Closed isabelmontoyaa closed 2 months ago
This is a really unhelpful error message from fortran, unfortunately! It doesn't give any clues about what's happening.
You are using a different version of python & fortran than others. I have a few suggestions for how you might search for a fix/workaround, but no guarantee this will work:
$ gfortran -I/Users/adam/repos/pyradex/Radex/src -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib -fno-automatic main.f
gfortran: warning: couldn’t understand kern.osversion ‘21.6.0
ld: warning: building for macOS 10.4 is deprecated
ld: library not found for -lgcc_s.10.4
collect2: error: ld returned 1 exit status
There may be missing libraries or flags you need to get pyradex to install, but we'll have to dig to figure out what.
Hi,
So I tried compiling gfortran alone, and this is what I get:
$ gfortran -I/Users/isabel/Documents/PhD_Oslo/personalPC/pyradex/Radex/src -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib main.f
Undefined symbols for architecture x86_64:
"_backrad_", referenced from:
_MAIN__ in ccsWQYpM.o
"_getinputs_", referenced from:
_MAIN__ in ccsWQYpM.o
"_matrix_", referenced from:
_MAIN__ in ccsWQYpM.o
"_output_", referenced from:
_MAIN__ in ccsWQYpM.o
"_readdata_", referenced from:
_MAIN__ in ccsWQYpM.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
What architecture is your system? Are you on an M1 or M2, or an older mac?
I am on an older Mac (2019), intel core i7
OK, weird, those are better-behaved than the new ARM ones. I'm not sure what to do about this. My best guess is that you have some incomplete libraries, but I don't know why.
...maybe try 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 gfortran -I/Users/isabel/Documents/PhD_Oslo/personalPC/pyradex/Radex/src -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib main.f
i.e., set all the flags before compiling, and see if that works?
Otherwise, you should try a conda installation
I tried that and still no luck.
$ 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' gfortran -I/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib main.f
Undefined symbols for architecture x86_64:
"_backrad_", referenced from:
_MAIN__ in ccZGTqx2.o
"_getinputs_", referenced from:
_MAIN__ in ccZGTqx2.o
"_matrix_", referenced from:
_MAIN__ in ccZGTqx2.o
"_output_", referenced from:
_MAIN__ in ccZGTqx2.o
"_readdata_", referenced from:
_MAIN__ in ccZGTqx2.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
Do you mean a conda installation of gfortran?
Maybe. I think on mac, conda defaults to using the built-in compilers. But it might install additional libraries?
Okay, after losing (what felt like) years of my life, the issue was apparently a non-compatible version of the linker (ld).
When checking which ld
it was using, it returned:
$ which -a ld
/opt/anaconda3/bin/ld
/opt/local/bin/ld
/usr/bin/ld
And after changing my $PATH variable to set /opt/local/bin/ld
as the first one, it worked.
I'm not sure why this happens, maybe it's a problem of the Anaconda version.
Wow, good work finding that - and I sympathize, I have spent similar ages debugging this sort of junk. I'm glad you solved it!
I'm closing this as solved, but thanks again @isabelmontoyaa for tracking down the issue... "Okay, after losing (what felt like) years of my life" is every time I do anything with f2py. (but it's still better than running radex on the command line)
Hello,
I have been trying to install pyradex with no success. I have a MacBook Pro, macOS Ventura 13.3.1
$ python -c "import sys, astropy, numpy; print(sys.version); print(numpy.version,astropy.version)" 3.10.11 (main, Apr 20 2023, 13:59:00) [Clang 14.0.6 ] 1.22.3 5.1
$ gfortran --version GNU Fortran (MacPorts gcc12 12.2.0_2+stdlib_flag) 12.2.0
By reading Issues #39 and #40, I have tried the following (with no success):
Inside the folder Radex/src I ran:
f2py -c -m radex --f77flags=-fno-automatic --fcompiler=gfortran -I/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src -L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib *.f
cd ../.. and then ran:
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_radex
And here is the prompt:
/opt/anaconda3/envs/py310/lib/python3.10/site-packages/setuptools/dist.py:529: UserWarning: Normalizing '0.4.2dev' to '0.4.2.dev0' warnings.warn(tmpl.format(*locals())) Downloading RADEX Download succeeded, or at least didn't obviously fail. Extracting RADEX source from file /Users/isabelmontoyaarroyave/.astropy/cache/download/url/df9a6b344f9b6851d8c799789754b74e/contents Reading fortran codes... Reading file 'main.f' (format:fix,strict) Reading file 'radex.inc' (format:fix) Line #25 in main.f:" integer niter ! iteration counter" updatevars: could not crack entity declaration "niter!". Ignoring. Line #26 in main.f:" integer imore ! are we running again?" updatevars: could not crack entity declaration "imore!". Ignoring. Line #26 in main.f:" integer imore ! are we running again?" updatevars: could not crack entity declaration "again?". Ignoring. Line #29 in main.f:" logical conv ! are we converged?" updatevars: could not crack entity declaration "conv!". Ignoring. Line #29 in main.f:" logical conv ! are we converged?" updatevars: attempt to change the type of "are" ("integer") to "logical". Ignoring. Line #29 in main.f:" logical conv ! are we converged?" updatevars: attempt to change the type of "we" ("integer") to "logical". Ignoring. Line #29 in main.f:" logical conv ! are we converged?" updatevars: could not crack entity declaration "converged?". Ignoring. Reading file 'background.f' (format:fix,strict) Reading file 'radex.inc' (format:fix) Reading file 'radex.inc' (format:fix) Reading file 'slatec.f' (format:fix,strict) Reading file 'matrix.f' (format:fix,strict) Reading file 'radex.inc' (format:fix) Line #25 in matrix.f:" integer niter ! iteration counter" updatevars: could not crack entity declaration "niter!". Ignoring. Line #26 in matrix.f:" integer ilev,jlev,klev ! to loop over energy levels" updatevars: could not crack entity declaration "klev!". Ignoring. Line #27 in matrix.f:" integer nplus ! to solve statistical equilibrium" updatevars: could not crack entity declaration "nplus!". Ignoring. Line #28 in matrix.f:" integer iline ! to loop over lines" updatevars: could not crack entity declaration "iline!". Ignoring. Line #29 in matrix.f:" integer m,n ! line upper/lower levels" updatevars: could not crack entity declaration "n!". Ignoring. Line #29 in matrix.f:" integer m,n ! line upper/lower levels" updatevars: could not crack entity declaration "upper/lower". Ignoring. Line #30 in matrix.f:" integer nthick ! counts optically thick lines" updatevars: could not crack entity declaration "nthick!". Ignoring. Line #31 in matrix.f:" integer nfat ! counts highly optically thick lines" updatevars: could not crack entity declaration "nfat!". Ignoring. Line #32 in matrix.f:" integer nreduce ! size of reduced rate matrix" updatevars: could not crack entity declaration "nreduce!". Ignoring. rmbadname1: Replacing "size" with "size_bn". Line #34 in matrix.f:" integer indx,dsign ! needed for NumRep equation solver" updatevars: could not crack entity declaration "dsign!". Ignoring. rmbadname1: Replacing "for" with "for_bn". Line #35 in matrix.f:" real8 rhs(maxlev) ! RHS of rate equation" updatevars: could not crack entity declaration "rhs(maxlev)!". Ignoring. Line #35 in matrix.f:" real8 rhs(maxlev) ! RHS of rate equation" updatevars: attempt to change the type of "of" ("integer") to "real". Ignoring. Line #35 in matrix.f:" real8 rhs(maxlev) ! RHS of rate equation" updatevars: attempt to change the type of "rate" ("integer") to "real". Ignoring. Line #35 in matrix.f:" real8 rhs(maxlev) ! RHS of rate equation" updatevars: attempt to change the type of "equation" ("integer") to "real". Ignoring. Line #37 in matrix.f:" real8 yrate(maxlev,maxlev) ! rate matrix" updatevars: could not crack entity declaration "yrate(maxlev,maxlev)!". Ignoring. Line #37 in matrix.f:" real8 yrate(maxlev,maxlev) ! rate matrix" updatevars: attempt to change the type of "rate" ("integer") to "real". Ignoring. Line #37 in matrix.f:" real8 yrate(maxlev,maxlev) ! rate matrix" updatevars: attempt to change the type of "matrix" ("integer") to "real". Ignoring. Line #38 in matrix.f:" real8 etr,exr ! to calculate radiative rates" updatevars: could not crack entity declaration "exr!". Ignoring. Line #38 in matrix.f:" real8 etr,exr ! to calculate radiative rates" updatevars: attempt to change the type of "to" ("integer") to "real". Ignoring. Line #39 in matrix.f:" real8 xt ! frequency cubed" updatevars: could not crack entity declaration "xt!". Ignoring. Line #40 in matrix.f:" real8 hnu ! photon energy" updatevars: could not crack entity declaration "hnu!". Ignoring. Line #40 in matrix.f:" real8 hnu ! photon energy" updatevars: attempt to change the type of "energy" ("integer") to "real". Ignoring. Line #41 in matrix.f:" real8 bnutex ! line source function" updatevars: could not crack entity declaration "bnutex!". Ignoring. Line #41 in matrix.f:" real8 bnutex ! line source function" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Line #42 in matrix.f:" real8 cddv ! N(mol) / delta V" updatevars: could not crack entity declaration "cddv!". Ignoring. Line #42 in matrix.f:" real8 cddv ! N(mol) / delta V" updatevars: attempt to change the type of "n" ("integer") to "real". Ignoring. Line #42 in matrix.f:" real8 cddv ! N(mol) / delta V" updatevars: could not crack entity declaration "n(mol)/delta". Ignoring. Line #43 in matrix.f:" real8 beta,escprob ! escape probability" updatevars: could not crack entity declaration "escprob!". Ignoring. Line #45 in matrix.f:" real8 bnu ! Planck function" updatevars: could not crack entity declaration "bnu!". Ignoring. Line #46 in matrix.f:" real8 uarray(maxlev,maxlev) ! reduced rate matrix" updatevars: could not crack entity declaration "uarray(maxlev,maxlev)!". Ignoring. Line #46 in matrix.f:" real8 uarray(maxlev,maxlev) ! reduced rate matrix" updatevars: attempt to change the type of "reduced" ("integer") to "real". Ignoring. Line #46 in matrix.f:" real8 uarray(maxlev,maxlev) ! reduced rate matrix" updatevars: attempt to change the type of "rate" ("integer") to "real". Ignoring. Line #46 in matrix.f:" real8 uarray(maxlev,maxlev) ! reduced rate matrix" updatevars: attempt to change the type of "matrix" ("integer") to "real". Ignoring. Line #47 in matrix.f:" real8 redcrit ! reduction criterion" updatevars: could not crack entity declaration "redcrit!". Ignoring. Line #48 in matrix.f:" real8 sumx ! summed radiative rate" updatevars: could not crack entity declaration "sumx!". Ignoring. Line #48 in matrix.f:" real8 sumx ! summed radiative rate" updatevars: attempt to change the type of "rate" ("integer") to "real". Ignoring. Line #49 in matrix.f:" real8 total ! to normalize populations" updatevars: could not crack entity declaration "total!". Ignoring. Line #49 in matrix.f:" real8 total ! to normalize populations" updatevars: attempt to change the type of "to" ("integer") to "real". Ignoring. Line #51 in matrix.f:" real8 tsum,thistex ! to check convergence" updatevars: could not crack entity declaration "thistex!". Ignoring. Line #51 in matrix.f:" real8 tsum,thistex ! to check convergence" updatevars: attempt to change the type of "to" ("integer") to "real". Ignoring. Line #54 in matrix.f:" logical conv ! are we converged?" updatevars: could not crack entity declaration "conv!". Ignoring. Line #54 in matrix.f:" logical conv ! are we converged?" updatevars: could not crack entity declaration "converged?". Ignoring. Reading file 'radex.inc' (format:fix) Line #329 in matrix.f:" real8 taur !optical radius" updatevars: could not crack entity declaration "taur!optical". Ignoring. Reading file 'io.f' (format:fix,strict) Reading file 'radex.inc' (format:fix) Line #24 in io.f:" integer length ! subroutine to determine" updatevars: could not crack entity declaration "length!". Ignoring. Line #26 in io.f:" integer ipart ! loop over collision partners" updatevars: could not crack entity declaration "ipart!". Ignoring. Line #27 in io.f:" character10 partner ! name of collision partner" updatevars: no name pattern found for entity='!'. Skipping. Line #27 in io.f:" character10 partner ! name of collision partner" updatevars: attempt to change the type of "collision" ("integer") to "character". Ignoring. updatevars:collision: attempt to change empty charselector to {'': '10'}. Ignoring. Line #30 in io.f:" integer id ! ID code of collision partner" updatevars: could not crack entity declaration "id!". Ignoring. Line #30 in io.f:" integer id ! ID code of collision partner" updatevars: attempt to change the type of "of" ("character") to "integer". Ignoring. Line #30 in io.f:" integer id ! ID code of collision partner" updatevars: attempt to change the type of "partner" ("character") to "integer". Ignoring. Reading file 'radex.inc' (format:fix) Line #162 in io.f:" integer ipart ! to loop over collision partners" updatevars: could not crack entity declaration "ipart!". Ignoring. Reading file 'radex.inc' (format:fix) Line #201 in io.f:" integer iline ! to loop over lines" updatevars: could not crack entity declaration "iline!". Ignoring. Line #202 in io.f:" integer m,n ! upper & lower level of the line" updatevars: could not crack entity declaration "n!". Ignoring. Line #202 in io.f:" integer m,n ! upper & lower level of the line" updatevars: no name pattern found for entity='&'. Skipping. Line #204 in io.f:" integer niter ! final number of iterations" updatevars: could not crack entity declaration "niter!". Ignoring. Line #208 in io.f:" real8 xt ! frequency cubed" updatevars: could not crack entity declaration "xt!". Ignoring. Line #209 in io.f:" real8 hnu ! photon energy" updatevars: could not crack entity declaration "hnu!". Ignoring. Line #210 in io.f:" real8 bnutex ! line source function" updatevars: could not crack entity declaration "bnutex!". Ignoring. Line #210 in io.f:" real8 bnutex ! line source function" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Line #211 in io.f:" real8 ftau ! exp(-tau)" updatevars: could not crack entity declaration "ftau!". Ignoring. Line #212 in io.f:" real8 toti ! background intensity" updatevars: could not crack entity declaration "toti!". Ignoring. Line #213 in io.f:" real8 tbl ! black body temperature" updatevars: could not crack entity declaration "tbl!". Ignoring. Line #214 in io.f:" real8 wh ! Planck correction" updatevars: could not crack entity declaration "wh!". Ignoring. Line #215 in io.f:" real8 tback ! background temperature" updatevars: could not crack entity declaration "tback!". Ignoring. Line #216 in io.f:" real8 ta ! line antenna temperature" updatevars: could not crack entity declaration "ta!". Ignoring. Line #216 in io.f:" real8 ta ! line antenna temperature" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Line #217 in io.f:" real8 tr ! line radiation temperature" updatevars: could not crack entity declaration "tr!". Ignoring. Line #217 in io.f:" real8 tr ! line radiation temperature" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Line #218 in io.f:" real8 beta,escprob ! escape probability" updatevars: no name pattern found for entity='!'. Skipping. Line #220 in io.f:" real8 bnu ! Planck function" updatevars: could not crack entity declaration "bnu!". Ignoring. Line #221 in io.f:" real8 kkms ! line integrated intensity (K km/s)" updatevars: could not crack entity declaration "kkms!". Ignoring. Line #221 in io.f:" real8 kkms ! line integrated intensity (K km/s)" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Line #222 in io.f:" real8 ergs ! line flux (erg / s / cm^2)" updatevars: could not crack entity declaration "ergs!". Ignoring. Line #222 in io.f:" real8 ergs ! line flux (erg / s / cm^2)" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Line #227 in io.f:" real8 wavel ! line wavelength (micron)" updatevars: could not crack entity declaration "wavel!". Ignoring. Line #227 in io.f:" real8 wavel ! line wavelength (micron)" updatevars: attempt to change the type of "line" ("integer") to "real". Ignoring. Reading file 'readdata.f' (format:fix,strict) Reading file 'radex.inc' (format:fix) Line #25 in readdata.f:" integer ilev,jlev ! to loop over energy levels" updatevars: could not crack entity declaration "jlev!". Ignoring. Line #26 in readdata.f:" integer iline ! to loop over lines" updatevars: could not crack entity declaration "iline!". Ignoring. Line #27 in readdata.f:" integer ipart,jpart ! to loop over collision partners" updatevars: no name pattern found for entity='!'. Skipping. Line #28 in readdata.f:" integer itemp ! to loop over collision temperatures" updatevars: could not crack entity declaration "itemp!". Ignoring. Line #29 in readdata.f:" integer icoll ! to loop over collisional transitions" updatevars: could not crack entity declaration "icoll!". Ignoring. Line #31 in readdata.f:" integer dummy ! to skip part of the file" updatevars: could not crack entity declaration "dummy!". Ignoring. Line #34 in readdata.f:" integer id(maxpart) ! to identify collision partners" updatevars: could not crack entity declaration "id(maxpart)!". Ignoring. Line #40 in readdata.f:" real8 temp(maxtemp) ! collision temperatures" updatevars: could not crack entity declaration "temp(maxtemp)!". Ignoring. Line #40 in readdata.f:" real8 temp(maxtemp) ! collision temperatures" updatevars: attempt to change the type of "collision" ("integer") to "real". Ignoring. Line #40 in readdata.f:" real8 temp(maxtemp) ! collision temperatures" updatevars: attempt to change the type of "temperatures" ("integer") to "real". Ignoring. Line #43 in readdata.f:" character120 collref ! text about source of collisional data" updatevars: no name pattern found for entity='!'. Skipping. Line #43 in readdata.f:" character120 collref ! text about source of collisional data" updatevars: attempt to change the type of "of" ("integer") to "character". Ignoring. updatevars:of: attempt to change empty charselector to {'': '120'}. Ignoring. Line #43 in readdata.f:" character120 collref ! text about source of collisional data" updatevars: attempt to change the type of "collisional" ("integer") to "character". Ignoring. updatevars:collisional: attempt to change empty charselector to {'': '120'}. Ignoring. Post-processing... Block: radex analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: backrad analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: galbr analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: splcoeff Block: splintrp Block: ludcmp Block: lubksb Block: sgeir Block: r1mach Block: sasum Block: scopy Block: sdsdot Block: sgefa Block: isamax Block: saxpy Block: sscal Block: sgesl Block: sdot Block: xermsg Block: j4save Block: xercnt Block: xerhlt Block: xerprn Block: i1mach Block: xgetua Block: xersve analyzevars: character array "character8 libtab(10)" is considered as "character libtab(10,8)"; "intent(c)" is forced. analyzevars: character array "character8 subtab(10)" is considered as "character subtab(10,8)"; "intent(c)" is forced. analyzevars: character array "character20 mestab(10)" is considered as "character mestab(10,20)"; "intent(c)" is forced. Block: fdump Block: matrix analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: escprob analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: getinputs analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: defaults analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Block: length Block: output analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. /opt/anaconda3/envs/py310/lib/python3.10/site-packages/numpy/f2py/symbolic.py:1508: ExprWarning: fromstring: treating 'k km' as symbol (original=k km/s) ewarn( /opt/anaconda3/envs/py310/lib/python3.10/site-packages/numpy/f2py/symbolic.py:1508: ExprWarning: fromstring: treating 'cm^2' as symbol (original=erg/s/cm^2) ewarn( Block: readdata analyzevars: character array "character6 qnum(2999)" is considered as "character qnum(2999,6)"; "intent(c)" is forced. Post-processing (stage 2)... Saving signatures to file "./radex.pyf" Running f2py with fcompiler=gfortran, f77exec=, include_path=-I/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src, linker_path= extra args = --f77flags="-fno-automatic" --fcompiler=gfortran -I/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src Current directory = /Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src Unknown vendor: "gfortran" running build running config_cc INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src INFO: build_src INFO: building extension "radex" sources INFO: f2py options: [] INFO: f2py:> /var/folders/4v/z0sz8nfx5k98v5qvmvljj4fh0000gq/T/tmpeyj33w4e/src.macosx-10.9-x86_64-3.10/radexmodule.c creating /var/folders/4v/z0sz8nfx5k98v5qvmvljj4fh0000gq/T/tmpeyj33w4e/src.macosx-10.9-x86_64-3.10 Reading fortran codes... Reading file '/var/folders/4v/z0sz8nfx5k98v5qvmvljj4fh0000gq/T/tmpafbwyq4p.f' (format:fix,strict)
Done running f2py in /Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src. r2=1 Unknown vendor: "gfortran" running build running config_cc INFO: unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc INFO: unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src INFO: build_src INFO: building extension "radex" sources INFO: f2py options: [] INFO: f2py:> /var/folders/4v/z0sz8nfx5k98v5qvmvljj4fh0000gq/T/tmpgnaxhn36/src.macosx-10.9-x86_64-3.10/radexmodule.c creating /var/folders/4v/z0sz8nfx5k98v5qvmvljj4fh0000gq/T/tmpgnaxhn36/src.macosx-10.9-x86_64-3.10 Reading fortran codes... Reading file '/var/folders/4v/z0sz8nfx5k98v5qvmvljj4fh0000gq/T/tmpojz6n_sr.f' (format:fix,strict)
Traceback (most recent call last): File "/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/setup.py", line 120, in
setup(name='pyradex',
File "/opt/anaconda3/envs/py310/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
File "/opt/anaconda3/envs/py310/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/opt/anaconda3/envs/py310/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 969, in run_commands
self.run_command(cmd)
File "/opt/anaconda3/envs/py310/lib/python3.10/site-packages/setuptools/dist.py", line 1208, in run_command
super().run_command(command)
File "/opt/anaconda3/envs/py310/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
cmd_obj.run()
File "/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/setup.py", line 44, in run
install_radex.install_radex()
File "/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/install_radex.py", line 25, in install_radex
compile_radex()
File "/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/install_radex.py", line 192, in compile_radex
raise SystemError(f"f2py failed with error {r2}\n"
SystemError: f2py failed with error 1
Try running the command:
cd Radex/src/ f2py -c -m radex --f77flags="-fno-automatic" --fcompiler=gfortran -I/Users/isabelmontoyaarroyave/Documents/PhD_Oslo/PhD/Research_tools/radex_emcee-master/pyradex/Radex/src .f cd - mv Radex/src/so pyradex/radex/
See also Github issues 39 and 40
I would appreciate any help! Thanks!