Error appears during pyradex installation #39
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fsalvest
changed the title
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Seems to be caused by an issue like this one: |
Dear Adam, |
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Could you please post the full error? There should be much more to the message than what you showed. |
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The following are the very last part of the messages printed on the terminal. I scrolled over the more than 700 lines, but no error messages are reported. adding '/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/fortranobject.c' to sources. creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var outfile = [] |
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I get the same traceback and error if I have the wrong SDK root specified (SDK = Software Development Kit, by mac). Try setting the variable with this command: export SDKROOT=$(xcrun -sdk macosx --show-sdk-path)and then re-try installing. |
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Neither this last suggestion worked, I get the same error. I also tried to install the code in a new conda environment, but it was an unsuccessful try. |
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I'm out of ideas of things to change, then. You could try running f2py yourself. ...there are some more arguments I have to look up, but you could reconstruct them from the install script |
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@fsalvest the problem appears to be with numpy 1.24. Try downgrading to 1.23. |
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You might need to use this command: f2py -c -m radex --f77flags=-fno-automatic --fcompiler=gfortran -I/Users/adam/repos/pyradex/Radex/src -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib *.fin the |
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Your solution works! I finally got this message: "Installation has completed. Make sure to set your RADEX_DATAPATH variable!".
I run this command in "Radex/src", but in a new conda environment, with python 3.10.9 and numpy 1.23.5. Thank you very much for your help! |
After running this command, some warnings occur. But what should I do then? |
Sorry I quote the wrong command line above, I meant this command. |
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if you're just getting warnings, that means everything is OK - there are supposed to be tons of warnings. If you get an error, otoh, that means something has gone wrong. If you get an error, please report it. |
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Oh, I meant I had run the command: And only warnings, no errors. So the next step, there seems to be a complied file "radex.cpython-39-darwin.so" in Radex/src/. I should move it to the pyradex/radex? |
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Good, that means it worked! Did running But yes, that's where it should go. |
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Yes. After "mv Radex/src/*so pyradex/radex/", I rerun the "python setup.py install_radex", still the same error as follows /Users/maple/opt/anaconda3/lib/python3.9/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires' Done running f2py in /Users/maple/pyradex/Radex/src. r2=1 Traceback (most recent call last): cd Radex/src/ |
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It seems there is something wrong with f2py.compile in the command line r2 = f2py.compile(source="merged_source.f", modulename='radex', |
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Agreed, this is where the problem happens. I haven't been able to figure out why, though. There is a difference between the behavior of |
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I'm keeping this open as I still think there should be a way to fix r2 = f2py.compile(source="merged_source.f", modulename='radex',
verbose=True,
# full_output=False,
extra_args=extra_args,)but I haven't found it yet. |
Hi to everybody,
I failed several times in installing pyradex. I have a macbook pro with
Python 3.7.13
numpy 1.21.5
astropy 4.3.1
GNU Fortran (GCC) 11.2.0
After having installed astroquery and specutils, I cloned pyradex from the repository.
Then I run "python setup.py install_radex install_myradex install", but the installation is interrupted by this message:
What can I do? Thank you for your help!
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