error: use of undeclared identifier 'environ'

[loranger]

Hello,

As I tried to install Kraken, I found a bug with the clstm dependency installation.

I tried with Python 3 and Python 2, but the result remains the same.
I use homebrewed python on macOS 10.13.3

Here is the output I get while running pip install clstm

Output

Collecting clstm
  Using cached clstm-0.0.5.tar.gz
Requirement already satisfied: numpy>=1.9.0 in /usr/local/lib/python3.6/site-packages (from clstm)
Building wheels for collected packages: clstm
  Running setup.py bdist_wheel for clstm: started
  Running setup.py bdist_wheel for clstm: finished with status 'error'
  Complete output from command /usr/local/opt/python3/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/35/8h9cj97x2sg8pxmk6l73fn8w0000gn/T/pip-build-rncsaq3b/clstm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /var/folders/35/8h9cj97x2sg8pxmk6l73fn8w0000gn/T/tmpi5jp5zoypip-wheel- --python-tag cp36:
  making proto file
  clstm.proto: No such file or directory
  running bdist_wheel
  running build_ext
  building '_clstm' extension
  swigging clstm.i to clstm_wrap.cpp
  swig -python -c++ -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -o clstm_wrap.cpp clstm.i
  clstm.i:35: Warning 451: Setting a const char * variable may leak memory.
  creating build
  creating build/temp.macosx-10.13-x86_64-3.6
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c clstm_wrap.cpp -o build/temp.macosx-10.13-x86_64-3.6/clstm_wrap.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c clstm.cc -o build/temp.macosx-10.13-x86_64-3.6/clstm.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c clstm_prefab.cc -o build/temp.macosx-10.13-x86_64-3.6/clstm_prefab.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
  clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c extras.cc -o build/temp.macosx-10.13-x86_64-3.6/extras.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
  extras.cc:679:17: error: use of undeclared identifier 'environ'
      char **ep = environ;
                  ^
  1 error generated.
  error: command 'clang' failed with exit status 1
  
  ----------------------------------------
  Running setup.py clean for clstm
Failed to build clstm
Installing collected packages: clstm
  Running setup.py install for clstm: started
    Running setup.py install for clstm: finished with status 'error'
    Complete output from command /usr/local/opt/python3/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/private/var/folders/35/8h9cj97x2sg8pxmk6l73fn8w0000gn/T/pip-build-rncsaq3b/clstm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /var/folders/35/8h9cj97x2sg8pxmk6l73fn8w0000gn/T/pip-noa4v0f4-record/install-record.txt --single-version-externally-managed --compile:
    making proto file
    clstm.proto: No such file or directory
    running install
    running build
    running build_ext
    building '_clstm' extension
    swigging clstm.i to clstm_wrap.cpp
    swig -python -c++ -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -o clstm_wrap.cpp clstm.i
    clstm.i:35: Warning 451: Setting a const char * variable may leak memory.
    creating build
    creating build/temp.macosx-10.13-x86_64-3.6
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c clstm_wrap.cpp -o build/temp.macosx-10.13-x86_64-3.6/clstm_wrap.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c clstm.cc -o build/temp.macosx-10.13-x86_64-3.6/clstm.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c clstm_prefab.cc -o build/temp.macosx-10.13-x86_64-3.6/clstm_prefab.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
    clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/usr/include/eigen3 -I/usr/local/include/eigen3 -I/usr/local/include -I/usr/include/hdf5/serial -I/usr/local/include -I/usr/local/opt/openssl/include -I/usr/local/opt/sqlite/include -I/usr/local/Cellar/python3/3.6.4_2/Frameworks/Python.framework/Versions/3.6/include/python3.6m -I/usr/local/lib/python3.6/site-packages/numpy/core/include -c extras.cc -o build/temp.macosx-10.13-x86_64-3.6/extras.o -std=c++11 -w -Dadd_raw=add -DNODISPLAY=1 -DTHROW=throw -DHGVERSION="\"unknown\""
    extras.cc:679:17: error: use of undeclared identifier 'environ'
        char **ep = environ;
                    ^
    1 error generated.
    error: command 'clang' failed with exit status 1
    
    ----------------------------------------

[mittagessen]

Apologies to the maintainers, I've packaged the separate-derivs branch with the working python bindings to pypi a while ago.

I don't know if clstm works on OSX but I'll look into the error right now and adjust the travis packaging if I get it working somehow

[amitdo]

See #34

[mittagessen]

I've got travis to produce osx builds. Either I'm getting better at the whole CI packaging shebang or the goat sacrifice the last time actually helped. @loranger, give it half an hour or so to build and push the tag to pypi and give it another try.

[amitdo]

What patch(es) did you apply to make it work?
Just the one in #34? @ryanfb patch? @tmbdev suggestion?
Something else?

[loranger]

I've got no more issue regarding the clstm install.
Thanks @mittagessen !

[mittagessen]

I just applied @ryanfb's patch and forced clang to use libc++ instead of libstdc++. As I don't have a OSX machine to test on and debugging changes through travis is not my idea of a fun evening I kept it at that. Have a look at the main branch of mittagessen/clstm; it has some other stop gap changes to make it auto-deploy to pypi through travis and actually built in a single pass with setuptools. Caveat emptor, all of it is rather ugly as it is only intended to keep people off my back with kraken installation related questions until I've finished the pytorch port.