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replicahq / doppelganger

A Python package of tools to support population synthesizers
Apache License 2.0
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Pomegrenate issues on CentOS 7.3 #23

Closed sdpoueme closed 7 years ago

sdpoueme commented 7 years ago

Trying to get my setup working. I am running the pip install command on a CentOS server. I checked my gcc version and it does not require an upgrade at the moment:

[camidus@urbanizer doppelganger]$ gcc --version gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-11)

Errors returned below:

` gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/base.c -o build/temp.linux-x86_64-2.7/pomegranate/base.o In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from pomegranate/base.c:444: /usr/lib64/python2.7/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 " \

^

gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/base.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/base.so building 'pomegranate.BayesianNetwork' extension gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/BayesianNetwork.c -o build/temp.linux-x86_64-2.7/pomegranate/BayesianNetwork.o In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from pomegranate/BayesianNetwork.c:444: /usr/lib64/python2.7/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 " \

^

gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/BayesianNetwork.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/BayesianNetwork.so building 'pomegranate.FactorGraph' extension gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/FactorGraph.c -o build/temp.linux-x86_64-2.7/pomegranate/FactorGraph.o In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from pomegranate/FactorGraph.c:444: /usr/lib64/python2.7/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 " \

^

gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/FactorGraph.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/FactorGraph.so building 'pomegranate.distributions' extension gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/distributions.c -o build/temp.linux-x86_64-2.7/pomegranate/distributions.o In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from pomegranate/distributions.c:444: /usr/lib64/python2.7/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 " \

^

gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/distributions.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/distributions.so building 'pomegranate.fsm' extension gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/fsm.c -o build/temp.linux-x86_64-2.7/pomegranate/fsm.o gcc: error: pomegranate/fsm.c: No such file or directory gcc: fatal error: no input files compilation terminated. error: command 'gcc' failed with exit status 4

Failed building wheel for pomegranate Running setup.py clean for pomegranate Failed to build pomegranate Installing collected packages: pomegranate, chardet, idna, urllib3, requests, doppelganger Running setup.py install for pomegranate ... error Complete output from command /bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-hVt89H/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-iPa6Ki-record/install-record.txt --single-version-externally-managed --compile: running install running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pomegranate copying pomegranate/init.py -> build/lib.linux-x86_64-2.7/pomegranate running build_ext building 'pomegranate.base' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/pomegranate gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/base.c -o build/temp.linux-x86_64-2.7/pomegranate/base.o In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18, from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from pomegranate/base.c:444: /usr/lib64/python2.7/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 " \

  ^
gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/base.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/base.so
building 'pomegranate.BayesianNetwork' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/BayesianNetwork.c -o build/temp.linux-x86_64-2.7/pomegranate/BayesianNetwork.o
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from pomegranate/BayesianNetwork.c:444:
/usr/lib64/python2.7/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 " \
  ^
gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/BayesianNetwork.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/BayesianNetwork.so
building 'pomegranate.FactorGraph' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/FactorGraph.c -o build/temp.linux-x86_64-2.7/pomegranate/FactorGraph.o
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from pomegranate/FactorGraph.c:444:
/usr/lib64/python2.7/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 " \
  ^
gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/FactorGraph.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/FactorGraph.so
building 'pomegranate.distributions' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/distributions.c -o build/temp.linux-x86_64-2.7/pomegranate/distributions.o
In file included from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1809:0,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:18,
                 from /usr/lib64/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from pomegranate/distributions.c:444:
/usr/lib64/python2.7/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 " \
  ^
gcc -pthread -shared -Wl,-z,relro build/temp.linux-x86_64-2.7/pomegranate/distributions.o -L. -lpython2.7 -o build/lib.linux-x86_64-2.7/pomegranate/distributions.so
building 'pomegranate.fsm' extension
gcc -pthread -fno-strict-aliasing -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -DNDEBUG -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -D_GNU_SOURCE -fPIC -fwrapv -fPIC -I/usr/include/python2.7 -I/usr/lib64/python2.7/site-packages/numpy/core/include -c pomegranate/fsm.c -o build/temp.linux-x86_64-2.7/pomegranate/fsm.o
gcc: error: pomegranate/fsm.c: No such file or directory
gcc: fatal error: no input files
compilation terminated.
error: command 'gcc' failed with exit status 4

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

Command "/bin/python -u -c "import setuptools, tokenize;file='/tmp/pip-build-hVt89H/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-iPa6Ki-record/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /tmp/pip-build-hVt89H/pomegranate/ `

katbusch commented 7 years ago

Interesting. Thanks for the report. What version of numpy are you using and how did you install it?

sdpoueme commented 7 years ago

I am running numpy 1.13.0

[camidus@urbanizer ~]$ pip freeze | grep numpy numpy==1.13.0

I installed it by running: pip install numpy

katbusch commented 7 years ago

We recommend installing numpy with Anaconda or another pre-built option. Otherwise it can be quite a difficult and tedious process to get it build.

sdpoueme commented 7 years ago

Thanks @katbusch , Anaconda was also installed but not correctly. I removed both numpy and Anaconda and reinstalled Anaconda 2. Now everything is fine, installation was successful: [root@urbanizer doppelganger]# pip install . Processing /home/camidus/doppelganger Collecting cvxpy==0.4.8 (from doppelganger==0.1.0) Requirement already satisfied: numpy>=1.11.0 in /root/anaconda2/lib/python2.7/site-packages (from doppelganger==0.1.0) Requirement already satisfied: pandas>=0.19.0 in /root/.local/lib/python2.7/site-packages (from doppelganger==0.1.0) Collecting pomegranate>=0.7.1 (from doppelganger==0.1.0) Using cached pomegranate-0.7.3.tar.gz Requirement already satisfied: requests>=2.0.0 in /root/anaconda2/lib/python2.7/site-packages (from doppelganger==0.1.0) Requirement already satisfied: six>=1.10.0 in /root/.local/lib/python2.7/site-packages (from doppelganger==0.1.0) Collecting scs>=1.1.3 (from cvxpy==0.4.8->doppelganger==0.1.0) Collecting multiprocess (from cvxpy==0.4.8->doppelganger==0.1.0) Collecting CVXcanon>=0.0.22 (from cvxpy==0.4.8->doppelganger==0.1.0) Collecting ecos>=2 (from cvxpy==0.4.8->doppelganger==0.1.0) Requirement already satisfied: toolz in /root/anaconda2/lib/python2.7/site-packages (from cvxpy==0.4.8->doppelganger==0.1.0) Requirement already satisfied: scipy>=0.15 in /root/.local/lib/python2.7/site-packages (from cvxpy==0.4.8->doppelganger==0.1.0) Requirement already satisfied: fastcache in /root/anaconda2/lib/python2.7/site-packages (from cvxpy==0.4.8->doppelganger==0.1.0) Requirement already satisfied: pytz>=2011k in /root/.local/lib/python2.7/site-packages (from pandas>=0.19.0->doppelganger==0.1.0) Requirement already satisfied: python-dateutil in /root/.local/lib/python2.7/site-packages (from pandas>=0.19.0->doppelganger==0.1.0) Collecting joblib>=0.9.0b4 (from pomegranate>=0.7.1->doppelganger==0.1.0) Using cached joblib-0.11-py2.py3-none-any.whl Requirement already satisfied: networkx>=1.8.1 in /root/anaconda2/lib/python2.7/site-packages (from pomegranate>=0.7.1->doppelganger==0.1.0) Collecting dill>=0.2.6 (from multiprocess->cvxpy==0.4.8->doppelganger==0.1.0) Requirement already satisfied: decorator>=3.4.0 in /root/anaconda2/lib/python2.7/site-packages (from networkx>=1.8.1->pomegranate>=0.7.1->doppelganger==0.1.0) Building wheels for collected packages: pomegranate Running setup.py bdist_wheel for pomegranate ... done Stored in directory: /root/.cache/pip/wheels/e7/32/98/8b89b0775c143e2520ac966981c0382c77c45723caf0cccf6a Successfully built pomegranate Installing collected packages: scs, dill, multiprocess, CVXcanon, ecos, cvxpy, joblib, pomegranate, doppelganger Running setup.py install for doppelganger ... done Successfully installed CVXcanon-0.1.1 cvxpy-0.4.8 dill-0.2.6 doppelganger-0.1.0 ecos-2.0.4 joblib-0.11 multiprocess-0.70.5 pomegranate-0.7.3 scs-1.2.6 [root@urbanizer doppelganger]#

katbusch commented 7 years ago

Yay!