Pomegranate: pip install fails on pomegranate-0.7.3

[xkortex]

Installing v 0.7.3 via pip seems problematic. The short of it is:

...
    x86_64-linux-gnu-gcc: error: pomegranate/fsm.c: No such file or directory
    x86_64-linux-gnu-gcc: fatal error: no input files
    compilation terminated.
    error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

pip install --upgrade numpy
Collecting numpy
Downloading numpy-1.13.0-cp35-cp35m-manylinux1_x86_64.whl (16.9MB)
100% |████████████████████████████████| 16.9MB 109kB/s
Installing collected packages: numpy
Found existing installation: numpy 1.12.0
Uninstalling numpy-1.12.0:
Successfully uninstalled numpy-1.12.0
Successfully installed numpy-1.13.0
(ml) ➜ pip install pomegranate
Collecting pomegranate
Using cached pomegranate-0.7.3.tar.gz
Requirement already satisfied: numpy>=1.8.0 in /home/mike/ve/ml/lib/python3.5/site-packages (from pomegranate)
Collecting joblib>=0.9.0b4 (from pomegranate)
Using cached joblib-0.11-py2.py3-none-any.whl
Requirement already satisfied: networkx>=1.8.1 in /home/mike/ve/ml/lib/python3.5/site-packages (from pomegranate)
Requirement already satisfied: scipy>=0.17.0 in /home/mike/ve/ml/lib/python3.5/site-packages (from pomegranate)
Requirement already satisfied: decorator>=3.4.0 in /home/mike/ve/ml/lib/python3.5/site-packages (from networkx>=1.8.1->pomegranate)
Building wheels for collected packages: pomegranate
Running setup.py bdist_wheel for pomegranate ... error
Complete output from command /home/mike/ve/ml/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-kjrpfg37/pomegranate/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 /tmp/tmpsuj26fy6pip-wheel- --python-tag cp35:
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/pomegranate
copying pomegranate/__init__.py -> build/lib.linux-x86_64-3.5/pomegranate
running build_ext
building 'pomegranate.base' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/pomegranate
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/base.c -o build/temp.linux-x86_64-3.5/pomegranate/base.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/base.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/base.o -o build/lib.linux-x86_64-3.5/pomegranate/base.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.BayesianNetwork' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/BayesianNetwork.c -o build/temp.linux-x86_64-3.5/pomegranate/BayesianNetwork.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/BayesianNetwork.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/BayesianNetwork.o -o build/lib.linux-x86_64-3.5/pomegranate/BayesianNetwork.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.FactorGraph' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/FactorGraph.c -o build/temp.linux-x86_64-3.5/pomegranate/FactorGraph.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/FactorGraph.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/FactorGraph.o -o build/lib.linux-x86_64-3.5/pomegranate/FactorGraph.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.distributions' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/distributions.c -o build/temp.linux-x86_64-3.5/pomegranate/distributions.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/distributions.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/distributions.o -o build/lib.linux-x86_64-3.5/pomegranate/distributions.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.fsm' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/fsm.c -o build/temp.linux-x86_64-3.5/pomegranate/fsm.o
x86_64-linux-gnu-gcc: error: pomegranate/fsm.c: No such file or directory
x86_64-linux-gnu-gcc: fatal error: no input files
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

---

Failed building wheel for pomegranate
Running setup.py clean for pomegranate
Failed to build pomegranate
Installing collected packages: joblib, pomegranate
Running setup.py install for pomegranate ... error
Complete output from command /home/mike/ve/ml/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-kjrpfg37/pomegranate/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-ok07d_5y-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/mike/ve/ml/include/site/python3.5/pomegranate:
running install
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.5
creating build/lib.linux-x86_64-3.5/pomegranate
copying pomegranate/__init__.py -> build/lib.linux-x86_64-3.5/pomegranate
running build_ext
building 'pomegranate.base' extension
creating build/temp.linux-x86_64-3.5
creating build/temp.linux-x86_64-3.5/pomegranate
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/base.c -o build/temp.linux-x86_64-3.5/pomegranate/base.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/base.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/base.o -o build/lib.linux-x86_64-3.5/pomegranate/base.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.BayesianNetwork' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/BayesianNetwork.c -o build/temp.linux-x86_64-3.5/pomegranate/BayesianNetwork.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/BayesianNetwork.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/BayesianNetwork.o -o build/lib.linux-x86_64-3.5/pomegranate/BayesianNetwork.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.FactorGraph' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/FactorGraph.c -o build/temp.linux-x86_64-3.5/pomegranate/FactorGraph.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/FactorGraph.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/FactorGraph.o -o build/lib.linux-x86_64-3.5/pomegranate/FactorGraph.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.distributions' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/distributions.c -o build/temp.linux-x86_64-3.5/pomegranate/distributions.o
In file included from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
from /home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pomegranate/distributions.c:444:
/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it by " \
^
x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.5/pomegranate/distributions.o -o build/lib.linux-x86_64-3.5/pomegranate/distributions.cpython-35m-x86_64-linux-gnu.so
building 'pomegranate.fsm' extension
x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/ml/include/python3.5m -I/home/mike/ve/ml/lib/python3.5/site-packages/numpy/core/include -c pomegranate/fsm.c -o build/temp.linux-x86_64-3.5/pomegranate/fsm.o
x86_64-linux-gnu-gcc: error: pomegranate/fsm.c: No such file or directory
x86_64-linux-gnu-gcc: fatal error: no input files
compilation terminated.
error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

----------------------------------------

Command "/home/mike/ve/ml/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-build-kjrpfg37/pomegranate/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-ok07d_5y-record/install-record.txt --single-version-externally-managed --compile --install-headers /home/mike/ve/ml/include/site/python3.5/pomegranate" failed with error code 1 in /tmp/pip-build-kjrpfg37/pomegranate/

0.7.0. 0.7.1, and 0.7.2 work.

Let me know if you need any other details.

[jmschrei]

I think the problem lies in that I removed fsm's in 7.3, so if you have older files somewhere that pip can read them it might cause an error. Try going to your site-packages folder and delete the pomegranate folders and egg files and using pip again.

[jmschrei]

This is what I get when I try on Ubuntu:

jmschr@ubuntu:~/Desktop/pomegranate$ pip install pomegranate
Collecting pomegranate
  Downloading pomegranate-0.7.3.tar.gz (7.5MB)
    100% |████████████████████████████████| 7.5MB 40kB/s 
Requirement already satisfied: numpy>=1.8.0 in /home/jmschr/anaconda2/lib/python2.7/site-packages (from pomegranate)
Requirement already satisfied: joblib>=0.9.0b4 in /home/jmschr/anaconda2/lib/python2.7/site-packages (from pomegranate)
Requirement already satisfied: networkx>=1.8.1 in /home/jmschr/anaconda2/lib/python2.7/site-packages (from pomegranate)
Requirement already satisfied: scipy>=0.17.0 in /home/jmschr/anaconda2/lib/python2.7/site-packages (from pomegranate)
Requirement already satisfied: decorator>=3.4.0 in /home/jmschr/anaconda2/lib/python2.7/site-packages (from networkx>=1.8.1->pomegranate)
Building wheels for collected packages: pomegranate
  Running setup.py bdist_wheel for pomegranate ... done
  Stored in directory: /home/jmschr/.cache/pip/wheels/e7/32/98/8b89b0775c143e2520ac966981c0382c77c45723caf0cccf6a
Successfully built pomegranate
Installing collected packages: pomegranate
Successfully installed pomegranate-0.7.3

This is when I try to install on Windows:

C:\Users\Jacob>pip install pomegranate
Collecting pomegranate
  Downloading pomegranate-0.7.3-cp27-cp27m-win_amd64.whl (1.3MB)
    100% |################################| 1.3MB 123kB/s
Requirement already satisfied (use --upgrade to upgrade): numpy>=1.8.0 in c:\anaconda\lib\site-packages (from pomegranate)
Requirement already satisfied (use --upgrade to upgrade): scipy>=0.17.0 in c:\anaconda\lib\site-packages (from pomegranate)
Requirement already satisfied (use --upgrade to upgrade): networkx>=1.8.1 in c:\anaconda\lib\site-packages (from pomegranate)
Requirement already satisfied (use --upgrade to upgrade): joblib>=0.9.0b4 in c:\anaconda\lib\site-packages (from pomegranate)
Requirement already satisfied (use --upgrade to upgrade): decorator>=3.4.0 in c:\anaconda\lib\site-packages (from networkx>=1.8.1->pomegranate)
Installing collected packages: pomegranate
Successfully installed pomegranate-0.7.3

[xkortex]

This was on my first attempt at installing pomegranate. Also occurred on a fresh virtualenv. Also I'm not using anaconda, perhaps anaconda is providing some dependency? Or perhaps something with virtualenv?

Just ran it again on Ubuntu, on a different computer:

virtualenv -p `which python3` pom
source ~/ve/pom/bin/activate
pip install numpy scipy joblib networkx
pip install pomegranate

Identical error.

I think this is the line causing the issue, emphasis mine:

x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.5m -I/home/mike/ve/pom/include/python3.5m -I/home/mike/ve/pom/lib/python3.5/site-packages/numpy/core/include -c pomegranate/fsm.c -o build/temp.linux-x86_64-3.5/pomegranate/fsm.o

My intuition is you still have hooks in the setup script somewhere for FSMs. I'm not familiar enough with the python build system though, so I'm not sure where that line is called from. If I had to wager, I would guess that the calls to build fsm shouldn't be in the manifest or setup.py.

https://github.com/jmschrei/pomegranate/blob/master/MANIFEST#L26
https://github.com/jmschrei/pomegranate/blob/master/setup.py#L18

[jmschrei]

I removed those references to fsms and pushed the changes. Can you try installing again and let me know what happens?

[jmschrei]

I'm going to assume this is resolved. Re-open if not the case.

[CermakM]

I faced this issue with 0.7.3, when bisecting through the earlier versions, I noticed that they install cython as dependency, make sure that you have it installed before trying to install 0.7.3