Build fails with Python 3.9.1 under MacOS 10.15

[mfkenney]

I attempted to build the package under MacOS (clang 12.0.0) and it failed with the error shown below. I suspect that the code generation scripts might need to be updated ...

src/_ufuncs.c:646:37: error: use of undeclared identifier 'gsw_o2sol_sp_pt'; did you mean 'data_o2sol_sp_pt'?
  static void *data_o2sol_sp_pt[] = {&gsw_o2sol_sp_pt};
                                      ^~~~~~~~~~~~~~~
                                      data_o2sol_sp_pt
  src/_ufuncs.c:646:14: note: 'data_o2sol_sp_pt' declared here
  static void *data_o2sol_sp_pt[] = {&gsw_o2sol_sp_pt};
               ^
  src/_ufuncs.c:660:40: error: use of undeclared identifier 'gsw_sp_salinometer'; did you mean 'data_sp_salinometer'?
  static void *data_sp_salinometer[] = {&gsw_sp_salinometer};
                                         ^~~~~~~~~~~~~~~~~~
                                         data_sp_salinometer
  src/_ufuncs.c:660:14: note: 'data_sp_salinometer' declared here
  static void *data_sp_salinometer[] = {&gsw_sp_salinometer};
               ^
  src/_ufuncs.c:733:31: error: use of undeclared identifier 'gsw_o2sol'
  static void *data_o2sol[] = {&gsw_o2sol};
                                ^
  In file included from src/_ufuncs.c:773:
  src/method_bodies.c:131:11: error: implicit declaration of function 'gsw_geo_strf_dyn_height_1' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
      ret = gsw_geo_strf_dyn_height_1((double *)PyArray_DATA(sa_a),
            ^
  src/method_bodies.c:204:11: error: implicit declaration of function 'gsw_util_pchip_interp' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
      ret = gsw_util_pchip_interp((double *)PyArray_DATA(xa),
            ^
  src/method_bodies.c:204:11: note: did you mean 'util_pchip_interp'?
  src/method_bodies.c:156:1: note: 'util_pchip_interp' declared here
  util_pchip_interp(PyObject *NPY_UNUSED(self), PyObject *args)
  ^
  13 warnings and 5 errors generated.
  error: command '/usr/bin/clang' failed with exit code 1

[DocOtak]

Hi @mfkenney this looks like the header c_gsw/gswteos-10.h is not being found/included. Do you have access to the clang command that was run? E.g. when I do a python setup.py build there is a line in the terminal output that looks like this (it's really long):

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/include -I/Users/abarna/.pyenv/versions/jupyter/lib/python3.9/site-packages/numpy/core/include -I/Users/abarna/work/software/GSW-Python/src/c_gsw -I/Users/abarna/.pyenv/versions/jupyter/include -I/Users/abarna/.pyenv/versions/3.9.6/include/python3.9 -c src/_ufuncs.c -o build/temp.macosx-11.4-x86_64-3.9/src/_ufuncs.o

[mfkenney]

@DocOtak, that's it. The clang invocation does not include the src/c_gsw directory.

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -I/private/var/folders/7x/cxkm6r217vbbsp40bd6_4pnc0000gn/T/pip-build-env-m_6emw_q/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python@3.9/3.9.1_2/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c src/_ufuncs.c -o build/temp.macosx-10.15-x86_64-3.9/src/_ufuncs.o

[mfkenney]

@DocOtak, unfortunately, that is not the cause. I used the include_dirs=['src/c_gsw'] option to setuptools.Extension and I get the same result:

clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -I/usr/local/include -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/usr/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/Tk.framework/Versions/8.5/Headers -Isrc/c_gsw -I/usr/local/lib/python3.9/site-packages/numpy/core/include -I/usr/local/include -I/usr/local/opt/openssl@1.1/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python@3.9/3.9.1_2/Frameworks/Python.framework/Versions/3.9/include/python3.9 -c src/_ufuncs.c -o build/temp.macosx-10.15-x86_64-3.9/src/_ufuncs.o
.
.
.
src/_ufuncs.c:646:37: error: use of undeclared identifier 'gsw_o2sol_sp_pt'; did you mean
      'data_o2sol_sp_pt'?
static void *data_o2sol_sp_pt[] = {&gsw_o2sol_sp_pt};
                                    ^~~~~~~~~~~~~~~
                                    data_o2sol_sp_pt
src/_ufuncs.c:646:14: note: 'data_o2sol_sp_pt' declared here
static void *data_o2sol_sp_pt[] = {&gsw_o2sol_sp_pt};
             ^
src/_ufuncs.c:660:40: error: use of undeclared identifier 'gsw_sp_salinometer'; did you mean
      'data_sp_salinometer'?
static void *data_sp_salinometer[] = {&gsw_sp_salinometer};
                                       ^~~~~~~~~~~~~~~~~~
                                       data_sp_salinometer
src/_ufuncs.c:660:14: note: 'data_sp_salinometer' declared here
static void *data_sp_salinometer[] = {&gsw_sp_salinometer};
             ^
src/_ufuncs.c:733:31: error: use of undeclared identifier 'gsw_o2sol'
static void *data_o2sol[] = {&gsw_o2sol};
                              ^
In file included from src/_ufuncs.c:773:
src/method_bodies.c:131:11: error: implicit declaration of function 'gsw_geo_strf_dyn_height_1' is
      invalid in C99 [-Werror,-Wimplicit-function-declaration]
    ret = gsw_geo_strf_dyn_height_1((double *)PyArray_DATA(sa_a),
          ^
src/method_bodies.c:204:11: error: implicit declaration of function 'gsw_util_pchip_interp' is invalid
      in C99 [-Werror,-Wimplicit-function-declaration]
    ret = gsw_util_pchip_interp((double *)PyArray_DATA(xa),
          ^
src/method_bodies.c:204:11: note: did you mean 'util_pchip_interp'?
src/method_bodies.c:156:1: note: 'util_pchip_interp' declared here
util_pchip_interp(PyObject *NPY_UNUSED(self), PyObject *args)
^
13 warnings and 5 errors generated.
error: command '/usr/bin/clang' failed with exit code 1

[mfkenney]

@DocOtak, problem solved. There was another copy of gswteos-10.h in /usr/local/include on my system that was being read in preference to the copy in src/c_gsw. Once I removed the old version, the package compiled fine.

[DocOtak]

Hm... I'm not sure why, the include dir is being configured here in the setup.py:

GSW-Python/setup.py

Line 55 in 63a7747

"include_dirs": [os.path.join(rootpath, 'src', 'c_gsw')],

Maybe we don't have that include_dirs in the right place the setuptools docs have this under the Extension class. it does warn slightly about having absolute paths in there.

---

Ah too fast for me, ignore the above since you already tried it. It also would have failed with an error like src/_ufuncs.c:14:10: fatal error: 'gswteos-10.h' file not found really quickly.

---

Too fast for me again, glad you solved it!

[mfkenney]

@DocOtak, the include_dirs option to setup might be deprecated. I have setuptools version 51.0.0 and I had to use the include_dirs option to the Extension function ...

[ocefpaf]

@mfkenney while looking into this error is important are you trying this route b/c there are no wheels for py39? I'll work on that ASAP but is conda an option for you?

[mfkenney]

@ocefpaf I was originally trying to install with pip but was able to build my own wheel from the source after fixing setup.py.