Comments (6)
To be 100% clear, are you saying you booted a clean ubuntu 16 instance and it failed to build there? Or is this on an already customized machine?
from deepvariant.
It is customised. And Python 2.7 was installed using Anaconda.
from deepvariant.
To make it clearer, I put the path structure here.
/deepvariant/core/
cloud_utils_test.py
math.py
...
And in cloud_utils_test.py
:
"""Tests for deepvariant .core.cloud_utils."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import httplib
...
Through httplib
, it imports mimetools
, which imports tempfile
, which imports ramdom
, which imports math
.
But since there is a math.py
in the same path, it shadows the math
module in python's standard library, causing an error.
To test the hypothesis, simply importing httplib
in the same path caused the following error:
>>> import httplib
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "xx/anaconda/envs/Python27/lib/python2.7/httplib.py", line 80, in <module>
import mimetools
File "xx/anaconda/envs/Python27/lib/python2.7/mimetools.py", line 6, in <module>
import tempfile
File "xx/anaconda/envs/Python27/lib/python2.7/tempfile.py", line 35, in <module>
from random import Random as _Random
File "xx/anaconda/envs/Python27/lib/python2.7/random.py", line 45, in <module>
from math import log as _log, exp as _exp, pi as _pi, e as _e, ceil as _ceil
***File "math.py", line 79, in <module>***
import numpy as np
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/__init__.py", line 142, in <module>
from . import add_newdocs
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
from numpy.lib import add_newdoc
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
from .type_check import *
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
import numpy.core.numeric as _nx
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/core/__init__.py", line 74, in <module>
from numpy.testing.nosetester import _numpy_tester
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/testing/__init__.py", line 12, in <module>
from . import decorators as dec
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/testing/decorators.py", line 20, in <module>
from .utils import SkipTest, assert_warns
File "xx/anaconda/envs/Python27/lib/python2.7/site-packages/numpy/testing/utils.py", line 15, in <module>
from tempfile import mkdtemp, mkstemp
ImportError: cannot import name mkdtemp
>>>
As you can see, it attempts to load the local math.py
, shadowing the standard math
module.
On the other hand, cd to another path and import httplib
does not have any problem.
from deepvariant.
I agree this is a problem. We have an internal bug tracking this. Probably we will just rename deepvariant/core/math.py to core_math.py or equivalent. I'll update this bug when the change is in internally and it'll show up in the next push of deepvariant to github. Note you can workaround this issue just like https://github.com/notoraptor/deepvariant/commit/15c2deb211672a8ba32c1cbe609d81e1a2b0fb74
from deepvariant.
Many thanks for pointing me to the workaround! Looking forward to the next push!
from deepvariant.
A fix is in in google, renaming math.py to genomics_math.py, which should fix the problem. The next major push of functional changes to DeepVariant will include this update.
from deepvariant.
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from deepvariant.