# PyMC3 installation issue

**URL:** <https://discourse.pymc.io/t/pymc3-installation-issue/7068>\
**Category:** Questions\
**Created:** [March 24, 2021, 3:56am UTC](https://discourse.pymc.io/t/pymc3-installation-issue/7068 "2021-03-24T03:56:48Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![hgu](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/hgu/32/3842_2.png) [@hgu](https://discourse.pymc.io/u/hgu)\
**Post date:** [March 24, 2021, 3:56am UTC](https://discourse.pymc.io/t/pymc3-installation-issue/7068/1 "2021-03-24T03:56:49Z")

</div>

I have followed the installation for macOS page but still could not load properly. I read a lot of similar posts and have uninstalled/installed many times. Any help is much appreciated 🙂

Machine: M1 MacBook Air  
OS: macOS 11.2.3  
Python: 3.8 via Conda, all related packages up to date with PyMC3 3.10 requirements

Issues:  
_when importing theano:_

```
You can find the C code in this temporary file: /var/folders/_c/frfzc_f54tbgbycvmnlj9v_w0000gn/T/theano_compilation_error_j2azim5s
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
     75 if version != actual_version:
---> 76 raise ImportError(
     77 "Version check of the existing lazylinker compiled file."

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:

ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
     98 if version != actual_version:
---> 99 raise ImportError(
    100 "Version check of the existing lazylinker compiled file."

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:

Exception Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/vm.py in <module>
    696 )
--> 697 from . import lazylinker_c
    698 

~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
    138 args = cmodule.GCC_compiler.compile_args()
--> 139 cmodule.GCC_compiler.compile_str(dirname, code, location=loc, preargs=args)
    140 # Save version into the __init__.py file.

~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
   2555 # difficult to read.
-> 2556 raise Exception(
   2557 "Compilation failed (return status=%s): %s"

Exception: Compilation failed (return status=1): In file included from /Users/hgu/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.5-64/lazylinker_ext/mod.cpp:1:. In file included from /Users/hgu/opt/anaconda3/include/python3.8/Python.h:25:. /Users/hgu/opt/anaconda3/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found. #include_next <stdio.h>. ^ ~~~~~~~~. 1 error generated.. 

During handling of the above exception, another exception occurred:

AttributeError Traceback (most recent call last)
<ipython-input-4-e2d3ee711e72> in <module>
----> 1 import theano

~/opt/anaconda3/lib/python3.8/site-packages/theano/ __init__.py in <module>
     76 __api_version__ = 1
     77 
---> 78 from theano import scalar, tensor
     79 from theano.compile import (
     80 In,

~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/ __init__.py in <module>
----> 1 from .basic import *
      2 from .basic_scipy import *

~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/basic.py in <module>
     22 
     23 import theano
---> 24 from theano import config, gof, printing
     25 from theano.gof import Apply, Constant, FunctionGraph, Op, Type, Variable, utils
     26 from theano.gradient import DisconnectedType, grad_undefined

~/opt/anaconda3/lib/python3.8/site-packages/theano/printing.py in <module>
     17 import theano
     18 from theano import config, gof
---> 19 from theano.compile import Function, SharedVariable, debugmode
     20 from theano.gof import Apply, Op
     21 

~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/ __init__.py in <module>
----> 1 from theano.compile.debugmode import DebugMode
      2 from theano.compile.function.pfunc import Param, pfunc, rebuild_collect_shared
      3 from theano.compile.function.types import (
      4 AliasedMemoryError,
      5 Function,

~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/debugmode.py in <module>
     25 std_fgraph,
     26 )
---> 27 from theano.compile.mode import Mode, register_mode
     28 from theano.compile.ops import OutputGuard, _output_guard
     29 from theano.gof import graph, link, ops_with_inner_function, utils

~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/mode.py in <module>
      8 
      9 import theano
---> 10 import theano.gof.vm
     11 from theano import config, gof
     12 from theano.compile.function.types import Supervisor

~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/vm.py in <module>
    705 except ImportError:
    706 pass
--> 707 except (OSError, theano.gof.cmodule.MissingGXX) as e:
    708 # OSError happens when g++ is not installed. In that case, we
    709 # already changed the default linker to something else then CVM.

AttributeError: partially initialized module 'theano' has no attribute 'gof' (most likely due to a circular import)

```

_when importing Pymc3_

```
You can find the C code in this temporary file: /var/folders/_c/frfzc_f54tbgbycvmnlj9v_w0000gn/T/theano_compilation_error_nlrt8_5r
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
     75 if version != actual_version:
---> 76 raise ImportError(
     77 "Version check of the existing lazylinker compiled file."

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:

ImportError Traceback (most recent call last)
~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
     98 if version != actual_version:
---> 99 raise ImportError(
    100 "Version check of the existing lazylinker compiled file."

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:

Exception Traceback (most recent call last)
<ipython-input-1-0668865beb19> in <module>
      1 import numpy as np
----> 2 import pymc3 as pm
      3 from scipy.interpolate import griddata, interp2d
      4 import theano.tensor as tt
      5 from matplotlib import pyplot as plt

~/opt/anaconda3/lib/python3.8/site-packages/pymc3/ __init__.py in <module>
     37 
     38 
---> 39 __set_compiler_flags()
     40 
     41 from . import gp, ode, sampling

~/opt/anaconda3/lib/python3.8/site-packages/pymc3/ __init__.py in __set_compiler_flags()
     31 def __set_compiler_flags():
     32 # Workarounds for Theano compiler problems on various platforms
---> 33 import theano
     34 
     35 current = theano.config.gcc.cxxflags

~/opt/anaconda3/lib/python3.8/site-packages/theano/ __init__.py in <module>
     76 __api_version__ = 1
     77 
---> 78 from theano import scalar, tensor
     79 from theano.compile import (
     80 In,

~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/ __init__.py in <module>
----> 1 from .basic import *
      2 from .basic_scipy import *

~/opt/anaconda3/lib/python3.8/site-packages/theano/scalar/basic.py in <module>
     22 
     23 import theano
---> 24 from theano import config, gof, printing
     25 from theano.gof import Apply, Constant, FunctionGraph, Op, Type, Variable, utils
     26 from theano.gradient import DisconnectedType, grad_undefined

~/opt/anaconda3/lib/python3.8/site-packages/theano/printing.py in <module>
     17 import theano
     18 from theano import config, gof
---> 19 from theano.compile import Function, SharedVariable, debugmode
     20 from theano.gof import Apply, Op
     21 

~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/ __init__.py in <module>
----> 1 from theano.compile.debugmode import DebugMode
      2 from theano.compile.function.pfunc import Param, pfunc, rebuild_collect_shared
      3 from theano.compile.function.types import (
      4 AliasedMemoryError,
      5 Function,

~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/debugmode.py in <module>
     25 std_fgraph,
     26 )
---> 27 from theano.compile.mode import Mode, register_mode
     28 from theano.compile.ops import OutputGuard, _output_guard
     29 from theano.gof import graph, link, ops_with_inner_function, utils

~/opt/anaconda3/lib/python3.8/site-packages/theano/compile/mode.py in <module>
      8 
      9 import theano
---> 10 import theano.gof.vm
     11 from theano import config, gof
     12 from theano.compile.function.types import Supervisor

~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/vm.py in <module>
    695 "lazylinker will not be imported if theano.config.cxx is not set."
    696 )
--> 697 from . import lazylinker_c
    698 
    699 class CVM(lazylinker_c.CLazyLinker, VM):

~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/lazylinker_c.py in <module>
    137 
    138 args = cmodule.GCC_compiler.compile_args()
--> 139 cmodule.GCC_compiler.compile_str(dirname, code, location=loc, preargs=args)
    140 # Save version into the __init__.py file.
    141 init_py = os.path.join(loc, " __init__.py")

~/opt/anaconda3/lib/python3.8/site-packages/theano/gof/cmodule.py in compile_str(module_name, src_code, location, include_dirs, lib_dirs, libs, preargs, py_module, hide_symbols)
   2554 # prints the exception, having '\n' in the text makes it more
   2555 # difficult to read.
-> 2556 raise Exception(
   2557 "Compilation failed (return status=%s): %s"
   2558 % (status, compile_stderr.replace("\n", ". "))

Exception: Compilation failed (return status=1): In file included from /Users/hgu/.theano/compiledir_macOS-10.16-x86_64-i386-64bit-i386-3.8.5-64/lazylinker_ext/mod.cpp:1:. In file included from /Users/hgu/opt/anaconda3/include/python3.8/Python.h:25:. /Users/hgu/opt/anaconda3/bin/../include/c++/v1/stdio.h:107:15: fatal error: 'stdio.h' file not found. #include_next <stdio.h>. ^ ~~~~~~~~. 1 error generated..
```

---

<div class="post-metadata">

**Author:** ![RichardJM](https://yyz2.discourse-cdn.com/flex036/user_avatar/discourse.pymc.io/richardjm/32/3274_2.png) [@RichardJM](https://discourse.pymc.io/u/RichardJM)\
**Post date:** [March 24, 2021, 8:01am UTC](https://discourse.pymc.io/t/pymc3-installation-issue/7068/2 "2021-03-24T08:01:47Z")

</div>

Hi, I had a similar set of error messages when trying to install PyMC3.

From my perspective, the problem was installing the packages with conda - for whatever reason I couldn’t get a working set of dependencies.

I ended up re-installing conda (just to ensure I removed any issues with previous versions on packages). Then, with a clean conda installation I installed PyMC with pip. Worked fine after that.