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0.kind: bugSomething is brokenSomething is broken6.topic: pythonPython is a high-level, general-purpose programming language.Python is a high-level, general-purpose programming language.
Description
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:
- 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
'';
}- 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 brokenSomething is broken6.topic: pythonPython is a high-level, general-purpose programming language.Python is a high-level, general-purpose programming language.