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python36Packages.scipy: segmentation fault when running tests #92458

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Description

@Enteee

Describe the bug
On current nixos-unstable Scipy fails to build with a segmentation fault during testing:

../cluster/tests/test_vq.py::TestKMean::test_kmeans2_init <- ../../nix/store/d00fds078va595ifakggj6srmky01jq2-python3.6-scipy-1.4.1/lib/python3.6/site-packages/scipy/cluster/tests/test_vq.py PASSED [  0%]
../cluster/tests/test_vq.py::TestKMean::test_krandinit <- ../../nix/store/d00fds078va595ifakggj6srmky01jq2-python3.6-scipy-1.4.1/lib/python3.6/site-packages/scipy/cluster/tests/test_vq.py Fatal Python error: Segmentation fault

Current thread 0x00007ffff7898f40 (most recent call first):
  File "/nix/store/d00fds078va595ifakggj6srmk/nix/store/ds7r5c4z1vzrm0jw7ay712zs59p64hf7-stdenv-linux/setup: line 1302:  9640 Segmentation fault      (core dumped) /nix/store/acwrn1di4lgiz80qxam9vk28b2mkr2py-python3-3.6.10/bin/python3.6 -c 'import scipy; scipy.test("fast", verbose=10)'
builder for '/nix/store/2sa0mm8g3rb2l4x4j4y2i7qihb2lbdpy-python3.6-scipy-1.4.1.drv' failed with exit code 139
cannot build derivation '/nix/store/0mxrinnvr4f43h17wpcfpfisc3kbqywk-python3-3.6.10-env.drv': 1 dependencies couldn't be built
error: build of '/nix/store/0mxrinnvr4f43h17wpcfpfisc3kbqywk-python3-3.6.10-env.drv' failed

To Reproduce
Steps to reproduce the behavior:

  1. save the following as shell.nix
{
  nixpkgs ?  import (builtins.fetchGit {
    url = "https://github.com/nixos/nixpkgs-channels/";

    #
    # Commit hash for nixos-unstable
    # `git ls-remote https://github.com/nixos/nixpkgs-channels nixos-unstable`
    name = "nixos-unstable-2020-07-06";
    ref = "refs/heads/nixos-unstable";
    rev = "dc80d7bc4a244120b3d766746c41c0d9c5f81dfa";

    #
    # Commit hash for nixos-20.03
    # `git ls-remote https://github.com/nixos/nixpkgs-channels nixos-20.03`
    #name = "nixos-20.03-2020-07-06";
    #ref = "refs/heads/nixos-20.03";
    #rev = "afa9ca61924f05aacfe495a7ad0fd84709d236cc";
  }) {}
}:

with nixpkgs;

let
  python = python36;
  python-with-base-packages = python.withPackages(ps: with ps; [
    # the following packages are related to the dependencies of your python
    # project.
    # In this particular example the python modules listed in the
    # requirements.txt require the following packages to be installed locally
    # in order to compile any binary extensions they may require.
    #

    scipy
  ]);

in mkShell {

  buildInputs = [
    python-with-base-packages
    python3Packages.venvShellHook
  ];

  shellHook = ''
    # set SOURCE_DATE_EPOCH so that we can use python wheels
    SOURCE_DATE_EPOCH=$(date +%s)
    venvShellHook
  '';
}
  1. run nix-shell

Expected behavior

Should not segfault during test.

Additional context
SciPY seems to build just fine on current 20.03 release.

Notify maintainers
cc @FRidh , @matthewbauer

Metadata

  • system: "x86_64-linux"
  • host os: Linux 5.4.46, NixOS, 20.09pre232692.7db146538e4 (Nightingale)
  • multi-user?: yes
  • sandbox: yes
  • version: nix-env (Nix) 2.3.6
  • channels(root): "home-manager, nixos-20.09pre233323.dc80d7bc4a2, nixos-hardware, nixpkgs-20.09pre233075.6e139365424"
  • channels(ente): ""
  • nixpkgs: /nix/var/nix/profiles/per-user/root/channels/nixos

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    0.kind: bugSomething is broken6.topic: pythonPython is a high-level, general-purpose programming language.

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