0s autopkgtest [11:37:57]: starting date and time: 2025-11-17 11:37:57+0000 0s autopkgtest [11:37:57]: git checkout: 508d4a25 a-v-ssh wait_for_ssh: demote "ssh connection failed" to a debug message 0s autopkgtest [11:37:57]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.5ml8zhqe/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_proxy=127.0.0.1,127.0.1.1,localhost,localdomain,internal,login.ubuntu.com,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com,radosgw.ps5.canonical.com\n" >> /etc/environment' --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 -- lxd -r lxd-armhf-10.145.243.142 lxd-armhf-10.145.243.142:autopkgtest/ubuntu/resolute/armhf 22s autopkgtest [11:38:19]: testbed dpkg architecture: armhf 24s autopkgtest [11:38:21]: testbed apt version: 3.1.11 28s autopkgtest [11:38:25]: @@@@@@@@@@@@@@@@@@@@ test bed setup 30s autopkgtest [11:38:27]: testbed release detected to be: None 38s autopkgtest [11:38:35]: updating testbed package index (apt update) 39s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 40s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [87.8 kB] 40s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 40s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 40s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB] 40s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 40s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 40s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB] 40s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [138 kB] 40s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 40s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [536 kB] 40s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9684 B] 40s Get:13 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 41s Get:14 http://ftpmaster.internal/ubuntu resolute/main Sources [1416 kB] 41s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1369 kB] 42s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.2 MB] 45s Fetched 41.1 MB in 6s (7214 kB/s) 46s Reading package lists... 52s autopkgtest [11:38:49]: upgrading testbed (apt dist-upgrade and autopurge) 54s Reading package lists... 54s Building dependency tree... 54s Reading state information... 54s Calculating upgrade... 55s The following packages will be upgraded: 55s libpython3-stdlib python3 python3-minimal usbutils 55s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 55s Need to get 140 kB of archives. 55s After this operation, 0 B of additional disk space will be used. 55s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.13.7-2 [27.8 kB] 55s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.13.7-2 [23.9 kB] 55s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.13.7-2 [10.6 kB] 55s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf usbutils armhf 1:019-1 [77.7 kB] 56s Fetched 140 kB in 0s (387 kB/s) 56s (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 ... 65904 files and directories currently installed.) 56s Preparing to unpack .../python3-minimal_3.13.7-2_armhf.deb ... 56s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 56s Setting up python3-minimal (3.13.7-2) ... 57s (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 ... 65904 files and directories currently installed.) 57s Preparing to unpack .../python3_3.13.7-2_armhf.deb ... 57s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 57s Preparing to unpack .../libpython3-stdlib_3.13.7-2_armhf.deb ... 57s Unpacking libpython3-stdlib:armhf (3.13.7-2) over (3.13.7-1) ... 57s Preparing to unpack .../usbutils_1%3a019-1_armhf.deb ... 57s Unpacking usbutils (1:019-1) over (1:018-2) ... 57s Setting up usbutils (1:019-1) ... 57s Setting up libpython3-stdlib:armhf (3.13.7-2) ... 57s Setting up python3 (3.13.7-2) ... 57s Processing triggers for man-db (2.13.1-1) ... 60s Reading package lists... 61s Building dependency tree... 61s Reading state information... 61s Solving dependencies... 62s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 63s autopkgtest [11:39:00]: rebooting testbed after setup commands that affected boot 106s autopkgtest [11:39:43]: testbed running kernel: Linux 6.8.0-86-generic #87~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 29 09:26:46 UTC 2 131s autopkgtest [11:40:08]: @@@@@@@@@@@@@@@@@@@@ apt-source cyvcf2 143s Get:1 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.4-1 (dsc) [2498 B] 143s Get:2 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.4-1 (tar) [421 kB] 143s Get:3 http://ftpmaster.internal/ubuntu resolute/universe cyvcf2 0.31.4-1 (diff) [6836 B] 143s gpgv: Signature made Mon Nov 3 21:31:49 2025 UTC 143s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 143s gpgv: issuer "emollier@debian.org" 143s gpgv: Can't check signature: No public key 143s dpkg-source: warning: cannot verify inline signature for ./cyvcf2_0.31.4-1.dsc: no acceptable signature found 143s autopkgtest [11:40:20]: testing package cyvcf2 version 0.31.4-1 146s autopkgtest [11:40:23]: build not needed 149s autopkgtest [11:40:26]: test run-unit-test: preparing testbed 151s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s Solving dependencies... 152s The following NEW packages will be installed: 152s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 152s libpython3.14-minimal libpython3.14-stdlib python3-all python3-click 152s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-iniconfig 152s python3-numpy python3-numpy-dev python3-pluggy python3-pytest python3.14 152s python3.14-minimal 152s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. 152s Need to get 14.6 MB of archives. 152s After this operation, 55.9 MB of additional disk space will be used. 152s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 152s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7 [133 kB] 152s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-7ubuntu1 [334 kB] 152s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7 [2091 kB] 153s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 153s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.0-4 [892 kB] 153s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.0-4 [2146 kB] 153s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 153s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 153s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 153s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.0-4 [2270 kB] 153s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.0-4 [805 kB] 153s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all armhf 3.13.7-2 [890 B] 153s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 153s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-humanfriendly all 10.0-6 [70.8 kB] 153s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 153s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-cyvcf2 armhf 0.31.4-1 [1060 kB] 153s Get:18 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-iniconfig all 2.1.0-1 [6840 B] 153s Get:19 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pluggy all 1.6.0-1 [21.0 kB] 153s Get:20 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-pytest all 8.3.5-2 [252 kB] 154s Fetched 14.6 MB in 1s (13.7 MB/s) 154s Selecting previously unselected package python3-numpy-dev:armhf. 154s (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 ... 65904 files and directories currently installed.) 154s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 154s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 154s Selecting previously unselected package libblas3:armhf. 154s Preparing to unpack .../01-libblas3_3.12.1-7_armhf.deb ... 154s Unpacking libblas3:armhf (3.12.1-7) ... 154s Selecting previously unselected package libgfortran5:armhf. 154s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_armhf.deb ... 154s Unpacking libgfortran5:armhf (15.2.0-7ubuntu1) ... 154s Selecting previously unselected package liblapack3:armhf. 154s Preparing to unpack .../03-liblapack3_3.12.1-7_armhf.deb ... 154s Unpacking liblapack3:armhf (3.12.1-7) ... 154s Selecting previously unselected package python3-numpy. 154s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 154s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 154s Selecting previously unselected package libpython3.14-minimal:armhf. 154s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_armhf.deb ... 154s Unpacking libpython3.14-minimal:armhf (3.14.0-4) ... 155s Selecting previously unselected package python3.14-minimal. 155s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_armhf.deb ... 155s Unpacking python3.14-minimal (3.14.0-4) ... 155s Selecting previously unselected package libdeflate0:armhf. 155s Preparing to unpack .../07-libdeflate0_1.23-2_armhf.deb ... 155s Unpacking libdeflate0:armhf (1.23-2) ... 155s Selecting previously unselected package libhtscodecs2:armhf. 155s Preparing to unpack .../08-libhtscodecs2_1.6.1-2_armhf.deb ... 155s Unpacking libhtscodecs2:armhf (1.6.1-2) ... 155s Selecting previously unselected package libhts3t64:armhf. 155s Preparing to unpack .../09-libhts3t64_1.22.1+ds2-1_armhf.deb ... 155s Unpacking libhts3t64:armhf (1.22.1+ds2-1) ... 155s Selecting previously unselected package libpython3.14-stdlib:armhf. 155s Preparing to unpack .../10-libpython3.14-stdlib_3.14.0-4_armhf.deb ... 155s Unpacking libpython3.14-stdlib:armhf (3.14.0-4) ... 155s Selecting previously unselected package python3.14. 155s Preparing to unpack .../11-python3.14_3.14.0-4_armhf.deb ... 155s Unpacking python3.14 (3.14.0-4) ... 155s Selecting previously unselected package python3-all. 155s Preparing to unpack .../12-python3-all_3.13.7-2_armhf.deb ... 155s Unpacking python3-all (3.13.7-2) ... 155s Selecting previously unselected package python3-click. 155s Preparing to unpack .../13-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 155s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 155s Selecting previously unselected package python3-humanfriendly. 155s Preparing to unpack .../14-python3-humanfriendly_10.0-6_all.deb ... 155s Unpacking python3-humanfriendly (10.0-6) ... 155s Selecting previously unselected package python3-coloredlogs. 155s Preparing to unpack .../15-python3-coloredlogs_15.0.1-1_all.deb ... 155s Unpacking python3-coloredlogs (15.0.1-1) ... 155s Selecting previously unselected package python3-cyvcf2. 155s Preparing to unpack .../16-python3-cyvcf2_0.31.4-1_armhf.deb ... 155s Unpacking python3-cyvcf2 (0.31.4-1) ... 155s Selecting previously unselected package python3-iniconfig. 156s Preparing to unpack .../17-python3-iniconfig_2.1.0-1_all.deb ... 156s Unpacking python3-iniconfig (2.1.0-1) ... 156s Selecting previously unselected package python3-pluggy. 156s Preparing to unpack .../18-python3-pluggy_1.6.0-1_all.deb ... 156s Unpacking python3-pluggy (1.6.0-1) ... 156s Selecting previously unselected package python3-pytest. 156s Preparing to unpack .../19-python3-pytest_8.3.5-2_all.deb ... 156s Unpacking python3-pytest (8.3.5-2) ... 156s Setting up libhtscodecs2:armhf (1.6.1-2) ... 156s Setting up python3-iniconfig (2.1.0-1) ... 156s Setting up libpython3.14-minimal:armhf (3.14.0-4) ... 156s Setting up libdeflate0:armhf (1.23-2) ... 156s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 157s Setting up libblas3:armhf (3.12.1-7) ... 157s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 157s Setting up python3-humanfriendly (10.0-6) ... 157s /usr/lib/python3/dist-packages/humanfriendly/testing.py:546: SyntaxWarning: 'return' in a 'finally' block 157s return super(MockedProgram, self).__exit__(*args, **kw) 157s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 157s Setting up libgfortran5:armhf (15.2.0-7ubuntu1) ... 157s Setting up python3-pluggy (1.6.0-1) ... 157s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 157s Setting up python3-coloredlogs (15.0.1-1) ... 158s Setting up python3.14-minimal (3.14.0-4) ... 159s Setting up liblapack3:armhf (3.12.1-7) ... 159s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 159s Setting up libpython3.14-stdlib:armhf (3.14.0-4) ... 159s Setting up python3-pytest (8.3.5-2) ... 160s 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) ... 166s Processing triggers for systemd (257.9-0ubuntu2) ... 166s Processing triggers for man-db (2.13.1-1) ... 166s Processing triggers for libc-bin (2.42-2ubuntu2) ... 174s autopkgtest [11:40:51]: test run-unit-test: [----------------------- 177s Testing with python3.14 in /tmp/autopkgtest.7jK0tp/autopkgtest_tmp: 177s ============================= test session starts ============================== 177s platform linux -- Python 3.14.0, pytest-8.3.5, pluggy-1.6.0 -- /usr/bin/python3.14 177s cachedir: .pytest_cache 177s rootdir: /tmp/autopkgtest.7jK0tp/autopkgtest_tmp 177s plugins: typeguard-4.4.2 178s collecting ... collected 0 items / 4 errors 178s 178s ==================================== ERRORS ==================================== 178s __________________ ERROR collecting cyvcf2/tests/test_cli.py ___________________ 178s ImportError while importing test module '/tmp/autopkgtest.7jK0tp/autopkgtest_tmp/cyvcf2/tests/test_cli.py'. 178s Hint: make sure your test modules/packages have valid Python names. 178s Traceback: 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 178s from . import multiarray 178s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 178s from . import overrides 178s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 178s from numpy._core._multiarray_umath import ( 178s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 178s 178s During handling of the above exception, another exception occurred: 178s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 178s from numpy.__config__ import show_config 178s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 178s from numpy._core._multiarray_umath import ( 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 178s raise ImportError(msg) 178s E ImportError: 178s E 178s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 178s E 178s E Importing the numpy C-extensions failed. This error can happen for 178s E many reasons, often due to issues with your setup or how NumPy was 178s E installed. 178s E 178s E We have compiled some common reasons and troubleshooting tips at: 178s E 178s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 178s E 178s E Please note and check the following: 178s E 178s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 178s E * The NumPy version is: "2.2.4" 178s E 178s E and make sure that they are the versions you expect. 178s E Please carefully study the documentation linked above for further help. 178s E 178s E Original error was: No module named 'numpy._core._multiarray_umath' 178s 178s The above exception was the direct cause of the following exception: 178s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 178s return _bootstrap._gcd_import(name[level:], package, level) 178s cyvcf2/__init__.py:1: in 178s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 178s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 178s #cython: profile=False 178s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 178s raise ImportError(msg) from e 178s E ImportError: Error importing numpy: you should not try to import numpy from 178s E its source directory; please exit the numpy source tree, and relaunch 178s E your python interpreter from there. 178s __________________ ERROR collecting cyvcf2/tests/test_hemi.py __________________ 178s ImportError while importing test module '/tmp/autopkgtest.7jK0tp/autopkgtest_tmp/cyvcf2/tests/test_hemi.py'. 178s Hint: make sure your test modules/packages have valid Python names. 178s Traceback: 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 178s from . import multiarray 178s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 178s from . import overrides 178s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 178s from numpy._core._multiarray_umath import ( 178s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 178s 178s During handling of the above exception, another exception occurred: 178s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 178s from numpy.__config__ import show_config 178s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 178s from numpy._core._multiarray_umath import ( 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 178s raise ImportError(msg) 178s E ImportError: 178s E 178s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 178s E 178s E Importing the numpy C-extensions failed. This error can happen for 178s E many reasons, often due to issues with your setup or how NumPy was 178s E installed. 178s E 178s E We have compiled some common reasons and troubleshooting tips at: 178s E 178s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 178s E 178s E Please note and check the following: 178s E 178s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 178s E * The NumPy version is: "2.2.4" 178s E 178s E and make sure that they are the versions you expect. 178s E Please carefully study the documentation linked above for further help. 178s E 178s E Original error was: No module named 'numpy._core._multiarray_umath' 178s 178s The above exception was the direct cause of the following exception: 178s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 178s return _bootstrap._gcd_import(name[level:], package, level) 178s cyvcf2/__init__.py:1: in 178s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 178s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 178s #cython: profile=False 178s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 178s raise ImportError(msg) from e 178s E ImportError: Error importing numpy: you should not try to import numpy from 178s E its source directory; please exit the numpy source tree, and relaunch 178s E your python interpreter from there. 178s _________________ ERROR collecting cyvcf2/tests/test_reader.py _________________ 178s ImportError while importing test module '/tmp/autopkgtest.7jK0tp/autopkgtest_tmp/cyvcf2/tests/test_reader.py'. 178s Hint: make sure your test modules/packages have valid Python names. 178s Traceback: 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 178s from . import multiarray 178s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 178s from . import overrides 178s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 178s from numpy._core._multiarray_umath import ( 178s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 178s 178s During handling of the above exception, another exception occurred: 178s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 178s from numpy.__config__ import show_config 178s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 178s from numpy._core._multiarray_umath import ( 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 178s raise ImportError(msg) 178s E ImportError: 178s E 178s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 178s E 178s E Importing the numpy C-extensions failed. This error can happen for 178s E many reasons, often due to issues with your setup or how NumPy was 178s E installed. 178s E 178s E We have compiled some common reasons and troubleshooting tips at: 178s E 178s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 178s E 178s E Please note and check the following: 178s E 178s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 178s E * The NumPy version is: "2.2.4" 178s E 178s E and make sure that they are the versions you expect. 178s E Please carefully study the documentation linked above for further help. 178s E 178s E Original error was: No module named 'numpy._core._multiarray_umath' 178s 178s The above exception was the direct cause of the following exception: 178s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 178s return _bootstrap._gcd_import(name[level:], package, level) 178s cyvcf2/__init__.py:1: in 178s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 178s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 178s #cython: profile=False 178s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 178s raise ImportError(msg) from e 178s E ImportError: Error importing numpy: you should not try to import numpy from 178s E its source directory; please exit the numpy source tree, and relaunch 178s E your python interpreter from there. 178s _________________ ERROR collecting cyvcf2/tests/test_writer.py _________________ 178s ImportError while importing test module '/tmp/autopkgtest.7jK0tp/autopkgtest_tmp/cyvcf2/tests/test_writer.py'. 178s Hint: make sure your test modules/packages have valid Python names. 178s Traceback: 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:23: in 178s from . import multiarray 178s /usr/lib/python3/dist-packages/numpy/_core/multiarray.py:10: in 178s from . import overrides 178s /usr/lib/python3/dist-packages/numpy/_core/overrides.py:7: in 178s from numpy._core._multiarray_umath import ( 178s E ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 178s 178s During handling of the above exception, another exception occurred: 178s /usr/lib/python3/dist-packages/numpy/__init__.py:114: in 178s from numpy.__config__ import show_config 178s /usr/lib/python3/dist-packages/numpy/__config__.py:4: in 178s from numpy._core._multiarray_umath import ( 178s /usr/lib/python3/dist-packages/numpy/_core/__init__.py:49: in 178s raise ImportError(msg) 178s E ImportError: 178s E 178s E IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 178s E 178s E Importing the numpy C-extensions failed. This error can happen for 178s E many reasons, often due to issues with your setup or how NumPy was 178s E installed. 178s E 178s E We have compiled some common reasons and troubleshooting tips at: 178s E 178s E https://numpy.org/devdocs/user/troubleshooting-importerror.html 178s E 178s E Please note and check the following: 178s E 178s E * The Python version is: Python3.14 from "/usr/bin/python3.14" 178s E * The NumPy version is: "2.2.4" 178s E 178s E and make sure that they are the versions you expect. 178s E Please carefully study the documentation linked above for further help. 178s E 178s E Original error was: No module named 'numpy._core._multiarray_umath' 178s 178s The above exception was the direct cause of the following exception: 178s /usr/lib/python3.14/importlib/__init__.py:88: in import_module 178s return _bootstrap._gcd_import(name[level:], package, level) 178s cyvcf2/__init__.py:1: in 178s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 178s cyvcf2/cyvcf2.pyx:1: in init cyvcf2.cyvcf2 178s #cython: profile=False 178s /usr/lib/python3/dist-packages/numpy/__init__.py:119: in 178s raise ImportError(msg) from e 178s E ImportError: Error importing numpy: you should not try to import numpy from 178s E its source directory; please exit the numpy source tree, and relaunch 178s E your python interpreter from there. 178s =========================== short test summary info ============================ 178s ERROR cyvcf2/tests/test_cli.py 178s ERROR cyvcf2/tests/test_hemi.py 178s ERROR cyvcf2/tests/test_reader.py 178s ERROR cyvcf2/tests/test_writer.py 178s !!!!!!!!!!!!!!!!!!! Interrupted: 4 errors during collection !!!!!!!!!!!!!!!!!!!! 178s ============================== 4 errors in 0.38s =============================== 178s autopkgtest [11:40:55]: test run-unit-test: -----------------------] 182s run-unit-test FAIL non-zero exit status 2 182s autopkgtest [11:40:59]: test run-unit-test: - - - - - - - - - - results - - - - - - - - - - 186s autopkgtest [11:41:03]: test autodep8-python3: preparing testbed 209s autopkgtest [11:41:26]: testbed dpkg architecture: armhf 211s autopkgtest [11:41:28]: testbed apt version: 3.1.11 215s autopkgtest [11:41:32]: @@@@@@@@@@@@@@@@@@@@ test bed setup 216s autopkgtest [11:41:33]: testbed release detected to be: resolute 224s autopkgtest [11:41:41]: updating testbed package index (apt update) 226s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed InRelease [87.8 kB] 227s Get:2 http://ftpmaster.internal/ubuntu resolute InRelease [87.8 kB] 227s Hit:3 http://ftpmaster.internal/ubuntu resolute-updates InRelease 227s Hit:4 http://ftpmaster.internal/ubuntu resolute-security InRelease 227s Get:5 http://ftpmaster.internal/ubuntu resolute-proposed/universe Sources [868 kB] 227s Get:6 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse Sources [22.9 kB] 227s Get:7 http://ftpmaster.internal/ubuntu resolute-proposed/main Sources [81.1 kB] 227s Get:8 http://ftpmaster.internal/ubuntu resolute-proposed/restricted Sources [9848 B] 227s Get:9 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf Packages [138 kB] 227s Get:10 http://ftpmaster.internal/ubuntu resolute-proposed/restricted armhf Packages [940 B] 227s Get:11 http://ftpmaster.internal/ubuntu resolute-proposed/universe armhf Packages [536 kB] 228s Get:12 http://ftpmaster.internal/ubuntu resolute-proposed/multiverse armhf Packages [9684 B] 228s Get:13 http://ftpmaster.internal/ubuntu resolute/main Sources [1416 kB] 228s Get:14 http://ftpmaster.internal/ubuntu resolute/universe Sources [21.3 MB] 230s Get:15 http://ftpmaster.internal/ubuntu resolute/main armhf Packages [1369 kB] 230s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf Packages [15.2 MB] 234s Fetched 41.1 MB in 7s (5572 kB/s) 235s Reading package lists... 240s autopkgtest [11:41:57]: upgrading testbed (apt dist-upgrade and autopurge) 242s Reading package lists... 242s Building dependency tree... 242s Reading state information... 243s Calculating upgrade... 243s The following packages will be upgraded: 243s libpython3-stdlib python3 python3-minimal usbutils 243s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 243s Need to get 140 kB of archives. 243s After this operation, 0 B of additional disk space will be used. 243s Get:1 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-minimal armhf 3.13.7-2 [27.8 kB] 244s Get:2 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3 armhf 3.13.7-2 [23.9 kB] 244s Get:3 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf libpython3-stdlib armhf 3.13.7-2 [10.6 kB] 244s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf usbutils armhf 1:019-1 [77.7 kB] 244s Fetched 140 kB in 0s (362 kB/s) 244s (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 ... 65904 files and directories currently installed.) 244s Preparing to unpack .../python3-minimal_3.13.7-2_armhf.deb ... 244s Unpacking python3-minimal (3.13.7-2) over (3.13.7-1) ... 244s Setting up python3-minimal (3.13.7-2) ... 245s (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 ... 65904 files and directories currently installed.) 245s Preparing to unpack .../python3_3.13.7-2_armhf.deb ... 245s Unpacking python3 (3.13.7-2) over (3.13.7-1) ... 245s Preparing to unpack .../libpython3-stdlib_3.13.7-2_armhf.deb ... 245s Unpacking libpython3-stdlib:armhf (3.13.7-2) over (3.13.7-1) ... 245s Preparing to unpack .../usbutils_1%3a019-1_armhf.deb ... 245s Unpacking usbutils (1:019-1) over (1:018-2) ... 245s Setting up usbutils (1:019-1) ... 245s Setting up libpython3-stdlib:armhf (3.13.7-2) ... 245s Setting up python3 (3.13.7-2) ... 245s Processing triggers for man-db (2.13.1-1) ... 248s Reading package lists... 248s Building dependency tree... 248s Reading state information... 248s Solving dependencies... 249s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 251s autopkgtest [11:42:08]: rebooting testbed after setup commands that affected boot 317s Reading package lists... 318s Building dependency tree... 318s Reading state information... 318s Solving dependencies... 318s The following NEW packages will be installed: 318s libblas3 libdeflate0 libgfortran5 libhts3t64 libhtscodecs2 liblapack3 318s libpython3.14-minimal libpython3.14-stdlib python3-all python3-click 318s python3-coloredlogs python3-cyvcf2 python3-humanfriendly python3-numpy 318s python3-numpy-dev python3.14 python3.14-minimal 319s 0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded. 319s Need to get 14.3 MB of archives. 319s After this operation, 54.5 MB of additional disk space will be used. 319s Get:1 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy-dev armhf 1:2.2.4+ds-1ubuntu1 [141 kB] 319s Get:2 http://ftpmaster.internal/ubuntu resolute/main armhf libblas3 armhf 3.12.1-7 [133 kB] 319s Get:3 http://ftpmaster.internal/ubuntu resolute/main armhf libgfortran5 armhf 15.2.0-7ubuntu1 [334 kB] 319s Get:4 http://ftpmaster.internal/ubuntu resolute/main armhf liblapack3 armhf 3.12.1-7 [2091 kB] 319s Get:5 http://ftpmaster.internal/ubuntu resolute/main armhf python3-numpy armhf 1:2.2.4+ds-1ubuntu1 [3724 kB] 319s Get:6 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-minimal armhf 3.14.0-4 [892 kB] 319s Get:7 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14-minimal armhf 3.14.0-4 [2146 kB] 319s Get:8 http://ftpmaster.internal/ubuntu resolute/main armhf libdeflate0 armhf 1.23-2 [38.7 kB] 319s Get:9 http://ftpmaster.internal/ubuntu resolute/universe armhf libhtscodecs2 armhf 1.6.1-2 [67.5 kB] 319s Get:10 http://ftpmaster.internal/ubuntu resolute/universe armhf libhts3t64 armhf 1.22.1+ds2-1 [408 kB] 319s Get:11 http://ftpmaster.internal/ubuntu resolute/main armhf libpython3.14-stdlib armhf 3.14.0-4 [2270 kB] 319s Get:12 http://ftpmaster.internal/ubuntu resolute/main armhf python3.14 armhf 3.14.0-4 [805 kB] 319s Get:13 http://ftpmaster.internal/ubuntu resolute-proposed/main armhf python3-all armhf 3.13.7-2 [890 B] 319s Get:14 http://ftpmaster.internal/ubuntu resolute/main armhf python3-click all 8.2.0+0.really.8.1.8-1 [80.0 kB] 319s Get:15 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-humanfriendly all 10.0-6 [70.8 kB] 319s Get:16 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-coloredlogs all 15.0.1-1 [38.2 kB] 319s Get:17 http://ftpmaster.internal/ubuntu resolute/universe armhf python3-cyvcf2 armhf 0.31.4-1 [1060 kB] 320s Fetched 14.3 MB in 1s (14.7 MB/s) 320s Selecting previously unselected package python3-numpy-dev:armhf. 320s (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 ... 65904 files and directories currently installed.) 320s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 320s Unpacking python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 320s Selecting previously unselected package libblas3:armhf. 320s Preparing to unpack .../01-libblas3_3.12.1-7_armhf.deb ... 320s Unpacking libblas3:armhf (3.12.1-7) ... 320s Selecting previously unselected package libgfortran5:armhf. 320s Preparing to unpack .../02-libgfortran5_15.2.0-7ubuntu1_armhf.deb ... 320s Unpacking libgfortran5:armhf (15.2.0-7ubuntu1) ... 320s Selecting previously unselected package liblapack3:armhf. 320s Preparing to unpack .../03-liblapack3_3.12.1-7_armhf.deb ... 320s Unpacking liblapack3:armhf (3.12.1-7) ... 320s Selecting previously unselected package python3-numpy. 320s Preparing to unpack .../04-python3-numpy_1%3a2.2.4+ds-1ubuntu1_armhf.deb ... 320s Unpacking python3-numpy (1:2.2.4+ds-1ubuntu1) ... 320s Selecting previously unselected package libpython3.14-minimal:armhf. 320s Preparing to unpack .../05-libpython3.14-minimal_3.14.0-4_armhf.deb ... 320s Unpacking libpython3.14-minimal:armhf (3.14.0-4) ... 321s Selecting previously unselected package python3.14-minimal. 321s Preparing to unpack .../06-python3.14-minimal_3.14.0-4_armhf.deb ... 321s Unpacking python3.14-minimal (3.14.0-4) ... 321s Selecting previously unselected package libdeflate0:armhf. 321s Preparing to unpack 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Selecting previously unselected package python3-click. 321s Preparing to unpack .../13-python3-click_8.2.0+0.really.8.1.8-1_all.deb ... 321s Unpacking python3-click (8.2.0+0.really.8.1.8-1) ... 321s Selecting previously unselected package python3-humanfriendly. 321s Preparing to unpack .../14-python3-humanfriendly_10.0-6_all.deb ... 321s Unpacking python3-humanfriendly (10.0-6) ... 321s Selecting previously unselected package python3-coloredlogs. 321s Preparing to unpack .../15-python3-coloredlogs_15.0.1-1_all.deb ... 321s Unpacking python3-coloredlogs (15.0.1-1) ... 321s Selecting previously unselected package python3-cyvcf2. 321s Preparing to unpack .../16-python3-cyvcf2_0.31.4-1_armhf.deb ... 321s Unpacking python3-cyvcf2 (0.31.4-1) ... 321s Setting up libhtscodecs2:armhf (1.6.1-2) ... 321s Setting up libpython3.14-minimal:armhf (3.14.0-4) ... 321s Setting up libdeflate0:armhf (1.23-2) ... 321s Setting up python3-click (8.2.0+0.really.8.1.8-1) ... 322s Setting up libblas3:armhf (3.12.1-7) ... 322s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 322s Setting up python3-humanfriendly (10.0-6) ... 322s /usr/lib/python3/dist-packages/humanfriendly/testing.py:546: SyntaxWarning: 'return' in a 'finally' block 322s return super(MockedProgram, self).__exit__(*args, **kw) 322s Setting up python3-numpy-dev:armhf (1:2.2.4+ds-1ubuntu1) ... 322s Setting up libgfortran5:armhf (15.2.0-7ubuntu1) ... 322s Setting up libhts3t64:armhf (1.22.1+ds2-1) ... 322s Setting up python3-coloredlogs (15.0.1-1) ... 322s Setting up python3.14-minimal (3.14.0-4) ... 323s Setting up liblapack3:armhf (3.12.1-7) ... 323s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 323s Setting up libpython3.14-stdlib:armhf (3.14.0-4) ... 323s Setting up python3-numpy (1:2.2.4+ds-1ubuntu1) ... 328s Setting up python3.14 (3.14.0-4) ... 329s Setting up python3-all (3.13.7-2) ... 329s Setting up python3-cyvcf2 (0.31.4-1) ... 329s Processing triggers for systemd (257.9-0ubuntu2) ... 329s Processing triggers for man-db (2.13.1-1) ... 330s Processing triggers for libc-bin (2.42-2ubuntu2) ... 344s autopkgtest [11:43:41]: 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 344s autopkgtest [11:43:41]: test autodep8-python3: [----------------------- 346s Testing with python3.14: 346s Traceback (most recent call last): 346s File "/usr/lib/python3/dist-packages/numpy/_core/__init__.py", line 23, in 346s from . import multiarray 346s File "/usr/lib/python3/dist-packages/numpy/_core/multiarray.py", line 10, in 346s from . import overrides 346s File "/usr/lib/python3/dist-packages/numpy/_core/overrides.py", line 7, in 346s from numpy._core._multiarray_umath import ( 346s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 346s ModuleNotFoundError: No module named 'numpy._core._multiarray_umath' 346s 346s During handling of the above exception, another exception occurred: 346s 346s Traceback (most recent call last): 346s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 114, in 346s from numpy.__config__ import show_config 346s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 346s from numpy._core._multiarray_umath import ( 346s ...<3 lines>... 346s ) 346s File "/usr/lib/python3/dist-packages/numpy/_core/__init__.py", line 49, in 346s raise ImportError(msg) 346s ImportError: 346s 346s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 346s 346s Importing the numpy C-extensions failed. This error can happen for 346s many reasons, often due to issues with your setup or how NumPy was 346s installed. 346s 346s We have compiled some common reasons and troubleshooting tips at: 346s 346s https://numpy.org/devdocs/user/troubleshooting-importerror.html 346s 346s Please note and check the following: 346s 346s * The Python version is: Python3.14 from "/usr/bin/python3.14" 346s * The NumPy version is: "2.2.4" 346s 346s and make sure that they are the versions you expect. 346s Please carefully study the documentation linked above for further help. 346s 346s Original error was: No module named 'numpy._core._multiarray_umath' 346s 346s 346s The above exception was the direct cause of the following exception: 346s 346s Traceback (most recent call last): 346s File "", line 1, in 346s import cyvcf2; print(cyvcf2) 346s ^^^^^^^^^^^^^ 346s File "/usr/lib/python3/dist-packages/cyvcf2/__init__.py", line 1, in 346s from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness, 346s par_het) 346s File "cyvcf2/cyvcf2.pyx", line 1, in init cyvcf2.cyvcf2 346s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 119, in 346s raise ImportError(msg) from e 346s ImportError: Error importing numpy: you should not try to import numpy from 346s its source directory; please exit the numpy source tree, and relaunch 346s your python interpreter from there. 347s autopkgtest [11:43:44]: test autodep8-python3: -----------------------] 350s autodep8-python3 FAIL non-zero exit status 1 350s autopkgtest [11:43:47]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 354s autopkgtest [11:43:51]: @@@@@@@@@@@@@@@@@@@@ summary 354s run-unit-test FAIL non-zero exit status 2 354s autodep8-python3 FAIL non-zero exit status 1