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.