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pymc3 does not run under nixos #73051

@idontgetoutmuch

Description

@idontgetoutmuch

Describe the bug
import pymc3 as pm fails
To Reproduce

nix-shell --pure -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/19.09.tar.gz -p 'python37.withPackages(ps: with ps; [ numpy pymc3 ])'

[nix-shell:~]$ python
Python 3.7.4 (default, Jul  8 2019, 18:31:06) 
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pymc3 as pm

You can find the C code in this temporary file: /run/user/1000/theano_compilation_error_8381jg5y
Traceback (most recent call last):
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/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 "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/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 "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/pymc3/__init__.py", line 5, in <module>
    from .distributions import *
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/pymc3/distributions/__init__.py", line 1, in <module>
    from . import timeseries
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/pymc3/distributions/timeseries.py", line 1, in <module>
    import theano.tensor as tt
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/theano/__init__.py", line 110, in <module>
    from theano.compile import (
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/theano/compile/__init__.py", line 12, in <module>
    from theano.compile.mode import *
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/theano/compile/mode.py", line 11, in <module>
    import theano.gof.vm
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/theano/gof/vm.py", line 674, in <module>
    from . import lazylinker_c
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/theano/gof/lazylinker_c.py", line 140, in <module>
    preargs=args)
  File "/nix/store/d7wqg2xi972hahp9g7fwk7njsvv58pwi-python3-3.7.4-env/lib/python3.7/site-packages/theano/gof/cmodule.py", line 2396, in compile_str
    (status, compile_stderr.replace('\n', '. ')))
Exception: Compilation failed (return status=1): impure path `/run/user/1000/ccJEQmOq.o' used in link. collect2: error: ld returned 1 exit status. 

Expected behavior
The package should be imported and be available to use.

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Additional context
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Metadata
Please run nix run nixpkgs.nix-info -c nix-info -m and paste the result.

[sundials@CUDA:~]$ nix run nixpkgs.nix-info -c nix-info -m
 - system: `"x86_64-linux"`
 - host os: `Linux 4.19.69, NixOS, 19.09.git.latest0 (Loris)`
 - multi-user?: `yes`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.2.2`
 - nixpkgs: `/nix/var/nix/profiles/per-user/root/channels/nixos`

Maintainer information:

# a list of nixpkgs attributes affected by the problem
attribute:
# a list of nixos modules affected by the problem
module:

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