Installing error in the compilation of "build_FortFlex.sh"

[envhyf]

Following the instruction, I have installed all the packages and met error when compiling the setup.py file.
I found out that the issue was in the process of the compilation of build_FortFlex.sh
The error shows like this:

ld: symbol(s) not found for architecture i386
collect2: ld returned 1 exit status
error: Command "/usr/local/bin/gfortran -Wall -g -L/usr/local/NETCDF/lib  /var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpmru57eln/var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpmru57eln/src.macosx-10.9-x86_64-3.5/FortFlexmodule.o /var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpmru57eln/var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpmru57eln/src.macosx-10.9-x86_64-3.5/fortranobject.o /var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpmru57eln/FortFlex.o -L/usr/local/lib/gcc/i686-apple-darwin8/4.2.3 -L/Users/HYF/anaconda/envs/py35/lib -lgfortran -o ./FortFlex.cpython-35m-darwin.so" failed with exit status 1

I would like to have an advice how to proceed.

PS: essential information about my compilation environment:

Darwin I.local 14.3.0 Darwin Kernel Version 14.3.0: Mon Mar 23 11:59:05 PDT 2015; root:xnu-2782.20.48~5/RELEASE_X86_64 x86_64 i386 MacBookAir7,2 Darwin        
Python 3.5, gcc 4.9.4

[FrancescAlted]

That's weird. I have just tried the master branch on my OSX box and it correctly compiles the extension. My context:

$ python -c "import reflexible; reflexible.print_versions()"
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
reflexible version: 0.5.0
NumPy version:     1.14.2
Python version:    3.6.5 |Anaconda, Inc.| (default, Apr 26 2018, 08:42:37) 
[GCC 4.2.1 Compatible Clang 4.0.1 (tags/RELEASE_401/final)]
Platform:          darwin-x86_64
Byte-ordering:     little
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

I suppose this is unrelated, but which version of gfortran do you have? Mine is 8.1.0:

$ gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/8.1.0/libexec/gcc/x86_64-apple-darwin17.5.0/8.1.0/lto-wrapper
Target: x86_64-apple-darwin17.5.0
Configured with: ../configure --build=x86_64-apple-darwin17.5.0 --prefix=/usr/local/Cellar/gcc/8.1.0 --libdir=/usr/local/Cellar/gcc/8.1.0/lib/gcc/8 --enable-languages=c,c++,objc,obj-c++,fortran --program-suffix=-8 --with-gmp=/usr/local/opt/gmp --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc --with-isl=/usr/local/opt/isl --with-system-zlib --enable-checking=release --with-pkgversion='Homebrew GCC 8.1.0' --with-bugurl=https://github.com/Homebrew/homebrew-core/issues --disable-nls
Thread model: posix
gcc version 8.1.0 (Homebrew GCC 8.1.0) 

[envhyf]

@FrancescAlted, thanks for your reply. I have found out some issues related with this problem.

1. I read that reflexible was built on Python3 environment, while the default f2py environment in my computer was based on Python 2.7.

2. The computer was in X86_64 architecture, while the compilation processe seems to be with i386 architecture. Thus, I change the archflag to x86_64 by adding "--arch=X86_64".

The revised ./build_FortFlex.sh shows as follows:

#!/bin/bash
#"/Users/HYF/anaconda/envs/py35/bin/f2py " is the path to call f2py function in python3
rm -f FortFlex.pyf
/Users/HYF/anaconda/envs/py35/bin/f2py -m FortFlex -h FortFlex.pyf FortFlex.f
/Users/HYF/anaconda/envs/py35/bin/f2py  -c --fcompiler=gfortran --arch=X86_64 FortFlex.pyf FortFlex.f
mv *.so ..

By this way, the error "ld: symbol(s) not found for architecture i386" disappers.
However, a new error just appears.

Warning: Unused variable ylat0 declared at (1)
FortFlex.f: In function ‘sumgrid’:
FortFlex.f:256: warning: ‘co’ is used uninitialized in this function
FortFlex.f:256: note: ‘co’ was declared here
FortFlex.f: In function ‘readheader’:
FortFlex.f:529: warning: ‘ltopo’ is used uninitialized in this function
FortFlex.f: In function ‘readgrid_v6’:
FortFlex.f:382: warning: ‘smallnum’ is used uninitialized in this function
FortFlex.f:418: warning: ‘lspec2’ is used uninitialized in this function
FortFlex.f:384: warning: ‘n’ may be used uninitialized in this function
FortFlex.f: In function ‘readgrid’:
FortFlex.f:112: warning: ‘n’ may be used uninitialized in this function
error: Command "gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops X86_64 -I/var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpdcd8m5an/src.macosx-10.9-x86_64-3.5 -I/Users/HYF/anaconda/envs/py35/lib/python3.5/site-packages/numpy/core/include -I/Users/HYF/anaconda/envs/py35/include/python3.5m -c -c FortFlex.f -o /var/folders/wg/d26_jxbj2p9gp7nkl90q0fbm0000gn/T/tmpdcd8m5an/FortFlex.o" failed with exit status 1

I don't know how to fix it. Is it related with my gcc version (4.9.2) which is lower than yours (8.1.0) ?

[FrancescAlted]

That's a good question; I only see warnings in your output, so this should not be a problem Just in case, you might want to try an updated gfortran and try. I installed my version via $ brew install gcc.