Cannot install fitsio with pip on MacOS Monterrey #413
Description
Hi, I'm trying to install the most recent version of fitsio using pip, but I'm getting errors related to compiling C fitsio code. Could I get some insights into how to resolve this?
Here are some specifications of my machine:
- MacOS Monterey 12.7.6
- Apple M1 Max
- XCode 14.2
- Python 3.10.14
Here is the error message I'm getting:
Collecting fitsio (from -r requirements.txt (line 65))
Using cached fitsio-1.2.4.tar.gz (4.5 MB)
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: async-timeout<5.0,>=4.0 in /Users/[user]/.pyenv/versions/3.10.14/lib/python3.10/site-packages (from aiohttp==3.9.0->-r requirements.txt (line 2)) (4.0.3)
Requirement already satisfied: lxml>=4.6.0 in /Users/[user]/.pyenv/versions/3.10.14/lib/python3.10/site-packages (from zeep==4.2.1->-r requirements.txt (line 62)) (5.3.0)
Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /Users/[user]/.pyenv/versions/3.10.14/lib/python3.10/site-packages (from numba->-r requirements.txt (line 64)) (0.43.0)
Building wheels for collected packages: fitsio
Building wheel for fitsio (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for fitsio (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [169 lines of output]
running bdist_wheel
running build
running build_py
creating build/lib.macosx-12.2-arm64-cpython-310/fitsio
copying fitsio/header.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio
copying fitsio/util.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio
copying fitsio/fits_exceptions.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio
copying fitsio/fitslib.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio
copying fitsio/__init__.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio
creating build/lib.macosx-12.2-arm64-cpython-310/fitsio/hdu
copying fitsio/hdu/__init__.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/hdu
copying fitsio/hdu/table.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/hdu
copying fitsio/hdu/image.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/hdu
copying fitsio/hdu/base.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/hdu
creating build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_warnings.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_image_compression.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_table.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_empty_slice.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/checks.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_image.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/__init__.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_lib.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_header.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/makedata.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
copying fitsio/tests/test_header_junk.py -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/tests
running egg_info
writing fitsio.egg-info/PKG-INFO
writing dependency_links to fitsio.egg-info/dependency_links.txt
writing requirements to fitsio.egg-info/requires.txt
writing top-level names to fitsio.egg-info/top_level.txt
reading manifest file 'fitsio.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.txt'
writing manifest file 'fitsio.egg-info/SOURCES.txt'
/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/command/build_py.py:218: _Warning: Package 'fitsio.test_images' is absent from the `packages` configuration.
!!
********************************************************************************
############################
# Package would be ignored #
############################
Python recognizes 'fitsio.test_images' as an importable package[^1],
but it is absent from setuptools' `packages` configuration.
This leads to an ambiguous overall configuration. If you want to distribute this
package, please make sure that 'fitsio.test_images' is explicitly added
to the `packages` configuration field.
Alternatively, you can also rely on setuptools' discovery methods
(for example by using `find_namespace_packages(...)`/`find_namespace:`
instead of `find_packages(...)`/`find:`).
You can read more about "package discovery" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/package_discovery.html
If you don't want 'fitsio.test_images' to be distributed and are
already explicitly excluding 'fitsio.test_images' via
`find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`,
you can try to use `exclude_package_data`, or `include-package-data=False` in
combination with a more fine grained `package-data` configuration.
You can read more about "package data files" on setuptools documentation page:
- https://setuptools.pypa.io/en/latest/userguide/datafiles.html
[^1]: For Python, any directory (with suitable naming) can be imported,
even if it does not contain any `.py` files.
On the other hand, currently there is no concept of package data
directory, all directories are treated like packages.
********************************************************************************
!!
check.warn(importable)
copying fitsio/fitsio_pywrap.c -> build/lib.macosx-12.2-arm64-cpython-310/fitsio
creating build/lib.macosx-12.2-arm64-cpython-310/fitsio/test_images
copying fitsio/test_images/test_gzip_compressed_image.fits.fz -> build/lib.macosx-12.2-arm64-cpython-310/fitsio/test_images
running build_ext
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/configure
Hunk #3 succeeded at 3787 (offset 1162 lines).
Hunk #4 succeeded at 3816 with fuzz 1 (offset 1162 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/configure
Hunk #3 succeeded at 3787 (offset 1162 lines).
Hunk #4 succeeded at 3816 with fuzz 1 (offset 1162 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/fitsio.h
Hunk #1 succeeded at 809 (offset -1 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/fitsio.h
Hunk #1 succeeded at 809 (offset -1 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/fitsio2.h
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/fitsio2.h
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/putcols.c
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/putcols.c
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/fitscore.c
Hunk #1 succeeded at 197 (offset 3 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/fitscore.c
Hunk #1 succeeded at 197 (offset 3 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/[configure.in](http://configure.in/)
Hunk #1 succeeded at 129 (offset 76 lines).
Hunk #2 succeeded at 153 (offset 76 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/[configure.in](http://configure.in/)
Hunk #1 succeeded at 129 (offset 76 lines).
Hunk #2 succeeded at 153 (offset 76 lines).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/Makefile.in
Hunk #1 succeeded at 70 (offset 1 line).
patching file build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617/Makefile.in
Hunk #1 succeeded at 70 (offset 1 line).
checking build system type... aarch64-apple-darwin21.6.0
checking host system type... aarch64-apple-darwin21.6.0
checking target system type... aarch64-apple-darwin21.6.0
checking for clang... clang
Gabba Hey!: EXT=darwin and CC=clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-install-un00d5qq/fitsio_d78e5d1f2dc04db79bd6808ac06d91d4/build/temp.macosx-12.2-arm64-cpython-310/cfitsio-4.4.1-20240617':
configure: error: C compiler cannot create executables
See `config.log' for more details
Traceback (most recent call last):
File "/Users/[user]/.pyenv/versions/3.10.14/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/Users/[user]/.pyenv/versions/3.10.14/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/Users/[user]/.pyenv/versions/3.10.14/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 421, in build_wheel
return self._build_with_temp_dir(
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 403, in _build_with_temp_dir
self.run_setup()
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 503, in run_setup
super().run_setup(setup_script=setup_script)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 318, in run_setup
exec(code, locals())
File "<string>", line 319, in <module>
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 117, in setup
return distutils.core.setup(**attrs)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 183, in setup
return run_commands(dist)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 199, in run_commands
dist.run_commands()
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 954, in run_commands
self.run_command(cmd)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 950, in run_command
super().run_command(command)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/command/bdist_wheel.py", line 398, in run
self.run_command("build")
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 950, in run_command
super().run_command(command)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 316, in run_command
self.distribution.run_command(command)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/dist.py", line 950, in run_command
super().run_command(command)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 973, in run_command
cmd_obj.run()
File "<string>", line 106, in run
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 98, in run
_build_ext.run(self)
File "/private/var/folders/yv/whcx9ccx5cx0ln0dbq_9lz6m000mqx/T/pip-build-env-dmog1cg2/overlay/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 359, in run
self.build_extensions()
File "<string>", line 130, in build_extensions
File "<string>", line 272, in configure_cfitsio
ValueError: could not configure cfitsio 4.4.1-20240617
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for fitsio
Failed to build fitsio
ERROR: ERROR: Failed to build installable wheels for some pyproject.toml based projects (fitsio)
Many thanks in advance for your help!