Compilation fails on myradex part

[aqingo3o]

Hiii,
After I install specutils and astroquery, I try to install pyradex on macOS and here is environment info:

$ python -c "import sys, astropy, numpy; print(sys.version); print(numpy.__version__,astropy.__version__)"
3.10.18 (main, Jun  5 2025, 08:13:51) [Clang 14.0.6 ]
1.26.2 6.1.2
$ gfortran --version
GNU Fortran (Homebrew GCC 15.2.0) 15.2.0
Copyright (C) 2025 Free Software Foundation, Inc.

• OS: macOS Sequoia 15.6.1
• arch: x86-64 (by Rosetta2)
• gfortran version: GNU Fortran (Homebrew GCC 15.2.0)
• Python: 3.10 (conda venv)
• numpy: 1.26.2
• astropy: 6.1.2

I run the installation command and successfully got share object for RADEX (radex.so).
(so I remove the install_radex in the command.)

$ python3 setup.py install_myradex install

And the Fortran build step fails with a type mismatch error:

opkda1.f:1309:72:

 1309 |      2   IPFLAG, F, JAC)
      |                                                                        1
Error: Type mismatch in argument 'iwk' at (1); passed REAL(8) to INTEGER(4)
opkda1.f:9825:72:

 9825 |      5   ADDA)
      |                                                                        1
Error: Type mismatch in argument 'iwk' at (1); passed REAL(8) to INTEGER(4)

The full message appear in terminal belike:

Found shared object files=['radex.so'] for RADEX.  (if that is a blank, it means radex didn't install successfully)
Found shared object files=[] for RADEX.  (if that is a blank, it means fjdu's myradex didn't install successfully)
/Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages/setuptools/dist.py:530: UserWarning: Normalizing '0.4.2dev' to '0.4.2.dev0'
  warnings.warn(tmpl.format(**locals()))
running install_myradex
rm ./*.mod ./*.o
rm: ./*.mod: No such file or directory
rm: ./*.o: No such file or directory
make: *** [clean] Error 1
gfortran -O3 -fPIC -c sub_global_variables.f90
gfortran -O3 -fPIC -c sub_trivials.f90
gfortran -O3 -fPIC -c nleq1.f
gfortran -O3 -fPIC -c linalg_nleq1.f
gfortran -O3 -fPIC -c statistic_equilibrium.f90
gfortran -O3 -fPIC -c my_radex.f90
gfortran -O3 -fPIC -c opkda1.f
opkda1.f:2804:72:

 2804 |   6     j = j-1
      |                                                                        1
Warning: Fortran 2018 deleted feature: DO termination statement which is not END DO or CONTINUE with label 6 at (1)
opkda1.f:1311:72:

 1311 |      4   JAC)
      |                                                                        1
Error: Type mismatch in argument 'iwk' at (1); passed REAL(8) to INTEGER(4)
opkda1.f:9827:72:

 9827 |      5   ADDA)
      |                                                                        1
Error: Type mismatch in argument 'iwk' at (1); passed REAL(8) to INTEGER(4)
make: *** [opkda1.o] Error 1
make: `sub_trivials.o' is up to date.
rm ./*.mod ./*.o
running install
/Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
running bdist_egg
running egg_info
writing pyradex.egg-info/PKG-INFO
writing dependency_links to pyradex.egg-info/dependency_links.txt
writing requirements to pyradex.egg-info/requires.txt
writing top-level names to pyradex.egg-info/top_level.txt
reading manifest file 'pyradex.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE.rst'
writing manifest file 'pyradex.egg-info/SOURCES.txt'
installing library code to build/bdist.macosx-10.15-x86_64/egg
running install_lib
running build_py
creating build/bdist.macosx-10.15-x86_64/egg
creating build/bdist.macosx-10.15-x86_64/egg/pyradex
creating build/bdist.macosx-10.15-x86_64/egg/pyradex/fjdu
copying build/lib/pyradex/fjdu/__init__.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/fjdu
copying build/lib/pyradex/fjdu/core.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/fjdu
copying build/lib/pyradex/version.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
creating build/bdist.macosx-10.15-x86_64/egg/pyradex/radex
copying build/lib/pyradex/radex/__init__.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/radex
copying build/lib/pyradex/radex/radex.so -> build/bdist.macosx-10.15-x86_64/egg/pyradex/radex
copying build/lib/pyradex/base_class.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
creating build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/test_fjdu.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/test_grid.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/__init__.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/test_synthspec.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/test_radex.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/test_radex_myradex_consistency.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/test_radex_install.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
copying build/lib/pyradex/tests/setup_package_data.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests
creating build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/data
copying build/lib/pyradex/tests/data/example.out -> build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/data
copying build/lib/pyradex/__init__.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
copying build/lib/pyradex/core.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
copying build/lib/pyradex/read_radex.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
copying build/lib/pyradex/utils.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
copying build/lib/pyradex/grid_wrapper.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
copying build/lib/pyradex/despotic_interface.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
copying build/lib/pyradex/synthspec.py -> build/bdist.macosx-10.15-x86_64/egg/pyradex
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/fjdu/__init__.py to __init__.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/fjdu/core.py to core.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/version.py to version.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/radex/__init__.py to __init__.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/base_class.py to base_class.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/test_fjdu.py to test_fjdu.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/test_grid.py to test_grid.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/__init__.py to __init__.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/test_synthspec.py to test_synthspec.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/test_radex.py to test_radex.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/test_radex_myradex_consistency.py to test_radex_myradex_consistency.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/test_radex_install.py to test_radex_install.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/tests/setup_package_data.py to setup_package_data.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/__init__.py to __init__.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/core.py to core.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/read_radex.py to read_radex.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/utils.py to utils.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/grid_wrapper.py to grid_wrapper.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/despotic_interface.py to despotic_interface.cpython-310.pyc
byte-compiling build/bdist.macosx-10.15-x86_64/egg/pyradex/synthspec.py to synthspec.cpython-310.pyc
creating build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying pyradex.egg-info/PKG-INFO -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying pyradex.egg-info/SOURCES.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying pyradex.egg-info/dependency_links.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying pyradex.egg-info/not-zip-safe -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying pyradex.egg-info/requires.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
copying pyradex.egg-info/top_level.txt -> build/bdist.macosx-10.15-x86_64/egg/EGG-INFO
writing build/bdist.macosx-10.15-x86_64/egg/EGG-INFO/native_libs.txt
creating 'dist/pyradex-0.4.2.dev0-py3.10.egg' and adding 'build/bdist.macosx-10.15-x86_64/egg' to it
removing 'build/bdist.macosx-10.15-x86_64/egg' (and everything under it)
Processing pyradex-0.4.2.dev0-py3.10.egg
removing '/Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages/pyradex-0.4.2.dev0-py3.10.egg' (and everything under it)
creating /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages/pyradex-0.4.2.dev0-py3.10.egg
Extracting pyradex-0.4.2.dev0-py3.10.egg to /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
pyradex 0.4.2.dev0 is already the active version in easy-install.pth

Installed /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages/pyradex-0.4.2.dev0-py3.10.egg
Processing dependencies for pyradex==0.4.2.dev0
Searching for requests==2.32.4
Best match: requests 2.32.4
Adding requests 2.32.4 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for astropy==6.1.2
Best match: astropy 6.1.2
Adding astropy 6.1.2 to easy-install.pth file
Installing fits2bitmap script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing fitscheck script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing fitsdiff script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing fitsheader script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing fitsinfo script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing samp_hub script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing showtable script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing volint script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin
Installing wcslint script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for certifi==2025.8.3
Best match: certifi 2025.8.3
Adding certifi 2025.8.3 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for urllib3==2.5.0
Best match: urllib3 2.5.0
Adding urllib3 2.5.0 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for idna==3.7
Best match: idna 3.7
Adding idna 3.7 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for charset-normalizer==3.3.2
Best match: charset-normalizer 3.3.2
Adding charset-normalizer 3.3.2 to easy-install.pth file
Installing normalizer script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for packaging==25.0
Best match: packaging 25.0
Adding packaging 25.0 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for PyYAML==6.0.2
Best match: PyYAML 6.0.2
Adding PyYAML 6.0.2 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for astropy-iers-data==0.2025.6.9.0.39.3
Best match: astropy-iers-data 0.2025.6.9.0.39.3
Adding astropy-iers-data 0.2025.6.9.0.39.3 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for pyerfa==2.0.1.5
Best match: pyerfa 2.0.1.5
Adding pyerfa 2.0.1.5 to easy-install.pth file

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Searching for numpy==1.26.2
Best match: numpy 1.26.2
Adding numpy 1.26.2 to easy-install.pth file
Installing f2py script to /Users/aqing/miniconda3_x86/envs/astro_py310/bin

Using /Users/aqing/miniconda3_x86/envs/astro_py310/lib/python3.10/site-packages
Finished processing dependencies for pyradex==0.4.2.dev0
Installation has completed.  Make sure to set your RADEX_DATAPATH variable!

I've try this command but nothing change :(

$ FFLAGS='-arch i686 -arch x86_64 -fPIC' CFLAGS='-fno-strict-aliasing -fno-common -dynamic -arch i386 -arch x86_64 -g -O2' LDFLAGS='-arch i686 -arch x86_64 -undefined dynamic_lookup -bundle' python setup.py install_myradex

Thanks everyone so much for maintaining and improving pyradex!

[keflavich]

Thanks for the detailed bug report. I'll investigate. It may be that the homebrew compiler requires some different flags than the conda compilers.

[aqingo3o]

Hiiiii,
thank you for the reply!
I’d like to provide an update on the compilation issue I previously reported.
I tried installing pyradex on Ubuntu20.04 in conda venv, and here is the environment information:

• gfortran: GNU Fortran 9.4.0 (Ubuntu 9.4.0-1ubuntu1~20.04.2)
• python==3.10
• astropy==6.1.2
• numpy==1.26.2

pyradex compiled successfully!
The previous error now appears only as a warning, without causing failure.
However, on macOS 15.6.1, the compilation error still persists.

I just wanted to share this update in case it helps narrow down the issue or confirm that it might be platform-specific?
I will continue working on the macOS side, Homebrew-installed compilers and the required compilation flags;)

[keflavich]

Thanks for the further investigation.

I updated the subpackage link to Fujun Du's myRadex, which might fix some of your errors. Try pulling that and reinstall?

[aqingo3o]

Thank you sooooo much for the update!
I ran into some (其實很多) arch-related issues when trying it on my local machine(MacOS, gfortran 15),
so it didn’t work right away.
I may need some more time to look into it properly, but I really appreciate your responsiveness and the update.

[keflavich]

alright, please post the errors here if you get any that look useful.