0s autopkgtest [13:29:17]: starting date and time: 2025-11-17 13:29:17+0000 0s autopkgtest [13:29:17]: git checkout: 4b346b80 nova: make wait_reboot return success even when a no-op 0s autopkgtest [13:29:17]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.kg_z9wzv/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults --apt-upgrade cyvcf2 --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=python3-defaults/3.13.7-2 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-1.secgroup --name adt-resolute-s390x-cyvcf2-20251117-121917-juju-7f2275-prod-proposed-migration-environment-15-f192bf51-6a71-4ca3-8027-962d8002c923 --image adt/ubuntu-resolute-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -e TERM=linux --mirror=http://ftpmaster.internal/ubuntu/ 3s Creating nova instance adt-resolute-s390x-cyvcf2-20251117-121917-juju-7f2275-prod-proposed-migration-environment-15-f192bf51-6a71-4ca3-8027-962d8002c923 from image adt/ubuntu-resolute-s390x-server-20251117.img (UUID a3a3e3b9-e6ba-478c-a5e9-fce6f0982a95)... 45s autopkgtest [13:30:02]: testbed dpkg architecture: s390x 45s autopkgtest [13:30:02]: testbed apt version: 3.1.11 46s autopkgtest [13:30:03]: @@@@@@@@@@@@@@@@@@@@ test bed setup 46s autopkgtest [13:30:03]: testbed release detected to be: None 46s autopkgtest [13:30:03]: updating testbed package index (apt update) 47s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 47s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 47s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 47s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 47s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 47s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 47s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB] 47s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB] 47s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [138 kB] 48s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 48s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [545 kB] 48s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [10.6 kB] 48s Fetched 1764 kB in 1s (1688 kB/s) 48s Reading package lists... 49s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 49s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 49s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 49s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 50s Reading package lists... 50s Reading package lists... 50s Building dependency tree... 50s Reading state information... 50s Calculating upgrade... 50s The following packages will be upgraded: 50s libpython3-stdlib python3 python3-minimal usbutils 50s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 50s Need to get 148 kB of archives. 50s After this operation, 4096 B disk space will be freed. 50s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.7-2 [27.8 kB] 50s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.7-2 [23.9 kB] 50s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.7-2 [10.6 kB] 50s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x usbutils s390x 1:019-1 [85.6 kB] 51s dpkg-preconfigure: unable to re-open stdin: No such file or directory 51s Fetched 148 kB in 0s (368 kB/s) 51s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61309 files and directories currently installed.) 51s Preparing to unpack .../python3-minimal_3.13.7-2_s390x.deb ... 51s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 51s Setting up python3-minimal (3.13.7-2) ... 51s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61309 files and directories currently installed.) 51s Preparing to unpack .../python3_3.13.7-2_s390x.deb ... 51s running python pre-rtupdate hooks for python3.13... 51s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 51s Preparing to unpack .../libpython3-stdlib_3.13.7-2_s390x.deb ... 51s Unpacking libpython3-stdlib:s390x (3.13.7-2) over (3.13.7-1) ... 51s Preparing to unpack .../usbutils_1%3a019-1_s390x.deb ... 51s Unpacking usbutils (1:019-1) over (1:018-2) ... 51s Setting up usbutils (1:019-1) ... 51s Setting up libpython3-stdlib:s390x (3.13.7-2) ... 51s Setting up python3 (3.13.7-2) ... 51s running python rtupdate hooks for python3.13... 51s running python post-rtupdate hooks for python3.13... 51s Processing triggers for man-db (2.13.1-1) ... 52s autopkgtest [13:30:09]: upgrading testbed (apt dist-upgrade and autopurge) 52s Reading package lists... 52s Building dependency tree... 52s Reading state information... 52s Calculating upgrade... 52s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 52s Reading package lists... 53s Building dependency tree... 53s Reading state information... 53s Solving dependencies... 53s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s autopkgtest [13:30:12]: testbed running kernel: Linux 6.17.0-5-generic #5-Ubuntu SMP Mon Sep 22 08:56:47 UTC 2025 55s autopkgtest [13:30:12]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 57s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.4-1 (dsc) [2498 B] 57s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.4-1 (tar) [421 kB] 57s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.4-1 (diff) [6836 B] 57s gpgv: Signature made Mon Nov 3 21:31:49 2025 UTC 57s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 57s gpgv: issuer "emollier@debian.org" 57s gpgv: Can't check signature: No public key 57s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.4-1.dsc: no acceptable signature found 57s autopkgtest [13:30:14]: testing package cyvcf2 version 0.31.4-1 58s autopkgtest [13:30:15]: build not needed 58s autopkgtest [13:30:15]: test run-unit-test: preparing testbed 59s Reading package lists... 59s Building dependency tree... 59s Reading state information... 59s Solving dependencies... 59s The following NEW packages will be installed: 59s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 59s libpython3.14-minimal libpython3.14-stdlib python3-all python3-click 59s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 59s python3-numpy python3-numpy-dev python3-pluggy python3-pytest python3.14 59s python3.14-minimal 59s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. 59s Need to get 17.2 MB of archives. 59s After this operation, 68.8 MB of additional disk space will be used. 59s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 59s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7 [254 kB] 59s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-7ubuntu1 [629 kB] 60s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7 [2983 kB] 60s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 60s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.0-4 [904 kB] 60s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.0-4 [2509 kB] 60s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 60s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 60s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x libhts3t64 s390x 1.22.1+ds2-1 [484 kB] 60s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.0-4 [2373 kB] 60s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.0-4 [805 kB] 60s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.13.7-2 [892 B] 60s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 60s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-humanfriendly all 10.0-6 [70.8 kB] 60s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-coloredlogs all 15.0.1-1 [38.2 kB] 60s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cyvcf2 s390x 0.31.4-1 [1105 kB] 60s Get:18 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-iniconfig all 2.1.0-1 [6840 B] 60s Get:19 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pluggy all 1.6.0-1 [21.0 kB] 60s Get:20 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-pytest all 8.3.5-2 [252 kB] 61s Fetched 17.2 MB in 1s (11.6 MB/s) 61s Selecting previously unselected package python3-numpy-dev:s390x. 61s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61309 files and directories currently installed.) 61s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 61s Unpacking python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 61s Selecting previously unselected package libblas3:s390x. 61s Preparing to unpack .../01-libblas3_3.12.1-7_s390x.deb ... 61s Unpacking libblas3:s390x (3.12.1-7) ... 61s Selecting previously unselected package libgfortran5:s390x. 61s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_s390x.deb ... 61s Unpacking libgfortran5:s390x (15.2.0-7ubuntu1) ... 61s Selecting previously unselected package liblapack3:s390x. 61s Preparing to unpack .../03-liblapack3_3.12.1-7_s390x.deb ... 61s Unpacking liblapack3:s390x (3.12.1-7) ... 61s Selecting previously unselected package python3-numpy. 61s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 61s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 61s Selecting previously unselected package libpython3.14-minimal:s390x. 61s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_s390x.deb ... 61s Unpacking libpython3.14-minimal:s390x (3.14.0-4) ... 61s Selecting previously unselected package python3.14-minimal. 61s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_s390x.deb ... 61s Unpacking python3.14-minimal (3.14.0-4) ... 61s Selecting previously unselected package libdeflate0:s390x. 61s Preparing to unpack .../07-libdeflate0_1.23-2_s390x.deb ... 61s Unpacking libdeflate0:s390x (1.23-2) ... 61s Selecting previously unselected package libhtscodecs2:s390x. 61s Preparing to unpack .../08-libhtscodecs2_1.6.1-2_s390x.deb ... 61s Unpacking libhtscodecs2:s390x (1.6.1-2) ... 61s Selecting previously unselected package libhts3t64:s390x. 61s Preparing to unpack .../09-libhts3t64_1.22.1+ds2-1_s390x.deb ... 61s Unpacking libhts3t64:s390x (1.22.1+ds2-1) ... 61s Selecting previously unselected package libpython3.14-stdlib:s390x. 61s Preparing to unpack .../10-libpython3.14-stdlib_3.14.0-4_s390x.deb ... 61s Unpacking libpython3.14-stdlib:s390x (3.14.0-4) ... 61s Selecting previously unselected package python3.14. 61s Preparing to unpack .../11-python3.14_3.14.0-4_s390x.deb ... 61s Unpacking python3.14 (3.14.0-4) ... 61s Selecting previously unselected package python3-all. 61s Preparing to unpack .../12-python3-all_3.13.7-2_s390x.deb ... 61s Unpacking python3-all (3.13.7-2) ... 61s Selecting previously unselected package python3-click. 61s Preparing to unpack .../13-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 61s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 61s Selecting previously unselected package python3-humanfriendly. 61s Preparing to unpack .../14-python3-humanfriendly_10.0-6_all.deb ... 61s Unpacking python3-humanfriendly (10.0-6) ... 61s Selecting previously unselected package python3-coloredlogs. 61s Preparing to unpack .../15-python3-coloredlogs_15.0.1-1_all.deb ... 61s Unpacking python3-coloredlogs (15.0.1-1) ... 61s Selecting previously unselected package python3-cyvcf2. 61s Preparing to unpack .../16-python3-cyvcf2_0.31.4-1_s390x.deb ... 61s Unpacking python3-cyvcf2 (0.31.4-1) ... 61s Selecting previously unselected package python3-iniconfig. 61s Preparing to unpack .../17-python3-iniconfig_2.1.0-1_all.deb ... 61s Unpacking python3-iniconfig (2.1.0-1) ... 61s Selecting previously unselected package python3-pluggy. 61s Preparing to unpack .../18-python3-pluggy_1.6.0-1_all.deb ... 61s Unpacking python3-pluggy (1.6.0-1) ... 61s Selecting previously unselected package python3-pytest. 61s Preparing to unpack .../19-python3-pytest_8.3.5-2_all.deb ... 61s Unpacking python3-pytest (8.3.5-2) ... 61s Setting up libhtscodecs2:s390x (1.6.1-2) ... 61s Setting up python3-iniconfig (2.1.0-1) ... 61s Setting up libpython3.14-minimal:s390x (3.14.0-4) ... 61s Setting up libdeflate0:s390x (1.23-2) ... 61s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 62s Setting up libblas3:s390x (3.12.1-7) ... 62s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 62s Setting up python3-humanfriendly (10.0-6) ... 62s /usr/lib/python3/dist-packages/humanfriendly/testing.py:546: SyntaxWarning: 'return' in a 'finally' block 62s return super(MockedProgram, self).__exit__(*args, **kw) 62s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 62s Setting up libgfortran5:s390x (15.2.0-7ubuntu1) ... 62s Setting up python3-pluggy (1.6.0-1) ... 62s Setting up libhts3t64:s390x (1.22.1+ds2-1) ... 62s Setting up python3-coloredlogs (15.0.1-1) ... 62s Setting up python3.14-minimal (3.14.0-4) ... 63s Setting up liblapack3:s390x (3.12.1-7) ... 63s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 63s Setting up libpython3.14-stdlib:s390x (3.14.0-4) ... 63s Setting up python3-pytest (8.3.5-2) ... 63s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 66s Setting up python3.14 (3.14.0-4) ... 66s Setting up python3-all (3.13.7-2) ... 66s Setting up python3-cyvcf2 (0.31.4-1) ... 66s Processing triggers for systemd (257.9-0ubuntu2) ... 66s Processing triggers for man-db (2.13.1-1) ... 67s Processing triggers for libc-bin (2.42-2ubuntu2) ... 68s autopkgtest [13:30:25]: test run-unit-test: [----------------------- 68s Testing with python3.14 in /tmp/autopkgtest.SF80Rc/autopkgtest_tmp: 68s ============================= test session starts ============================== 68s platform linux -- Python 3.14.0, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.14 68s cachedir: .pytest_cache 68s rootdir: /tmp/autopkgtest.SF80Rc/autopkgtest_tmp 68s plugins: typeguard-4.4.2 68s collecting ... collected 0 items / 4 errors 68s 68s ==================================== ERRORS ==================================== 68s __________________ ERROR collecting cyvcf2/tests/test_cli.py ___________________ 68s ImportError while importing test module '/tmp/autopkgtest.SF80Rc/autopkgtest_tmp/cyvcf2/tests/test_cli.py'. 68s Hint: make sure your test modules/packages have valid Python names. 68s Traceback: 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 68s from . import multiarray 68s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 68s from . import overrides 68s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 68s from numpy._core._multiarray_umath import ( 68s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 68s 68s During handling of the above exception, another exception occurred: 68s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 68s from numpy.__config__ import show_config 68s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 68s from numpy._core._multiarray_umath import ( 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 68s raise ImportError(msg) 68s E ImportError: 68s E 68s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 68s E 68s E Importing the numpy C-extensions failed. This error can happen for 68s E many reasons, often due to issues with your setup or how NumPy was 68s E installed. 68s E 68s E We have compiled some common reasons and troubleshooting tips at: 68s E 68s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 68s E 68s E Please note and check the following: 68s E 68s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 68s E * The NumPy version is: "2.2.4" 68s E 68s E and make sure that they are the versions you expect. 68s E Please carefully study the documentation linked above for further help. 68s E 68s E Original error was: No module named 'numpy._core._multiarray_umath' 68s 68s The above exception was the direct cause of the following exception: 68s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 68s return _bootstrap._gcd_import(name[level:], package, level) 68s cyvcf2/__init__.py:1: in 68s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 68s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 68s #cython: profile=False 68s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 68s raise ImportError(msg) from e 68s E ImportError: Error importing numpy: you should not try to import numpy from 68s E its source directory; please exit the numpy source tree, and relaunch 68s E your python interpreter from there. 68s __________________ ERROR collecting cyvcf2/tests/test_hemi.py __________________ 68s ImportError while importing test module '/tmp/autopkgtest.SF80Rc/autopkgtest_tmp/cyvcf2/tests/test_hemi.py'. 68s Hint: make sure your test modules/packages have valid Python names. 68s Traceback: 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 68s from . import multiarray 68s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 68s from . import overrides 68s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 68s from numpy._core._multiarray_umath import ( 68s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 68s 68s During handling of the above exception, another exception occurred: 68s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 68s from numpy.__config__ import show_config 68s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 68s from numpy._core._multiarray_umath import ( 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 68s raise ImportError(msg) 68s E ImportError: 68s E 68s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 68s E 68s E Importing the numpy C-extensions failed. This error can happen for 68s E many reasons, often due to issues with your setup or how NumPy was 68s E installed. 68s E 68s E We have compiled some common reasons and troubleshooting tips at: 68s E 68s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 68s E 68s E Please note and check the following: 68s E 68s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 68s E * The NumPy version is: "2.2.4" 68s E 68s E and make sure that they are the versions you expect. 68s E Please carefully study the documentation linked above for further help. 68s E 68s E Original error was: No module named 'numpy._core._multiarray_umath' 68s 68s The above exception was the direct cause of the following exception: 68s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 68s return _bootstrap._gcd_import(name[level:], package, level) 68s cyvcf2/__init__.py:1: in 68s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 68s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 68s #cython: profile=False 68s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 68s raise ImportError(msg) from e 68s E ImportError: Error importing numpy: you should not try to import numpy from 68s E its source directory; please exit the numpy source tree, and relaunch 68s E your python interpreter from there. 68s _________________ ERROR collecting cyvcf2/tests/test_reader.py _________________ 68s ImportError while importing test module '/tmp/autopkgtest.SF80Rc/autopkgtest_tmp/cyvcf2/tests/test_reader.py'. 68s Hint: make sure your test modules/packages have valid Python names. 68s Traceback: 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 68s from . import multiarray 68s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 68s from . import overrides 68s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 68s from numpy._core._multiarray_umath import ( 68s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 68s 68s During handling of the above exception, another exception occurred: 68s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 68s from numpy.__config__ import show_config 68s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 68s from numpy._core._multiarray_umath import ( 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 68s raise ImportError(msg) 68s E ImportError: 68s E 68s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 68s E 68s E Importing the numpy C-extensions failed. This error can happen for 68s E many reasons, often due to issues with your setup or how NumPy was 68s E installed. 68s E 68s E We have compiled some common reasons and troubleshooting tips at: 68s E 68s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 68s E 68s E Please note and check the following: 68s E 68s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 68s E * The NumPy version is: "2.2.4" 68s E 68s E and make sure that they are the versions you expect. 68s E Please carefully study the documentation linked above for further help. 68s E 68s E Original error was: No module named 'numpy._core._multiarray_umath' 68s 68s The above exception was the direct cause of the following exception: 68s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 68s return _bootstrap._gcd_import(name[level:], package, level) 68s cyvcf2/__init__.py:1: in 68s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 68s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 68s #cython: profile=False 68s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 68s raise ImportError(msg) from e 68s E ImportError: Error importing numpy: you should not try to import numpy from 68s E its source directory; please exit the numpy source tree, and relaunch 68s E your python interpreter from there. 68s _________________ ERROR collecting cyvcf2/tests/test_writer.py _________________ 68s ImportError while importing test module '/tmp/autopkgtest.SF80Rc/autopkgtest_tmp/cyvcf2/tests/test_writer.py'. 68s Hint: make sure your test modules/packages have valid Python names. 68s Traceback: 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 68s from . import multiarray 68s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 68s from . import overrides 68s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 68s from numpy._core._multiarray_umath import ( 68s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 68s 68s During handling of the above exception, another exception occurred: 68s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 68s from numpy.__config__ import show_config 68s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 68s from numpy._core._multiarray_umath import ( 68s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 68s raise ImportError(msg) 68s E ImportError: 68s E 68s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 68s E 68s E Importing the numpy C-extensions failed. This error can happen for 68s E many reasons, often due to issues with your setup or how NumPy was 68s E installed. 68s E 68s E We have compiled some common reasons and troubleshooting tips at: 68s E 68s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 68s E 68s E Please note and check the following: 68s E 68s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 68s E * The NumPy version is: "2.2.4" 68s E 68s E and make sure that they are the versions you expect. 68s E Please carefully study the documentation linked above for further help. 68s E 68s E Original error was: No module named 'numpy._core._multiarray_umath' 68s 68s The above exception was the direct cause of the following exception: 68s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 68s return _bootstrap._gcd_import(name[level:], package, level) 68s cyvcf2/__init__.py:1: in 68s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 68s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 68s #cython: profile=False 68s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 68s raise ImportError(msg) from e 68s E ImportError: Error importing numpy: you should not try to import numpy from 68s E its source directory; please exit the numpy source tree, and relaunch 68s E your python interpreter from there. 68s =========================== short test summary info ============================ 68s ERROR cyvcf2/tests/test_cli.py 68s ERROR cyvcf2/tests/test_hemi.py 68s ERROR cyvcf2/tests/test_reader.py 68s ERROR cyvcf2/tests/test_writer.py 68s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 68s ============================== 4 errors in 0.13s =============================== 69s autopkgtest [13:30:26]: test run-unit-test: -----------------------] 69s autopkgtest [13:30:26]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 69s run-unit-test FAIL non-zero exit status 2 69s autopkgtest [13:30:26]: test autodep8-python3: preparing testbed 90s Creating nova instance adt-resolute-s390x-cyvcf2-20251117-121917-juju-7f2275-prod-proposed-migration-environment-15-f192bf51-6a71-4ca3-8027-962d8002c923 from image adt/ubuntu-resolute-s390x-server-20251117.img (UUID a3a3e3b9-e6ba-478c-a5e9-fce6f0982a95)... 145s autopkgtest [13:31:42]: testbed dpkg architecture: s390x 145s autopkgtest [13:31:42]: testbed apt version: 3.1.11 145s autopkgtest [13:31:42]: @@@@@@@@@@@@@@@@@@@@ test bed setup 145s autopkgtest [13:31:42]: testbed release detected to be: resolute 146s autopkgtest [13:31:43]: updating testbed package index (apt update) 146s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 147s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 147s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 147s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 147s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB] 147s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB] 147s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 147s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 147s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x Packages [138 kB] 147s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted s390x Packages [940 B] 147s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe s390x Packages [545 kB] 148s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse s390x Packages [10.6 kB] 148s Fetched 1764 kB in 1s (1282 kB/s) 148s Reading package lists... 149s Hit:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease 149s Hit:2 http://ftpmaster.internal/ubuntu resolute InRelease 149s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 149s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 150s Reading package lists... 150s Reading package lists... 150s Building dependency tree... 150s Reading state information... 150s Calculating upgrade... 150s The following packages will be upgraded: 150s libpython3-stdlib python3 python3-minimal usbutils 150s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 150s Need to get 148 kB of archives. 150s After this operation, 4096 B disk space will be freed. 150s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-minimal s390x 3.13.7-2 [27.8 kB] 150s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3 s390x 3.13.7-2 [23.9 kB] 151s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x libpython3-stdlib s390x 3.13.7-2 [10.6 kB] 151s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x usbutils s390x 1:019-1 [85.6 kB] 151s dpkg-preconfigure: unable to re-open stdin: No such file or directory 151s Fetched 148 kB in 0s (347 kB/s) 151s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61309 files and directories currently installed.) 151s Preparing to unpack .../python3-minimal_3.13.7-2_s390x.deb ... 151s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 151s Setting up python3-minimal (3.13.7-2) ... 151s (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 61309 files and directories currently installed.) 151s Preparing to unpack .../python3_3.13.7-2_s390x.deb ... 151s running python pre-rtupdate hooks for python3.13... 151s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 151s Preparing to unpack .../libpython3-stdlib_3.13.7-2_s390x.deb ... 151s Unpacking libpython3-stdlib:s390x (3.13.7-2) over (3.13.7-1) ... 151s Preparing to unpack .../usbutils_1%3a019-1_s390x.deb ... 151s Unpacking usbutils (1:019-1) over (1:018-2) ... 151s Setting up usbutils (1:019-1) ... 151s Setting up libpython3-stdlib:s390x (3.13.7-2) ... 151s Setting up python3 (3.13.7-2) ... 151s running python rtupdate hooks for python3.13... 151s running python post-rtupdate hooks for python3.13... 151s Processing triggers for man-db (2.13.1-1) ... 152s autopkgtest [13:31:49]: upgrading testbed (apt dist-upgrade and autopurge) 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Calculating upgrade... 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 153s Solving dependencies... 153s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 156s Reading package lists... 156s Building dependency tree... 156s Reading state information... 156s Solving dependencies... 156s The following NEW packages will be installed: 156s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 156s libpython3.14-minimal libpython3.14-stdlib python3-all python3-click 156s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 156s python3-numpy-dev python3.14 python3.14-minimal 156s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 156s Need to get 16.9 MB of archives. 156s After this operation, 67.4 MB of additional disk space will be used. 156s Get:1 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy-dev s390x 1:2.2.4+ds-1ubuntu1 [147 kB] 157s Get:2 http://ftpmaster.internal/ubuntu resolute/main s390x libblas3 s390x 3.12.1-7 [254 kB] 157s Get:3 http://ftpmaster.internal/ubuntu resolute/main s390x libgfortran5 s390x 15.2.0-7ubuntu1 [629 kB] 157s Get:4 http://ftpmaster.internal/ubuntu resolute/main s390x liblapack3 s390x 3.12.1-7 [2983 kB] 158s Get:5 http://ftpmaster.internal/ubuntu resolute/main s390x python3-numpy s390x 1:2.2.4+ds-1ubuntu1 [4399 kB] 158s Get:6 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-minimal s390x 3.14.0-4 [904 kB] 159s Get:7 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14-minimal s390x 3.14.0-4 [2509 kB] 159s Get:8 http://ftpmaster.internal/ubuntu resolute/main s390x libdeflate0 s390x 1.23-2 [46.0 kB] 159s Get:9 http://ftpmaster.internal/ubuntu resolute/universe s390x libhtscodecs2 s390x 1.6.1-2 [91.0 kB] 159s Get:10 http://ftpmaster.internal/ubuntu resolute/universe s390x libhts3t64 s390x 1.22.1+ds2-1 [484 kB] 159s Get:11 http://ftpmaster.internal/ubuntu resolute/main s390x libpython3.14-stdlib s390x 3.14.0-4 [2373 kB] 159s Get:12 http://ftpmaster.internal/ubuntu resolute/main s390x python3.14 s390x 3.14.0-4 [805 kB] 159s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/main s390x python3-all s390x 3.13.7-2 [892 B] 159s Get:14 http://ftpmaster.internal/ubuntu resolute/main s390x python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 159s Get:15 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-humanfriendly all 10.0-6 [70.8 kB] 159s Get:16 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-coloredlogs all 15.0.1-1 [38.2 kB] 159s Get:17 http://ftpmaster.internal/ubuntu resolute/universe s390x python3-cyvcf2 s390x 0.31.4-1 [1105 kB] 159s Fetched 16.9 MB in 3s (5567 kB/s) 159s Selecting previously unselected package python3-numpy-dev:s390x. 159s (Reading database ... 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unpack .../02-libgfortran5_15.2.0-7ubuntu1_s390x.deb ... 159s Unpacking libgfortran5:s390x (15.2.0-7ubuntu1) ... 159s Selecting previously unselected package liblapack3:s390x. 159s Preparing to unpack .../03-liblapack3_3.12.1-7_s390x.deb ... 159s Unpacking liblapack3:s390x (3.12.1-7) ... 160s Selecting previously unselected package python3-numpy. 160s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_s390x.deb ... 160s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 160s Selecting previously unselected package libpython3.14-minimal:s390x. 160s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_s390x.deb ... 160s Unpacking libpython3.14-minimal:s390x (3.14.0-4) ... 160s Selecting previously unselected package python3.14-minimal. 160s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_s390x.deb ... 160s Unpacking python3.14-minimal (3.14.0-4) ... 160s Selecting previously unselected package libdeflate0:s390x. 160s Preparing to unpack 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Selecting previously unselected package python3-click. 160s Preparing to unpack .../13-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 160s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 160s Selecting previously unselected package python3-humanfriendly. 160s Preparing to unpack .../14-python3-humanfriendly_10.0-6_all.deb ... 160s Unpacking python3-humanfriendly (10.0-6) ... 160s Selecting previously unselected package python3-coloredlogs. 160s Preparing to unpack .../15-python3-coloredlogs_15.0.1-1_all.deb ... 160s Unpacking python3-coloredlogs (15.0.1-1) ... 160s Selecting previously unselected package python3-cyvcf2. 160s Preparing to unpack .../16-python3-cyvcf2_0.31.4-1_s390x.deb ... 160s Unpacking python3-cyvcf2 (0.31.4-1) ... 160s Setting up libhtscodecs2:s390x (1.6.1-2) ... 160s Setting up libpython3.14-minimal:s390x (3.14.0-4) ... 160s Setting up libdeflate0:s390x (1.23-2) ... 160s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 160s Setting up libblas3:s390x (3.12.1-7) ... 160s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 160s Setting up python3-humanfriendly (10.0-6) ... 160s /usr/lib/python3/dist-packages/humanfriendly/testing.py:546: SyntaxWarning: 'return' in a 'finally' block 160s return super(MockedProgram, self).__exit__(*args, **kw) 160s Setting up python3-numpy-dev:s390x (1:2.2.4+ds-1ubuntu1) ... 160s Setting up libgfortran5:s390x (15.2.0-7ubuntu1) ... 160s Setting up libhts3t64:s390x (1.22.1+ds2-1) ... 160s Setting up python3-coloredlogs (15.0.1-1) ... 161s Setting up python3.14-minimal (3.14.0-4) ... 161s Setting up liblapack3:s390x (3.12.1-7) ... 161s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 161s Setting up libpython3.14-stdlib:s390x (3.14.0-4) ... 161s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 164s Setting up python3.14 (3.14.0-4) ... 165s Setting up python3-all (3.13.7-2) ... 165s Setting up python3-cyvcf2 (0.31.4-1) ... 165s Processing triggers for systemd (257.9-0ubuntu2) ... 165s Processing triggers for man-db (2.13.1-1) ... 165s Processing triggers for libc-bin (2.42-2ubuntu2) ... 171s autopkgtest [13:32:08]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import cyvcf2; print(cyvcf2)" ; done 171s autopkgtest [13:32:08]: test autodep8-python3: [----------------------- 171s Testing with python3.14: 171s Traceback (most recent call last): 171s File "/usr/lib/python3/dist-packages/numpy/_core/__init__.py", line 23, in 171s from . import multiarray 171s File "/usr/lib/python3/dist-packages/numpy/_core/multiarray.py", line 10, in 171s from . import overrides 171s File "/usr/lib/python3/dist-packages/numpy/_core/overrides.py", line 7, in 171s from numpy._core._multiarray_umath import ( 171s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 171s ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 171s 171s During handling of the above exception, another exception occurred: 171s 171s Traceback (most recent call last): 171s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 114, in 171s from numpy.__config__ import show_config 171s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 171s from numpy._core._multiarray_umath import ( 171s ...<3 lines>... 171s ) 171s File "/usr/lib/python3/dist-packages/numpy/_core/__init__.py", line 49, in 171s raise ImportError(msg) 171s ImportError: 171s 171s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 171s 171s Importing the numpy C-extensions failed. This error can happen for 171s many reasons, often due to issues with your setup or how NumPy was 171s installed. 171s 171s We have compiled some common reasons and troubleshooting tips at: 171s 171s https://numpy.org/devdocs/user/troubleshooting-importerror.html 171s 171s Please note and check the following: 171s 171s * The Python version is: Python3.14 from "/usr/bin/python3.14" 171s * The NumPy version is: "2.2.4" 171s 171s and make sure that they are the versions you expect. 171s Please carefully study the documentation linked above for further help. 171s 171s Original error was: No module named 'numpy._core._multiarray_umath' 171s 171s 171s The above exception was the direct cause of the following exception: 171s 171s Traceback (most recent call last): 171s File "", line 1, in 171s import cyvcf2; print(cyvcf2) 171s ^^^^^^^^^^^^^ 171s File "/usr/lib/python3/dist-packages/cyvcf2/__init__.py", line 1, in 171s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 171s par_het) 171s File "cyvcf2/cyvcf2.pyx", line 1, in init cyvcf2.cyvcf2 171s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 119, in 171s raise ImportError(msg) from e 171s ImportError: Error importing numpy: you should not try to import numpy from 171s its source directory; please exit the numpy source tree, and relaunch 171s your python interpreter from there. 171s autopkgtest [13:32:08]: test autodep8-python3: -----------------------] 172s autodep8-python3 FAIL non-zero exit status 1 172s autopkgtest [13:32:09]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 172s autopkgtest [13:32:09]: @@@@@@@@@@@@@@@@@@@@ summary 172s run-unit-test FAIL non-zero exit status 2 172s autodep8-python3 FAIL non-zero exit status 1