automl / automl/random_forest_run

Installation error limits.h

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Description

Installed swig, cmake, gcc in conda, however we get the following error:
```

(gensim_env) dyn-160-39-178-198:~ prernakashyap$ pip install pyrfr

Collecting pyrfr

Using cached https://files.pythonhosted.org/packages/ed/0f/4d7e42a9dfef3a1898e03cffa8f1cfcd1f96507d718808b2db584c6f8401/pyrfr-0.8.0.tar.gz

Building wheels for collected packages: pyrfr

Running setup.py bdist_wheel for pyrfr ... error

Complete output from command /Users/prernakashyap/anaconda3/envs/gensim_env/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-install-9wu83pgt/pyrfr/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 /private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-wheel-ee82_ljr --python-tag cp36:

running bdist_wheel

running build

running build_ext

building 'pyrfr._regression' extension

swigging pyrfr/regression.i to pyrfr/regression_wrap.cpp

swig -python -c++ -modern -features nondynamic -I./include -o pyrfr/regression_wrap.cpp pyrfr/regression.i

creating build

creating build/temp.macosx-10.7-x86_64-3.6

creating build/temp.macosx-10.7-x86_64-3.6/pyrfr

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/prernakashyap/anaconda3/envs/gensim_env/include -arch x86_64 -I/Users/prernakashyap/anaconda3/envs/gensim_env/include -arch x86_64 -I./include -I/Users/prernakashyap/anaconda3/envs/gensim_env/include/python3.6m -c pyrfr/regression_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.6/pyrfr/regression_wrap.o -O2 -std=c++11

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]

In file included from /Users/prernakashyap/anaconda3/envs/gensim_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0,

from /Users/prernakashyap/anaconda3/envs/gensim_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34,

from /Users/prernakashyap/anaconda3/envs/gensim_env/include/python3.6m/Python.h:11,

from pyrfr/regression_wrap.cpp:173:

/Users/prernakashyap/anaconda3/envs/gensim_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

#include_next /* recurse down to the real one */

^

compilation terminated.

error: command 'gcc' failed with exit status 1

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

Failed building wheel for pyrfr

Running setup.py clean for pyrfr

Failed to build pyrfr

Installing collected packages: pyrfr

Running setup.py install for pyrfr ... error

Complete output from command /Users/prernakashyap/anaconda3/envs/gensim_env/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-install-9wu83pgt/pyrfr/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-record-9qiyacqw/install-record.txt --single-version-externally-managed --compile:

running install

running build_ext

building 'pyrfr._regression' extension

swigging pyrfr/regression.i to pyrfr/regression_wrap.cpp

swig -python -c++ -modern -features nondynamic -I./include -o pyrfr/regression_wrap.cpp pyrfr/regression.i

creating build

creating build/temp.macosx-10.7-x86_64-3.6

creating build/temp.macosx-10.7-x86_64-3.6/pyrfr

gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/prernakashyap/anaconda3/envs/gensim_env/include -arch x86_64 -I/Users/prernakashyap/anaconda3/envs/gensim_env/include -arch x86_64 -I./include -I/Users/prernakashyap/anaconda3/envs/gensim_env/include/python3.6m -c pyrfr/regression_wrap.cpp -o build/temp.macosx-10.7-x86_64-3.6/pyrfr/regression_wrap.o -O2 -std=c++11

cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++ [enabled by default]

In file included from /Users/prernakashyap/anaconda3/envs/gensim_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/syslimits.h:7:0,

from /Users/prernakashyap/anaconda3/envs/gensim_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:34,

from /Users/prernakashyap/anaconda3/envs/gensim_env/include/python3.6m/Python.h:11,

from pyrfr/regression_wrap.cpp:173:

/Users/prernakashyap/anaconda3/envs/gensim_env/lib/gcc/x86_64-apple-darwin11.4.2/4.8.5/include-fixed/limits.h:168:61: fatal error: limits.h: No such file or directory

#include_next /* recurse down to the real one */

^

compilation terminated.

error: command 'gcc' failed with exit status 1

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

Command "/Users/prernakashyap/anaconda3/envs/gensim_env/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-install-9wu83pgt/pyrfr/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-record-9qiyacqw/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/ty/2lwym9l571l4xvwp44x5c43c0000gn/T/pip-install-9wu83pgt/pyrfr/
```

Did someone encounter this problem before? Conda version is 4.5.X

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with setup.py and pyrfr/regression.i, then reproduce pip install pyrfr in the reported conda Python 3.6/macOS environment and inspect the gcc limits.h failure. Done means identifying and validating a repository-supported installation path that completes the pyrfr build.

Written by the indexing model from the issue text.

Assessment

Tech stack
cmake, cpp, python
Domain
build-system
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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