pandas: ValueError: numpy.dtype has the wrong size, try recompiling

I have been setting up a new CI server and I’m hitting a problem when running our tests on the new server - tests which use Pandas are giving this error:

File "/root/.virtualenvs/myproject/local/lib/python2.7/site-packages/pandas/__init__.py", line 7, in <module>
    from . import hashtable, tslib, lib
  File "pandas/src/numpy.pxd", line 157, in init pandas.lib (pandas/lib.c:78660)
ValueError: numpy.dtype has the wrong size, try recompiling

I have read other threads about the cause of this problem but they don’t seem to apply in my case.

We are running in a virtualenv, inside a Docker container (Debian Stretch).

There is no ‘system’ numpy, pandas or cython installed:

root@e00c968153d1:/# pip freeze | grep -i numpy
root@e00c968153d1:/# pip freeze | grep -i pandas
root@e00c968153d1:/# pip freeze | grep -i cython

In our requirements.txt we have:

numpy==1.9.1
pandas==0.15.2

but…

$ workon myproject
$ ipython
In [1]: import numpy
In [2]: numpy.version.full_version
Out[2]: '1.9.1'
In [3]: import pandas
numpy.dtype has the wrong size, try recompiling

Now, I have found a manual fix, which is to re-install pandas:

$ pip uninstall pandas
$ pip install --no-cache-dir pandas==0.15.2

The need for --no-cache-dir suggests something about the problem, but I don’t understand what exactly. I am installing in a ‘virgin’ docker container, there is no pip cache before I first install requirements.txt:

$ ls -l /root/.cache/pip/wheels
$ ls: cannot access /root/.cache/pip/wheels: No such file or directory

After pip install -r requirements.txt:

$ locate pandas
/root/.cache/pip/wheels/f7/7b/7c/6de5614135da1e25d864beec01ed40bb43fcafdeda870a05f6/pandas-0.15.2-cp27-none-linux_x86_64.whl
/root/.virtualenvs/myproject/lib/python2.7/site-packages/pandas
...
(only one installation of pandas found)

The manual fix is not acceptable as I need to automate the build.

Appreciate if you can suggest other avenues to explore towards a solution.