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astral-sh
Is `clang` required for compiling C extensions?
I wanted to uv pip install -e . a local package which contains a C extension, but I received an error: command 'clang' failed: No such file or directory. Is this something that uv requires, or is it some upstream package (setuptools maybe)? I'm asking because I already have a C compiler installed (cc -> gcc), so maybe this can be changed with an environment variable? Also, installing the package with the OG pip seems to use gcc.
Resolved 68 packages in 1.64s
error: Failed to prepare distributions
Caused by: Failed to fetch wheel: sleepecg @ file:///home/clemens/Projects/sleepecg
Caused by: Build backend failed to build editable through `build_editable` (exit status: 1)
[stdout]
No `packages` or `py_modules` configuration, performing automatic discovery.
`src-layout` detected -- analysing ./src
discovered packages -- ['sleepecg', 'sleepecg.classifiers', 'sleepecg.data', 'sleepecg.io']
discovered py_modules -- []
running editable_wheel
creating /home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info
writing /home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info/PKG-INFO
writing dependency_links to /home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info/dependency_links.txt
writing requirements to /home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info/requires.txt
writing top-level names to /home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info/top_level.txt
writing manifest file '/home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info/SOURCES.txt'
adding license file 'LICENSE'
writing manifest file '/home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg.egg-info/SOURCES.txt'
creating '/home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg-0.6.0.dev0.dist-info'
creating /home/clemens/.cache/uv/sdists-v4/editable/06d660b39b152d1a/jBYKEmid6Pcy_Yhu3Phiy/.tmp4dOrcC/.tmp-ea2n0bef/sleepecg-0.6.0.dev0.dist-info/WHEEL
running build_py
running build_ext
building 'sleepecg._heartbeat_detection' extension
creating /tmp/tmpwhxe1s8c.build-temp/src/sleepecg
clang -pthread -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -fPIC -fPIC -I/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/numpy/_core/include -I/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/include -I/home/clemens/.local/share/uv/python/cpython-3.13.0-linux-x86_64-gnu/include/python3.13 -c src/sleepecg/_heartbeat_detection.c -o /tmp/tmpwhxe1s8c.build-temp/src/sleepecg/_heartbeat_detection.o
[stderr]
Traceback (most recent call last):
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/spawn.py", line 70, in spawn
subprocess.check_call(cmd, env=_inject_macos_ver(env))
~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.local/share/uv/python/cpython-3.13.0-linux-x86_64-gnu/lib/python3.13/subprocess.py", line 414, in check_call
retcode = call(*popenargs, **kwargs)
File "/home/clemens/.local/share/uv/python/cpython-3.13.0-linux-x86_64-gnu/lib/python3.13/subprocess.py", line 395, in call
with Popen(*popenargs, **kwargs) as p:
~~~~~^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.local/share/uv/python/cpython-3.13.0-linux-x86_64-gnu/lib/python3.13/subprocess.py", line 1036, in __init__
self._execute_child(args, executable, preexec_fn, close_fds,
~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
pass_fds, cwd, env,
^^^^^^^^^^^^^^^^^^^
...<5 lines>...
gid, gids, uid, umask,
^^^^^^^^^^^^^^^^^^^^^^
start_new_session, process_group)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.local/share/uv/python/cpython-3.13.0-linux-x86_64-gnu/lib/python3.13/subprocess.py", line 1966, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'clang'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/unixccompiler.py", line 200, in _compile
self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/ccompiler.py", line 1045, in spawn
spawn(cmd, dry_run=self.dry_run, **kwargs)
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/spawn.py", line 72, in spawn
raise DistutilsExecError(
f"command {_debug(cmd)!r} failed: {exc.args[-1]}"
) from exc
distutils.errors.DistutilsExecError: command 'clang' failed: No such file or directory
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/command/editable_wheel.py", line 138, in run
self._create_wheel_file(bdist_wheel)
~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/command/editable_wheel.py", line 341, in _create_wheel_file
files, mapping = self._run_build_commands(dist_name, unpacked, lib, tmp)
~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/command/editable_wheel.py", line 264, in _run_build_commands
self._run_build_subcommands()
~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/command/editable_wheel.py", line 291, in _run_build_subcommands
self.run_command(name)
~~~~~~~~~~~~~~~~^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/dist.py", line 950, in run_command
super().run_command(command)
~~~~~~~~~~~~~~~~~~~^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
~~~~~~~~~~~^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/command/build_ext.py", line 98, in run
_build_ext.run(self)
~~~~~~~~~~~~~~^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
~~~~~~~~~~~~~~~~~~~~~^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 476, in build_extensions
self._build_extensions_serial()
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 502, in _build_extensions_serial
self.build_extension(ext)
~~~~~~~~~~~~~~~~~~~~^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/command/build_ext.py", line 263, in build_extension
_build_ext.build_extension(self, ext)
~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/command/build_ext.py", line 557, in build_extension
objects = self.compiler.compile(
sources,
...<5 lines>...
depends=ext.depends,
)
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/ccompiler.py", line 606, in compile
self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/unixccompiler.py", line 202, in _compile
raise CompileError(msg)
distutils.errors.CompileError: command 'clang' failed: No such file or directory
/home/clemens/.cache/uv/builds-v0/.tmpIpFClq/lib/python3.13/site-packages/setuptools/_distutils/dist.py:973: _DebuggingTips: Problem in editable installation.
!!
********************************************************************************
An error happened while installing `sleepecg` in editable mode.
The following steps are recommended to help debug this problem:
- Try to install the project normally, without using the editable mode.
Does the error still persist?
(If it does, try fixing the problem before attempting the editable mode).
- If you are using binary extensions, make sure you have all OS-level
dependencies installed (e.g. compilers, toolchains, binary libraries, ...).
- Try the latest version of setuptools (maybe the error was already fixed).
- If you (or your project dependencies) are using any setuptools extension
or customization, make sure they support the editable mode.
After following the steps above, if the problem still persists and
you think this is related to how setuptools handles editable installations,
please submit a reproducible example
(see https://stackoverflow.com/help/minimal-reproducible-example) to:
https://github.com/pypa/setuptools/issues
See https://setuptools.pypa.io/en/latest/userguide/development_mode.html for details.
********************************************************************************
!!
cmd_obj.run()
error: command 'clang' failed: No such file or directory
It's not required -- I believe you can override with export CC=gcc or similar when running a uv command.
Great, thanks! Yes, the CC env variable overwrites the behavior. However, I don't know if it is desired that uv pip behaves like pip in this case; if so, it seems like either pip has a different default (e.g. gcc), or it tries multiple options (e.g. clang, then gcc). I would think that this is a useful behavior, but it is certainly also OK to just set the env varbiable.
The Python binaries uv installs were built using clang so they have CC=clang in their sysconfig. Thus, when using a uv-managed python when clang isn't available, pip also fails to build.
❯ uvx -p3.13 pip wheel git+https://github.com/zeevro/cgeo.git
Installed 1 package in 19ms
Collecting git+https://github.com/zeevro/cgeo.git
Cloning https://github.com/zeevro/cgeo.git to /tmp/pip-req-build-n161azpl
Running command git clone --filter=blob:none --quiet https://github.com/zeevro/cgeo.git /tmp/pip-req-build-n161azpl
Resolved https://github.com/zeevro/cgeo.git to commit b5e0d92749982f69e943cb8774afdc148b44e877
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: cgeo
Building wheel for cgeo (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for cgeo (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [18 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.linux-x86_64-cpython-313/cgeo
copying cgeo/__init__.py -> build/lib.linux-x86_64-cpython-313/cgeo
copying cgeo/_cgeo.py -> build/lib.linux-x86_64-cpython-313/cgeo
running egg_info
writing cgeo.egg-info/PKG-INFO
writing dependency_links to cgeo.egg-info/dependency_links.txt
writing top-level names to cgeo.egg-info/top_level.txt
reading manifest file 'cgeo.egg-info/SOURCES.txt'
writing manifest file 'cgeo.egg-info/SOURCES.txt'
copying cgeo/py.typed -> build/lib.linux-x86_64-cpython-313/cgeo
running build_ext
building 'cgeo._cgeo' extension
creating build/temp.linux-x86_64-cpython-313
clang -pthread -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -g -O3 -Wall -fPIC -fPIC -I/home/zeev/.cache/uv/archive-v0/t0on_6b0HIdss7m2zNvDi/include -I/home/zeev/.local/share/uv/python/cpython-3.13.0rc2-linux-x86_64-gnu/include/python3.13 -c cgeo.c -o build/temp.linux-x86_64-cpython-313/cgeo.o
error: command 'clang' failed: No such file or directory
[end of output]
❯ CC=gcc uvx -p3.13 pip wheel git+https://github.com/zeevro/cgeo.git
Collecting git+https://github.com/zeevro/cgeo.git
Cloning https://github.com/zeevro/cgeo.git to /tmp/pip-req-build-fq2ez4y5
Running command git clone --filter=blob:none --quiet https://github.com/zeevro/cgeo.git /tmp/pip-req-build-fq2ez4y5
Resolved https://github.com/zeevro/cgeo.git to commit b5e0d92749982f69e943cb8774afdc148b44e877
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Building wheels for collected packages: cgeo
Building wheel for cgeo (pyproject.toml) ... done
Created wheel for cgeo: filename=cgeo-1.0-cp313-cp313-linux_x86_64.whl size=18227 sha256=01203422a85c84b1e8ac97d112ad88be319ff856b12106580a9f3e7913d22239
Stored in directory: /tmp/pip-ephem-wheel-cache-tynhz2z3/wheels/d8/4c/20/6dd73fbea92ad7bd766039212a97b3388b0aa903d3f2212fd3
Successfully built cgeo
Right, it was just a little surprising that on my Linux system, which uses gcc by default (and I assume this is true for most Linux distributions), pip installed via the package manager uses (was built with) gcc by default, so it worked. I'm not saying there's anything wrong with using clang by default, but it should probably be documented somewhere (my apologies if it already is and I missed it).
Can someone also tell me what the equivalent is for using g++ instead of clang++? I'm trying to install gdal, and I get a message saying clang++ not found. I wasn't sure what the equivalent CC was for clang++. I made a symlink from '/usr/bin/g++' to /usr/local/bin/clang++' and it worked ok, but would be better if I could do something like:
CC=gcc CPP=g++ uv pip install gdal==$(gdal-config --version)
Going to track improving this in https://github.com/astral-sh/uv/issues/8429
Hi, apologies for reviving this, but the suggested fixes are not working for me.
In a similar setup to @cbrnr I am trying to install a package with C extensions: https://github.com/21cmfast/21cmFAST/.
During the install the package makes a call to sysconfig.get_config_var("CC"), which in my case returns cc -pthread.
What I tried:
- I tried overwriting
CCandCXXenv vars for bot commands:CC=gcc CXX=g++ uv add 21cmfastCC=gcc CXX=g++ uv pip install 21cmfast
- I switched to bash end explicitly exported the variable
export CC=gcc - I removed and clean installed the virtual env:
uv sync --no-cache --build --no-binary.
Still during installation sysconfig.get_config_var("CC") returns cc -pthread.
I believe get_config_var("CC") is always going to return the value CPython was built with. It sounds like 21cmFAST should read the CC variable first and prefer that?
Interesting point, so using sysconfig.get_config_var("CC") is the wrong approach in that case? I will raise an issue on their side then. Thank you for your help!
I think so! At the very least, it doesn't allow overriding it to your preferred compiler. I'm not sure what downstream best practice is.