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afg1/error_log.txt

Created February 9, 2023 09:56
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Error log from trying to run `poetry add -vvvv git+https://github.com/afg1/pysam.git`
Raw
error_log.txt
Stack trace:
1 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1523 in _run
1521│
1522│ if input_:
→ 1523│ output = subprocess.run(
1524│ command,
1525│ stdout=subprocess.PIPE,
CalledProcessError
Command '['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/bin/python', '-']' returned non-zero exit status 1.
at ~/.pyenv/versions/3.11.0/lib/python3.11/subprocess.py:569 in run
565│ # We don't call process.wait() as .__exit__ does that for us.
566│ raise
567│ retcode = process.poll()
568│ if check and retcode:
→ 569│ raise CalledProcessError(retcode, process.args,
570│ output=stdout, stderr=stderr)
571│ return CompletedProcess(process.args, retcode, stdout, stderr)
572│
573│
The following error occurred when trying to handle this error:
Stack trace:
3 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/inspection/info.py:599 in get_pep517_metadata
597│ *PEP517_META_BUILD_DEPS,
598│ )
→ 599│ venv.run(
600│ "python",
601│ "-",
2 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1492 in run
1490│ def run(self, bin: str, *args: str, **kwargs: Any) -> str | int:
1491│ cmd = self.get_command_from_bin(bin) + list(args)
→ 1492│ return self._run(cmd, **kwargs)
1493│
1494│ def run_pip(self, *args: str, **kwargs: Any) -> int | str:
1 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1776 in _run
1774│ def _run(self, cmd: list[str], **kwargs: Any) -> int | str:
1775│ kwargs["env"] = self.get_temp_environ(environ=kwargs.get("env"))
→ 1776│ return super()._run(cmd, **kwargs)
1777│
1778│ def get_temp_environ(
EnvCommandError
Command ['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/bin/python', '-'] errored with the following return code 1, and output:
Traceback (most recent call last):
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/build/__init__.py", line 422, in _handle_backend
yield
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/build/__init__.py", line 310, in get_requires_for_build
return set(get_requires(config_settings))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/pep517/wrappers.py", line 172, in get_requires_for_build_wheel
return self._call_hook('get_requires_for_build_wheel', {
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/pep517/wrappers.py", line 322, in _call_hook
self._subprocess_runner(
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/build/__init__.py", line 261, in _runner
self._hook_runner(cmd, cwd, extra_environ)
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/pep517/wrappers.py", line 75, in quiet_subprocess_runner
check_output(cmd, cwd=cwd, env=env, stderr=STDOUT)
File "/Users/agreen/.pyenv/versions/3.11.0/lib/python3.11/subprocess.py", line 465, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/agreen/.pyenv/versions/3.11.0/lib/python3.11/subprocess.py", line 569, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/build-env-8k7_2aq_/bin/python', '/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/pep517/in_process/_in_process.py', 'get_requires_for_build_wheel', '/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmpygfbytod']' returned non-zero exit status 1.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 16, in <module>
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/build/__init__.py", line 309, in get_requires_for_build
with self._handle_backend(hook_name):
File "/Users/agreen/.pyenv/versions/3.11.0/lib/python3.11/contextlib.py", line 155, in __exit__
self.gen.throw(typ, value, traceback)
File "/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/lib/python3.11/site-packages/build/__init__.py", line 430, in _handle_backend
raise BuildBackendException(exception, f'Backend subproccess exited when trying to invoke {hook}')
build.BuildBackendException: Backend subproccess exited when trying to invoke get_requires_for_build_wheel
input was : import build
import build.env
import pep517
source = '/Users/agreen/Library/Caches/pypoetry/virtualenvs/rnacentral-pipeline-GU-1IkEM-py3.11/src/pysam'
dest = '/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/dist'
with build.env.IsolatedEnvBuilder() as env:
builder = build.ProjectBuilder(
srcdir=source,
scripts_dir=env.scripts_dir,
python_executable=env.executable,
runner=pep517.quiet_subprocess_runner,
)
env.install(builder.build_system_requires)
env.install(builder.get_requires_for_build('wheel'))
builder.metadata_path(dest)
at ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1540 in _run
1536│ output = subprocess.check_output(
1537│ command, stderr=subprocess.STDOUT, env=env, **kwargs
1538│ )
1539│ except CalledProcessError as e:
→ 1540│ raise EnvCommandError(e, input=input_)
1541│
1542│ return decode(output)
1543│
1544│ def execute(self, bin: str, *args: str, **kwargs: Any) -> int:
The following error occurred when trying to handle this error:
Stack trace:
2 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1536 in _run
1534│ )
1535│ else:
→ 1536│ output = subprocess.check_output(
1537│ command, stderr=subprocess.STDOUT, env=env, **kwargs
1538│ )
1 ~/.pyenv/versions/3.11.0/lib/python3.11/subprocess.py:465 in check_output
463│ kwargs['input'] = empty
464│
→ 465│ return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
466│ **kwargs).stdout
467│
CalledProcessError
Command '['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/bin/python', 'setup.py', 'egg_info']' returned non-zero exit status 1.
at ~/.pyenv/versions/3.11.0/lib/python3.11/subprocess.py:569 in run
565│ # We don't call process.wait() as .__exit__ does that for us.
566│ raise
567│ retcode = process.poll()
568│ if check and retcode:
→ 569│ raise CalledProcessError(retcode, process.args,
570│ output=stdout, stderr=stderr)
571│ return CompletedProcess(process.args, retcode, stdout, stderr)
572│
573│
The following error occurred when trying to handle this error:
Stack trace:
3 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/inspection/info.py:620 in get_pep517_metadata
618│ os.chdir(path.as_posix())
619│ try:
→ 620│ venv.run("python", "setup.py", "egg_info")
621│ info = PackageInfo.from_metadata(path)
622│ except EnvCommandError as fbe:
2 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1492 in run
1490│ def run(self, bin: str, *args: str, **kwargs: Any) -> str | int:
1491│ cmd = self.get_command_from_bin(bin) + list(args)
→ 1492│ return self._run(cmd, **kwargs)
1493│
1494│ def run_pip(self, *args: str, **kwargs: Any) -> int | str:
1 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1776 in _run
1774│ def _run(self, cmd: list[str], **kwargs: Any) -> int | str:
1775│ kwargs["env"] = self.get_temp_environ(environ=kwargs.get("env"))
→ 1776│ return super()._run(cmd, **kwargs)
1777│
1778│ def get_temp_environ(
EnvCommandError
Command ['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/bin/python', 'setup.py', 'egg_info'] errored with the following return code 1, and output:
# pysam: no cython available - using pre-compiled C
Traceback (most recent call last):
File "/Users/agreen/Library/Caches/pypoetry/virtualenvs/rnacentral-pipeline-GU-1IkEM-py3.11/src/pysam/setup.py", line 345, in <module>
raise ValueError(
ValueError: no cython installed, but can not find pysam/libchtslib.c.Make sure that cython is installed when building from the repository
at ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/env.py:1540 in _run
1536│ output = subprocess.check_output(
1537│ command, stderr=subprocess.STDOUT, env=env, **kwargs
1538│ )
1539│ except CalledProcessError as e:
→ 1540│ raise EnvCommandError(e, input=input_)
1541│
1542│ return decode(output)
1543│
1544│ def execute(self, bin: str, *args: str, **kwargs: Any) -> int:
The following error occurred when trying to handle this error:
Stack trace:
18 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/cleo/application.py:327 in run
325│
326│ try:
→ 327│ exit_code = self._run(io)
328│ except BrokenPipeError:
329│ # If we are piped to another process, it may close early and send a
17 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/console/application.py:190 in _run
188│ self._load_plugins(io)
189│
→ 190│ exit_code: int = super()._run(io)
191│ return exit_code
192│
16 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/cleo/application.py:431 in _run
429│ io.input.interactive(interactive)
430│
→ 431│ exit_code = self._run_command(command, io)
432│ self._running_command = None
433│
15 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/cleo/application.py:473 in _run_command
471│
472│ if error is not None:
→ 473│ raise error
474│
475│ return terminate_event.exit_code
14 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/cleo/application.py:457 in _run_command
455│
456│ if command_event.command_should_run():
→ 457│ exit_code = command.run(io)
458│ else:
459│ exit_code = ConsoleCommandEvent.RETURN_CODE_DISABLED
13 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/cleo/commands/base_command.py:119 in run
117│ io.input.validate()
118│
→ 119│ status_code = self.execute(io)
120│
121│ if status_code is None:
12 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/cleo/commands/command.py:62 in execute
60│
61│ try:
→ 62│ return self.handle()
63│ except KeyboardInterrupt:
64│ return 1
11 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/console/commands/add.py:158 in handle
156│ return 0
157│
→ 158│ requirements = self._determine_requirements(
159│ packages,
160│ allow_prereleases=self.option("allow-prereleases"),
10 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/console/commands/init.py:367 in _determine_requirements
365│
366│ result = []
→ 367│ for requirement in self._parse_requirements(requires):
368│ if "git" in requirement or "url" in requirement or "path" in requirement:
369│ result.append(requirement)
9 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/console/commands/init.py:426 in _parse_requirements
424│ cwd = Path.cwd()
425│
→ 426│ return [
427│ parse_dependency_specification(
428│ requirement=requirement,
8 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/console/commands/init.py:427 in <listcomp>
425│
426│ return [
→ 427│ parse_dependency_specification(
428│ requirement=requirement,
429│ env=self.env if isinstance(self, EnvCommand) else None,
7 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/dependency_specification.py:216 in parse_dependency_specification
214│
215│ specification = (
→ 216│ _parse_dependency_specification_url(requirement, env=env)
217│ or _parse_dependency_specification_path(requirement, cwd=cwd)
218│ or _parse_dependency_specification_simple(requirement)
6 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/dependency_specification.py:68 in _parse_dependency_specification_url
66│
67│ if url_parsed.scheme in ["git+https", "git+ssh"]:
→ 68│ return _parse_dependency_specification_git_url(requirement, env)
69│
70│ if url_parsed.scheme in ["http", "https"]:
5 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/utils/dependency_specification.py:49 in _parse_dependency_specification_git_url
47│
48│ source_root = env.path.joinpath("src") if env else None
→ 49│ package = Provider.get_package_from_vcs(
50│ "git",
51│ url=url.url,
4 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/puzzle/provider.py:382 in get_package_from_vcs
380│ raise ValueError(f"Unsupported VCS dependency {vcs}")
381│
→ 382│ return _get_package_from_git(
383│ url=url,
384│ branch=branch,
3 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/puzzle/provider.py:124 in _get_package_from_git
122│ path = path.joinpath(subdirectory)
123│
→ 124│ package = Provider.get_package_from_directory(path)
125│ package._source_type = "git"
126│ package._source_url = url
2 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/puzzle/provider.py:435 in get_package_from_directory
433│ @classmethod
434│ def get_package_from_directory(cls, directory: Path) -> Package:
→ 435│ return PackageInfo.from_directory(path=directory).to_package(root_dir=directory)
436│
437│ def _search_for_url(self, dependency: URLDependency) -> Package:
1 ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/inspection/info.py:497 in from_directory
495│ info = cls.from_setup_files(path)
496│ else:
→ 497│ info = get_pep517_metadata(path)
498│ except PackageInfoError:
499│ if not info:
PackageInfoError
Unable to determine package info for path: /Users/agreen/Library/Caches/pypoetry/virtualenvs/rnacentral-pipeline-GU-1IkEM-py3.11/src/pysam
Fallback egg_info generation failed.
Command ['/var/folders/sg/3858brmd79z4rz781g0q__940000gp/T/tmp3o_tpe0o/.venv/bin/python', 'setup.py', 'egg_info'] errored with the following return code 1, and output:
# pysam: no cython available - using pre-compiled C
Traceback (most recent call last):
File "/Users/agreen/Library/Caches/pypoetry/virtualenvs/rnacentral-pipeline-GU-1IkEM-py3.11/src/pysam/setup.py", line 345, in <module>
raise ValueError(
ValueError: no cython installed, but can not find pysam/libchtslib.c.Make sure that cython is installed when building from the repository
at ~/Library/Application Support/pypoetry/venv/lib/python3.11/site-packages/poetry/inspection/info.py:623 in get_pep517_metadata
619│ try:
620│ venv.run("python", "setup.py", "egg_info")
621│ info = PackageInfo.from_metadata(path)
622│ except EnvCommandError as fbe:
→ 623│ raise PackageInfoError(
624│ path, "Fallback egg_info generation failed.", fbe
625│ )
626│ finally:
627│ os.chdir(cwd.as_posix())
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