I am now able to reproduce the problem. It seems to be related with the 
presence of the topcom optional package. I am able to reproduce the issue 
with sage-8.7 + topcom + slabbe-0.5.1 and sage-8.8.rc2 + topcom + 
slabbe-0.5.1 :

$ ./sage -version
SageMath version 8.7, Release Date: 2019-03-23
$ ./sage -t ~/arXiv_1906_01104.rst 
Using --optional=cmake,dochtml,memlimit,mpir,python2,qhull,sage,topcom
Doctesting 1 file.
....
----------------------------------------------------------------------
sage -t /home/slabbe/arXiv_1906_01104.rst  # Timed out
----------------------------------------------------------------------
Total time for all tests: 304.2 seconds
    cpu time: 0.0 seconds
    cumulative wall time: 0.0 seconds

Do you know why and where topcom becomes automatically involved in my 
computations?

Is there an easy command to uninstall topcom?

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