fitsio
fitsio copied to clipboard
esheldon
Cannot install fitsio with pip on MacOS Monterrey
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!
You need to inspect the config.log and figure out why the compiler won't build C code.
It says checking whether the C compiler works... no
Does your environment not have a C compiler available?
It should have a C compiler available. I'm able to use clang on MacOS to compile other C programs.
Yeah you need to look at the config.log file to see what the compiler error is.
Do you have any workarounds to access the config.log file? Stackoverflow tells me that the config.log file should be in the folder where it errored in, but when I tried to cd into the the /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 folder, it said the folder didn't exist.
