Error appears during pyradex installation

[fsalvest]

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:

outfile = []
error: Did not find the correct .so file(s)! Compilation has failed.

What can I do? Thank you for your help!

[keflavich]

Seems to be caused by an issue like this one:
ponylang/ponyc#3684
Should now be fixed with this commit: e07704d

[fsalvest]

Seems to be caused by an issue like this one: ponylang/ponyc#3684 Should now be fixed with this commit: e07704d

Dear Adam,
thank you for your fast reply. I tried fixing install_radex.py as you suggested, but I get the same Error.

[keflavich]

Could you please post the full error? There should be much more to the message than what you showed.

[fsalvest]

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.
Many thanks for your time and help!

Wrote C/API module "radex" to file "/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/radexmodule.c"
Fortran 77 wrappers are saved to "/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/radex-f2pywrappers.f"

adding '/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/fortranobject.c' to sources.
adding '/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7' to include_dirs.
copying /Users/home/opt/anaconda3/envs/pyradex_demo/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.c -> /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7
copying /Users/home/opt/anaconda3/envs/pyradex_demo/lib/python3.7/site-packages/numpy/f2py/src/fortranobject.h -> /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7
adding '/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/radex-f2pywrappers.f' to sources.
build_src: building npy-pkg config files
running build_ext
customize UnixCCompiler
customize UnixCCompiler using build_ext
customize Gnu95FCompiler
Found executable /Users/home/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-gfortran
Found executable /Users/home/opt/anaconda3/envs/pyradex_demo/bin/x86_64-apple-darwin13.4.0-ld
Found executable /Users/home/opt/anaconda3/envs/pyradex_demo/bin/x86_64-apple-darwin13.4.0-ar
Found executable /Users/home/opt/anaconda3/envs/pyradex_demo/bin/x86_64-apple-darwin13.4.0-ranlib
customize Gnu95FCompiler using build_ext
building 'radex' extension
compiling C sources
C compiler: x86_64-apple-darwin13.4.0-clang -fno-strict-aliasing -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -pipe -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=/Users/home/opt/anaconda3/envs/pyradex_demo=/usr/local/src/conda-prefix -flto -Wl,-export_dynamic -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O3 -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/home/opt/anaconda3/include -D_FORTIFY_SOURCE=2 -isystem /Users/home/opt/anaconda3/include

creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var
creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var/folders
creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var/folders/m9
creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq
creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T
creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax
creating /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7
compile options: '-DNPY_DISABLE_OPTIMIZATION=1 -I/Users/home/RADEX/pyradex/Radex/src -I/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7 -I/Users/home/opt/anaconda3/envs/pyradex_demo/lib/python3.7/site-packages/numpy/core/include -I/Users/home/opt/anaconda3/envs/pyradex_demo/include/python3.7m -c'
x86_64-apple-darwin13.4.0-clang: /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/radexmodule.c
x86_64-apple-darwin13.4.0-clang: /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/fortranobject.c
compiling Fortran sources
Fortran f77 compiler: /Users/home/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-gfortran -fno-automatic -fPIC -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/home/opt/anaconda3/include -O3 -funroll-loops
Fortran f90 compiler: /Users/home/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-gfortran -Wall -g -fno-second-underscore -fPIC -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/home/opt/anaconda3/include -O3 -funroll-loops
Fortran fix compiler: /Users/home/opt/anaconda3/bin/x86_64-apple-darwin13.4.0-gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -fPIC -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem /Users/home/opt/anaconda3/include -O3 -funroll-loops
compile options: '-I/Users/home/RADEX/pyradex/Radex/src -I/var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7 -I/Users/home/opt/anaconda3/envs/pyradex_demo/lib/python3.7/site-packages/numpy/core/include -I/Users/home/opt/anaconda3/envs/pyradex_demo/include/python3.7m -c'
x86_64-apple-darwin13.4.0-gfortran:f77: /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmpnoltqy9_.f
x86_64-apple-darwin13.4.0-gfortran:f77: /var/folders/m9/jbqkxbmd265_mvfzkjvw34dr0000gq/T/tmp49_gplax/src.macosx-10.9-x86_64-3.7/radex-f2pywrappers.f

outfile = []
error: Did not find the correct .so file(s)! Compilation has failed.

[keflavich]

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.

[fsalvest]

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.

[keflavich]

I'm out of ideas of things to change, then. You could try running f2py yourself.

cd radex/src
f2py -m radex *.f

...there are some more arguments I have to look up, but you could reconstruct them from the install script

[keflavich]

@fsalvest the problem appears to be with numpy 1.24. Try downgrading to 1.23.

[keflavich]

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 *.f

in the Radex/src directory. I haven't yet figured out what's going wrong with the f2py.compile command, but something is.

[fsalvest]

Your solution works! I finally got this message: "Installation has completed. Make sure to set your RADEX_DATAPATH variable!".

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 *.f

I run this command in "Radex/src", but in a new conda environment, with python 3.10.9 and numpy 1.23.5.
I don't know why the code could not run in my base environment (info at the top of the thread).

Thank you very much for your help!

[XFengwei]

f2py -m radex *.f

After running this command, some warnings occur. But what should I do then?

[XFengwei]

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 *.f

in the Radex/src directory. I haven't yet figured out what's going wrong with the f2py.compile command, but something is.

Sorry I quote the wrong command line above, I meant this command.