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I've been using QGIS with the Semi-Automatic Classification plugin (SCP) at work, and am attempting to install and use it at home. Unfortunately, I am encountering an error which causes QGIS to crash when installing, disabling, or uninstalling SCP.

Upon opening QGIS 2.18.6, I get the following messages:

Semi-Automatic Classification Plugin: Please, restart QGIS for executing the Semi-Automatic Classification Plugin. Possible missing dependecies: SciPy

Semi-Automatic Classification Plugin: Please, restart QGIS for executing the Semi-Automatic Classification Plugin

From investigating the plugin's source, it looks like it is trying the following import before throwing the SciPy dependency exception:

import scipy.stats.distributions as statdistr

I tried the same import from the OSGeo4W Shell, and get the following traceback:

Taceback (most recen call last):
  File "<stdin>", line 1, in <module>
  File "C:\OSGEO4~1\apps\Python27\lib\site-packages\scipy\stats\__init__.py", line 334,
    in <module> from .stats import *
  File "C:\OSGEO4~1\apps\Python27\lib\site-packages\scipy\stats\stats.py", line 181,
    in <module> import scipy.special as special
  File "C:\OSGEO4~1\apps\Python27\lib\site-packages\scipy\special\__init__.py", line 546,
    in <module> from ._ufuncs import *

Additionally, doing a pip list does not display scipy but does display numpy and matplotlib, the other two dependencies for the plugin.

I've attempted to reinstall QGIS and supporting apps / libraries using the advanced and express installers, but run into the same problem each time I try to install SCP. The error also causes QGIS to crash and write a minidump on close. I'm also using Windows 10.


I am able to import scipy from the OSGeo4W Shell, but any module imports do not work, i.e. import scipy.stats or import scipy.linalg

How can I resolve this specific Scipy dependency issue within QGIS?

  • Welcome to GIS SE! As a new user be sure to take the Tour where you will see that there should be only one question asked per question under our focussed Q&A format. – PolyGeo Apr 8 '17 at 5:35
  • I thought I'd update with my solution for this issue, as it may help others in the future. I was able to resolve the Scipy dependency by forgoing the installation of Scipy through the OSGeo4W advanced installer, and instead installing it directly via Pip and a Scipy .whl. – Nick Apr 8 '17 at 18:18
  • I'll re-open your question do that you can provide that as a self-answer to your question. – PolyGeo Apr 8 '17 at 19:57
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Was able to resolve the issue by forgoing the installation of Scipy through the OSGeo4W advanced installer, and instead installing it directly via Pip (installed via OSGeo4W) and a Scipy .whl gotten from:

http://www.lfd.uci.edu/~gohlke/pythonlibs/

I grabbed:

numpy‑1.12.1+mkl‑cp27‑cp27m‑win_amd64.whl and scipy‑0.19.0‑cp27‑cp27m‑win_amd64.whl

Then used the OSGeo4W Shell to install directly:

pip install "C:\path\to\numpy‑1.12.1+mkl‑cp27‑cp27m‑win_amd64.whl"
pip install "C:\path\to\scipy‑0.19.0‑cp27‑cp27m‑win_amd64.whl"

I wanted to make sure that the Numpy installation was also correct because it is a dependency for Scipy, so that's the reason for installing both.

  • I had exactly the same problem yesterday after using the OSGeo4W installer. A couple of weeks ago the install worked fine with the OSGeo4W libraries, so I wonder if they've changed their packages recently. Either way, thank you for sharing your solution! – rudivonstaden Apr 10 '17 at 10:05
  • this worked for me on qgis2.18.13 – Elio Diaz Oct 3 '17 at 15:06

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