[theano-users] Theano Compile error with Anaconda, OSX

[Christopher Grubb]

After following the Theano installation instructions, attempting to import
Theano using Python 3.5 gives me the following error:

You can find the C code in this temporary file:
/var/folders/0f/ymnzcwzs7k75g9rybwgzc9hc0000gn/T/theano_compilation_error_o4xziccn

Traceback (most recent call last):

File "/anaconda3/lib/python3.5/site-packages/theano/gof/lazylinker_c.py",
line 81, in <module>

actual_version, force_compile, _need_reload))

ImportError: Version check of the existing lazylinker compiled file.
Looking for version 0.211, but found None. Extra debug information:
force_compile=False, _need_reload=True


During handling of the above exception, another exception occurred:


Traceback (most recent call last):

File "/anaconda3/lib/python3.5/site-packages/theano/gof/lazylinker_c.py",
line 105, in <module>

actual_version, force_compile, _need_reload))

ImportError: Version check of the existing lazylinker compiled file.
Looking for version 0.211, but found None. Extra debug information:
force_compile=False, _need_reload=True


During handling of the above exception, another exception occurred:


Traceback (most recent call last):

File "<stdin>", line 1, in <module>

File "/anaconda3/lib/python3.5/site-packages/theano/__init__.py", line
110, in <module>

from theano.compile import (

File "/anaconda3/lib/python3.5/site-packages/theano/compile/__init__.py",
line 12, in <module>

from theano.compile.mode import *

File "/anaconda3/lib/python3.5/site-packages/theano/compile/mode.py",
line 11, in <module>

import theano.gof.vm

File "/anaconda3/lib/python3.5/site-packages/theano/gof/vm.py", line 674,
in <module>

from . import lazylinker_c

File "/anaconda3/lib/python3.5/site-packages/theano/gof/lazylinker_c.py",
line 140, in <module>

preargs=args)

File "/anaconda3/lib/python3.5/site-packages/theano/gof/cmodule.py", line
2388, in compile_str

(status, compile_stderr.replace('\n', '. ')))

Exception: Compilation failed (return status=1): In file included from
/Users/chris/.theano/compiledir_Darwin-18.0.0-x86_64-i386-64bit-i386-3.5.6-64/lazylinker_ext/mod.cpp:1:.
In file included from /anaconda3/include/python3.5m/Python.h:25:.
/anaconda3/bin/../include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h'
file not found. #include_next <stdio.h>. ^~~~~~~~~. 1 error
generated..

I have installed Xcode command-line tools, all optional dependencies for
MacOS, uninstalled and re-installed Anaconda, etc.

Any help would be very much appreciated!

[Arnaud Bergeron]

You seem to have the same problem as this: https://github.com/Theano/Theano/issues/6645 <https://github.com/Theano/Theano/issues/6645>

Unfortunately as explained in that ticket the solution is rather involved and would require more time than we have available for now.

You can find the C code in this temporary file: /var/folders/0f/ymnzcwzs7k75g9rybwgzc9hc0000gn/T/theano_compilation_error_o4xziccn
File "/anaconda3/lib/python3.5/site-packages/theano/gof/lazylinker_c.py", line 81, in <module>
actual_version, force_compile, _need_reload))
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True
File "/anaconda3/lib/python3.5/site-packages/theano/gof/lazylinker_c.py", line 105, in <module>
actual_version, force_compile, _need_reload))
ImportError: Version check of the existing lazylinker compiled file. Looking for version 0.211, but found None. Extra debug information: force_compile=False, _need_reload=True
File "<stdin>", line 1, in <module>
File "/anaconda3/lib/python3.5/site-packages/theano/__init__.py", line 110, in <module>
from theano.compile import (
File "/anaconda3/lib/python3.5/site-packages/theano/compile/__init__.py", line 12, in <module>
from theano.compile.mode import *
File "/anaconda3/lib/python3.5/site-packages/theano/compile/mode.py", line 11, in <module>
import theano.gof.vm
File "/anaconda3/lib/python3.5/site-packages/theano/gof/vm.py", line 674, in <module>
from . import lazylinker_c
File "/anaconda3/lib/python3.5/site-packages/theano/gof/lazylinker_c.py", line 140, in <module>
preargs=args)
File "/anaconda3/lib/python3.5/site-packages/theano/gof/cmodule.py", line 2388, in compile_str
(status, compile_stderr.replace('\n', '. ')))
Exception: Compilation failed (return status=1): In file included from /Users/chris/.theano/compiledir_Darwin-18.0.0-x86_64-i386-64bit-i386-3.5.6-64/lazylinker_ext/mod.cpp:1:. In file included from /anaconda3/include/python3.5m/Python.h:25:. /anaconda3/bin/../include/c++/v1/stdio.h:108:15: fatal error: 'stdio.h' file not found. #include_next <stdio.h>. ^~~~~~~~~. 1 error generated..
I have installed Xcode command-line tools, all optional dependencies for MacOS, uninstalled and re-installed Anaconda, etc.
Any help would be very much appreciated!
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