0s autopkgtest [11:09:28]: starting date and time: 2024-11-13 11:09:28+0000 0s autopkgtest [11:09:28]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [11:09:28]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.j3mauv25/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:python3-defaults,src:python3-stdlib-extensions --apt-upgrade scikit-fmm --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=python3-defaults/3.12.7-1 python3-stdlib-extensions/3.12.7-1' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-49.secgroup --name adt-plucky-arm64-scikit-fmm-20241113-110928-juju-7f2275-prod-proposed-migration-environment-2-78557866-98d3-494e-89e0-616b5c0c51e0 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 93s autopkgtest [11:11:01]: testbed dpkg architecture: arm64 94s autopkgtest [11:11:02]: testbed apt version: 2.9.8 94s autopkgtest [11:11:02]: @@@@@@@@@@@@@@@@@@@@ test bed setup 95s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 95s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 96s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 96s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 96s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 96s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 96s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 96s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 96s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 96s Fetched 1794 kB in 1s (1942 kB/s) 96s Reading package lists... 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 102s Calculating upgrade... 103s The following NEW packages will be installed: 103s python3.13-gdbm 103s The following packages will be upgraded: 103s libpython3-stdlib python3 python3-gdbm python3-minimal 103s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 103s Need to get 101 kB of archives. 103s After this operation, 141 kB of additional disk space will be used. 103s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 103s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 103s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 103s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 103s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 104s Fetched 101 kB in 0s (281 kB/s) 104s (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 ... 79924 files and directories currently installed.) 104s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 104s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 104s Setting up python3-minimal (3.12.7-1) ... 105s (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 ... 79924 files and directories currently installed.) 105s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 105s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 105s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 105s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 105s Selecting previously unselected package python3.13-gdbm. 105s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 105s Unpacking python3.13-gdbm (3.13.0-2) ... 105s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 105s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 105s Setting up python3.13-gdbm (3.13.0-2) ... 105s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 105s Setting up python3 (3.12.7-1) ... 106s Setting up python3-gdbm:arm64 (3.12.7-1) ... 106s Processing triggers for man-db (2.12.1-3) ... 107s Reading package lists... 107s Building dependency tree... 107s Reading state information... 109s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 109s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 109s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 109s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 110s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 111s Reading package lists... 111s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Calculating upgrade... 114s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 114s Reading package lists... 115s Building dependency tree... 115s Reading state information... 116s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s autopkgtest [11:11:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 120s autopkgtest [11:11:28]: @@@@@@@@@@@@@@@@@@@@ apt-source scikit-fmm 122s Get:1 http://ftpmaster.internal/ubuntu plucky/universe scikit-fmm 2024.05.29-1 (dsc) [2068 B] 122s Get:2 http://ftpmaster.internal/ubuntu plucky/universe scikit-fmm 2024.05.29-1 (tar) [461 kB] 122s Get:3 http://ftpmaster.internal/ubuntu plucky/universe scikit-fmm 2024.05.29-1 (diff) [4072 B] 123s gpgv: Signature made Sat Jul 6 05:11:21 2024 UTC 123s gpgv: using RSA key 1E0BAAD85C2232A1B3CE92EBB7047105830B9FA1 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./scikit-fmm_2024.05.29-1.dsc: no acceptable signature found 123s autopkgtest [11:11:31]: testing package scikit-fmm version 2024.05.29-1 123s autopkgtest [11:11:31]: build not needed 123s autopkgtest [11:11:31]: test command1: preparing testbed 125s Reading package lists... 126s Building dependency tree... 126s Reading state information... 126s Starting pkgProblemResolver with broken count: 0 126s Starting 2 pkgProblemResolver with broken count: 0 126s Done 128s The following additional packages will be installed: 128s libblas3 libgfortran5 liblapack3 libpython3.13-minimal libpython3.13-stdlib 128s python3-all python3-numpy python3-scikit-fmm python3.13 python3.13-minimal 128s Suggested packages: 128s gcc gfortran python-numpy-doc python3-dev python3-pytest python3.13-venv 128s python3.13-doc binfmt-support 128s The following NEW packages will be installed: 128s autopkgtest-satdep libblas3 libgfortran5 liblapack3 libpython3.13-minimal 128s libpython3.13-stdlib python3-all python3-numpy python3-scikit-fmm python3.13 128s python3.13-minimal 128s 0 upgraded, 11 newly installed, 0 to remove and 0 not upgraded. 128s Need to get 12.4 MB/12.4 MB of archives. 128s After this operation, 51.9 MB of additional disk space will be used. 128s Get:1 /tmp/autopkgtest.72KLbG/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 128s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 129s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 129s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 129s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 129s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 129s Get:7 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 129s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 129s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 129s Get:10 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 129s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scikit-fmm arm64 2024.05.29-1 [59.0 kB] 130s Fetched 12.4 MB in 1s (10.9 MB/s) 130s Selecting previously unselected package libpython3.13-minimal:arm64. 130s (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 ... 79931 files and directories currently installed.) 130s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 130s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 130s Selecting previously unselected package python3.13-minimal. 130s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 130s Unpacking python3.13-minimal (3.13.0-2) ... 130s Selecting previously unselected package libblas3:arm64. 130s Preparing to unpack .../02-libblas3_3.12.0-3build2_arm64.deb ... 130s Unpacking libblas3:arm64 (3.12.0-3build2) ... 130s Selecting previously unselected package libgfortran5:arm64. 130s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 130s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 130s Selecting previously unselected package liblapack3:arm64. 130s Preparing to unpack .../04-liblapack3_3.12.0-3build2_arm64.deb ... 130s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 130s Selecting previously unselected package libpython3.13-stdlib:arm64. 130s Preparing to unpack .../05-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 130s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 131s Selecting previously unselected package python3.13. 131s Preparing to unpack .../06-python3.13_3.13.0-2_arm64.deb ... 131s Unpacking python3.13 (3.13.0-2) ... 131s Selecting previously unselected package python3-all. 131s Preparing to unpack .../07-python3-all_3.12.7-1_arm64.deb ... 131s Unpacking python3-all (3.12.7-1) ... 131s Selecting previously unselected package python3-numpy. 131s Preparing to unpack .../08-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 131s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 131s Selecting previously unselected package python3-scikit-fmm. 131s Preparing to unpack .../09-python3-scikit-fmm_2024.05.29-1_arm64.deb ... 131s Unpacking python3-scikit-fmm (2024.05.29-1) ... 131s Selecting previously unselected package autopkgtest-satdep. 131s Preparing to unpack .../10-1-autopkgtest-satdep.deb ... 131s Unpacking autopkgtest-satdep (0) ... 131s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 131s Setting up libblas3:arm64 (3.12.0-3build2) ... 131s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 131s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 131s Setting up python3.13-minimal (3.13.0-2) ... 132s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 132s Setting up liblapack3:arm64 (3.12.0-3build2) ... 132s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 132s Setting up python3.13 (3.13.0-2) ... 134s Setting up python3-all (3.12.7-1) ... 134s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 140s Setting up python3-scikit-fmm (2024.05.29-1) ... 140s Setting up autopkgtest-satdep (0) ... 140s Processing triggers for systemd (256.5-2ubuntu4) ... 141s Processing triggers for man-db (2.12.1-3) ... 141s Processing triggers for libc-bin (2.40-1ubuntu3) ... 146s (Reading database ... 81581 files and directories currently installed.) 146s Removing autopkgtest-satdep (0) ... 146s autopkgtest [11:11:54]: test command1: set -e ; for py in $(py3versions -s 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import skfmm, sys; sys.exit(skfmm.test())" ; done 146s autopkgtest [11:11:54]: test command1: [----------------------- 147s Testing with python3.13: 147s Traceback (most recent call last): 147s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 147s from . import multiarray 147s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 147s from . import overrides 147s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 147s from numpy.core._multiarray_umath import ( 147s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 147s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 147s 147s During handling of the above exception, another exception occurred: 147s 147s Traceback (most recent call last): 147s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 147s from numpy.__config__ import show as show_config 147s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 147s from numpy.core._multiarray_umath import ( 147s ...<3 lines>... 147s ) 147s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 147s raise ImportError(msg) 147s ImportError: 147s 147s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 147s 147s Importing the numpy C-extensions failed. This error can happen for 147s many reasons, often due to issues with your setup or how NumPy was 147s installed. 147s 147s We have compiled some common reasons and troubleshooting tips at: 147s 147s https://numpy.org/devdocs/user/troubleshooting-importerror.html 147s 147s Please note and check the following: 147s 147s * The Python version is: Python3.13 from "/usr/bin/python3.13" 147s * The NumPy version is: "1.26.4" 147s 147s and make sure that they are the versions you expect. 147s Please carefully study the documentation linked above for further help. 147s 147s Original error was: No module named 'numpy.core._multiarray_umath' 147s 147s 147s The above exception was the direct cause of the following exception: 147s 147s Traceback (most recent call last): 147s File "", line 1, in 147s import skfmm, sys; sys.exit(skfmm.test()) 147s ^^^^^^^^^^^^^^^^^ 147s File "/usr/lib/python3/dist-packages/skfmm/__init__.py", line 51, in 147s from .pfmm import distance, travel_time, extension_velocities 147s File "/usr/lib/python3/dist-packages/skfmm/pfmm.py", line 2, in 147s import numpy as np 147s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 147s raise ImportError(msg) from e 147s ImportError: Error importing numpy: you should not try to import numpy from 147s its source directory; please exit the numpy source tree, and relaunch 147s your python interpreter from there. 147s autopkgtest [11:11:55]: test command1: -----------------------] 148s command1 FAIL non-zero exit status 1 148s autopkgtest [11:11:56]: test command1: - - - - - - - - - - results - - - - - - - - - - 148s autopkgtest [11:11:56]: test command1: - - - - - - - - - - stderr - - - - - - - - - - 148s Traceback (most recent call last): 148s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 148s from . import multiarray 148s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 148s from . import overrides 148s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 148s from numpy.core._multiarray_umath import ( 148s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 148s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 148s 148s During handling of the above exception, another exception occurred: 148s 148s Traceback (most recent call last): 148s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 148s from numpy.__config__ import show as show_config 148s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 148s from numpy.core._multiarray_umath import ( 148s ...<3 lines>... 148s ) 148s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 148s raise ImportError(msg) 148s ImportError: 148s 148s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 148s 148s Importing the numpy C-extensions failed. This error can happen for 148s many reasons, often due to issues with your setup or how NumPy was 148s installed. 148s 148s We have compiled some common reasons and troubleshooting tips at: 148s 148s https://numpy.org/devdocs/user/troubleshooting-importerror.html 148s 148s Please note and check the following: 148s 148s * The Python version is: Python3.13 from "/usr/bin/python3.13" 148s * The NumPy version is: "1.26.4" 148s 148s and make sure that they are the versions you expect. 148s Please carefully study the documentation linked above for further help. 148s 148s Original error was: No module named 'numpy.core._multiarray_umath' 148s 148s 148s The above exception was the direct cause of the following exception: 148s 148s Traceback (most recent call last): 148s File "", line 1, in 148s import skfmm, sys; sys.exit(skfmm.test()) 148s ^^^^^^^^^^^^^^^^^ 148s File "/usr/lib/python3/dist-packages/skfmm/__init__.py", line 51, in 148s from .pfmm import distance, travel_time, extension_velocities 148s File "/usr/lib/python3/dist-packages/skfmm/pfmm.py", line 2, in 148s import numpy as np 148s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 148s raise ImportError(msg) from e 148s ImportError: Error importing numpy: you should not try to import numpy from 148s its source directory; please exit the numpy source tree, and relaunch 148s your python interpreter from there. 148s autopkgtest [11:11:56]: @@@@@@@@@@@@@@@@@@@@ summary 148s command1 FAIL non-zero exit status 1 164s virt: nova [W] Skipping flock in bos03-arm64 164s virt: Creating nova instance adt-plucky-arm64-scikit-fmm-20241113-110928-juju-7f2275-prod-proposed-migration-environment-2-78557866-98d3-494e-89e0-616b5c0c51e0 from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...