04:12:41,858 return (c for c in iterator if id(c) not in self._incompatible_ids) 2025-09-14T04:12:41,858 ^^^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built 2025-09-14T04:12:41,858 candidate = func() 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link 2025-09-14T04:12:41,858 base: Optional[BaseCandidate] = self._make_base_candidate_from_link( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 link, template, name, version 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link 2025-09-14T04:12:41,858 self._link_candidate_cache[link] = LinkCandidate( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 link, 2025-09-14T04:12:41,858 ^^^^^ 2025-09-14T04:12:41,858 ...<3 lines>... 2025-09-14T04:12:41,858 version=version, 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__ 2025-09-14T04:12:41,858 super().__init__( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 link=link, 2025-09-14T04:12:41,858 ^^^^^^^^^^ 2025-09-14T04:12:41,858 ...<4 lines>... 2025-09-14T04:12:41,858 version=version, 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__ 2025-09-14T04:12:41,858 self.dist = self._prepare() 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare 2025-09-14T04:12:41,858 dist = self._prepare_distribution() 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution 2025-09-14T04:12:41,858 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True) 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement 2025-09-14T04:12:41,858 return self._prepare_linked_requirement(req, parallel_builds) 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement 2025-09-14T04:12:41,858 dist = _get_prepared_distribution( 2025-09-14T04:12:41,858 req, 2025-09-14T04:12:41,858 ...<3 lines>... 2025-09-14T04:12:41,858 self.check_build_deps, 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution 2025-09-14T04:12:41,858 abstract_dist.prepare_distribution_metadata( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 finder, build_isolation, check_build_deps 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata 2025-09-14T04:12:41,858 self.req.prepare_metadata() 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~~~~~^^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata 2025-09-14T04:12:41,858 self.metadata_directory = generate_metadata_legacy( 2025-09-14T04:12:41,858 ~~~~~~~~~~~~~~~~~~~~~~~~^ 2025-09-14T04:12:41,858 build_env=self.build_env, 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ...<3 lines>... 2025-09-14T04:12:41,858 details=details, 2025-09-14T04:12:41,858 ^^^^^^^^^^^^^^^^ 2025-09-14T04:12:41,858 ) 2025-09-14T04:12:41,858 ^ 2025-09-14T04:12:41,858 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 70, in generate_metadata 2025-09-14T04:12:41,858 raise MetadataGenerationFailed(package_details=details) from error 2025-09-14T04:12:41,858 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed 2025-09-14T04:12:41,879 Removed samtool==0.0.1 from https://files.pythonhosted.org/packages/1f/f3/49433523caff950b141ca9c8ffb8498efb85cf397a5fb1e4e6cf9ea82e72/samtool-0.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-v9rmpghz' 2025-09-14T04:12:41,879 Removed build tracker: '/tmp/pip-build-tracker-v9rmpghz'