Subject: Python modules installed by pip in virtualenv can't find shared objects.
From: Fis Trivial <[email-masked]>
To: "[email-masked]" <[email-masked]>
Date: Tue, 23 Jan 2018 11:49:59 +0000
List-Id: <debbugs-submit.debbugs.gnu.org>

When a python module needs to load a dynamic shared object, it looks in the
path provided by *LD_LIBRARY_PATH*(1), but guix doesn't modify this environment
variable to export the needed path for python.

* Backtrace
In my case, it's lightgbm (installed by pip), needs libgomp.so from gcc:lib for
openmp support. Here is the backtrace:

--8<---------------cut here---------------start------------->8---
Traceback (most recent call last):
  File "ex1.py", line 5, in <module>
    import lightgbm as lgb
  File "/home/fis/Workspace/tianchi/medical_treatment/lib/python3.5/site-packages/lightgbm/__init__.py", line 8, in <module>
    from .basic import Booster, Dataset
  File "/home/fis/Workspace/tianchi/medical_treatment/lib/python3.5/site-packages/lightgbm/basic.py", line 32, in <module>
    _LIB = _load_lib()
  File "/home/fis/Workspace/tianchi/medical_treatment/lib/python3.5/site-packages/lightgbm/basic.py", line 27, in _load_lib
    lib = ctypes.cdll.LoadLibrary(lib_path[0])
  File "/gnu/store/jb3n0bsdpkhvyb8y70jyr8fcx8fqssr9-python-3.5.3/lib/python3.5/ctypes/__init__.py", line 425, in LoadLibrary
    return self._dlltype(name)
  File "/gnu/store/jb3n0bsdpkhvyb8y70jyr8fcx8fqssr9-python-3.5.3/lib/python3.5/ctypes/__init__.py", line 347, in __init__
    self._handle = _dlopen(self._name, mode)
OSError: libgomp.so.1: cannot open shared object file: No such file or directory
--8<---------------cut here---------------end--------------->8---

* Reproduce
To install lightgbm, simply use `pip install lightgbm`(in virtualenv).
Then in python shell:
import lightgbm as lgb

* Ad-hoc
export LD_LIBRARY_PATH=~/.guix-profile/lib:$LD_LIBRARY_PATH

[1]: https://stackoverflow.com/a/1100016