0s autopkgtest [10:10:19]: starting date and time: 2024-11-13 10:10:19+0000 0s autopkgtest [10:10:19]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [10:10:19]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.osmmgr47/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 python-pymbar --timeout-short=300 --timeout-copy=20000 --timeout-test=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-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-arm64-22.secgroup --name adt-plucky-arm64-python-pymbar-20241113-101019-juju-7f2275-prod-proposed-migration-environment-15-64b1fb99-4b5c-46b7-9f25-a8eecc1a267f --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --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/ 106s autopkgtest [10:12:05]: testbed dpkg architecture: arm64 107s autopkgtest [10:12:06]: testbed apt version: 2.9.8 107s autopkgtest [10:12:06]: @@@@@@@@@@@@@@@@@@@@ test bed setup 108s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 108s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 108s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 108s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 108s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 108s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 108s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 108s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 108s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 109s Fetched 1794 kB in 1s (1987 kB/s) 109s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 113s Calculating upgrade... 115s The following NEW packages will be installed: 115s python3.13-gdbm 115s The following packages will be upgraded: 115s libpython3-stdlib python3 python3-gdbm python3-minimal 115s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 115s Need to get 101 kB of archives. 115s After this operation, 141 kB of additional disk space will be used. 115s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 115s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 115s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 115s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 115s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 116s Fetched 101 kB in 0s (268 kB/s) 116s (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.) 116s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 116s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 116s Setting up python3-minimal (3.12.7-1) ... 116s (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.) 116s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 117s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 117s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 117s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 117s Selecting previously unselected package python3.13-gdbm. 117s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 117s Unpacking python3.13-gdbm (3.13.0-2) ... 117s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 117s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 117s Setting up python3.13-gdbm (3.13.0-2) ... 117s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 117s Setting up python3 (3.12.7-1) ... 118s Setting up python3-gdbm:arm64 (3.12.7-1) ... 118s Processing triggers for man-db (2.12.1-3) ... 118s Reading package lists... 119s Building dependency tree... 119s Reading state information... 120s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 120s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 120s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 120s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 120s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 122s Reading package lists... 122s Reading package lists... 123s Building dependency tree... 123s Reading state information... 124s Calculating upgrade... 125s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 125s Reading package lists... 125s Building dependency tree... 125s Reading state information... 126s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 130s autopkgtest [10:12:28]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 130s autopkgtest [10:12:29]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 132s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (dsc) [2234 B] 132s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (tar) [17.2 MB] 132s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (diff) [3444 B] 133s gpgv: Signature made Sat Jun 29 17:20:42 2024 UTC 133s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 133s gpgv: issuer "tchet@debian.org" 133s gpgv: Can't check signature: No public key 133s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_4.0.3-2.dsc: no acceptable signature found 133s autopkgtest [10:12:32]: testing package python-pymbar version 4.0.3-2 134s autopkgtest [10:12:33]: build not needed 136s autopkgtest [10:12:35]: test command1: preparing testbed 138s Reading package lists... 139s Building dependency tree... 139s Reading state information... 139s Starting pkgProblemResolver with broken count: 0 139s Starting 2 pkgProblemResolver with broken count: 0 139s Done 141s The following additional packages will be installed: 141s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 141s python3-iniconfig python3-numexpr python3-numpy python3-packaging 141s python3-pluggy python3-pymbar python3-pytest python3-scipy 141s Suggested packages: 141s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 141s Recommended packages: 141s g++ | c++-compiler python3-pil 141s The following NEW packages will be installed: 141s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 141s python3-decorator python3-iniconfig python3-numexpr python3-numpy 141s python3-packaging python3-pluggy python3-pymbar python3-pytest python3-scipy 141s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 141s Need to get 23.4 MB/23.4 MB of archives. 141s After this operation, 97.0 MB of additional disk space will be used. 141s Get:1 /tmp/autopkgtest.L5WCnl/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 141s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 142s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 142s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 142s Get:5 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 142s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 142s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 142s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 142s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 142s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.1-2 [114 kB] 142s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 142s Get:12 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 142s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymbar all 4.0.3-2 [80.7 kB] 142s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.3-1 [251 kB] 143s Fetched 23.4 MB in 1s (16.9 MB/s) 143s Selecting previously unselected package libblas3:arm64. 143s (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.) 143s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 143s Unpacking libblas3:arm64 (3.12.0-3build2) ... 143s Selecting previously unselected package libgfortran5:arm64. 143s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 143s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 143s Selecting previously unselected package liblapack3:arm64. 143s Preparing to unpack .../02-liblapack3_3.12.0-3build2_arm64.deb ... 143s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 143s Selecting previously unselected package liblbfgsb0:arm64. 143s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 143s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 143s Selecting previously unselected package python3-decorator. 143s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 143s Unpacking python3-decorator (5.1.1-5) ... 143s Selecting previously unselected package python3-iniconfig. 143s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 143s Unpacking python3-iniconfig (1.1.1-2) ... 143s Selecting previously unselected package python3-numpy. 143s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 143s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 144s Selecting previously unselected package python3-packaging. 144s Preparing to unpack .../07-python3-packaging_24.1-1_all.deb ... 144s Unpacking python3-packaging (24.1-1) ... 144s Selecting previously unselected package python3-numexpr. 144s Preparing to unpack .../08-python3-numexpr_2.10.1-2_arm64.deb ... 144s Unpacking python3-numexpr (2.10.1-2) ... 144s Selecting previously unselected package python3-pluggy. 144s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 144s Unpacking python3-pluggy (1.5.0-1) ... 144s Selecting previously unselected package python3-scipy. 144s Preparing to unpack .../10-python3-scipy_1.13.1-5_arm64.deb ... 144s Unpacking python3-scipy (1.13.1-5) ... 144s Selecting previously unselected package python3-pymbar. 144s Preparing to unpack .../11-python3-pymbar_4.0.3-2_all.deb ... 144s Unpacking python3-pymbar (4.0.3-2) ... 144s Selecting previously unselected package python3-pytest. 144s Preparing to unpack .../12-python3-pytest_8.3.3-1_all.deb ... 144s Unpacking python3-pytest (8.3.3-1) ... 144s Selecting previously unselected package autopkgtest-satdep. 144s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 144s Unpacking autopkgtest-satdep (0) ... 145s Setting up python3-iniconfig (1.1.1-2) ... 145s Setting up python3-decorator (5.1.1-5) ... 145s Setting up libblas3:arm64 (3.12.0-3build2) ... 145s 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 145s Setting up python3-packaging (24.1-1) ... 145s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 145s Setting up python3-pluggy (1.5.0-1) ... 145s Setting up liblapack3:arm64 (3.12.0-3build2) ... 145s 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 145s Setting up python3-pytest (8.3.3-1) ... 146s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 149s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 149s Setting up python3-scipy (1.13.1-5) ... 155s Setting up python3-numexpr (2.10.1-2) ... 155s Setting up python3-pymbar (4.0.3-2) ... 155s Setting up autopkgtest-satdep (0) ... 155s Processing triggers for man-db (2.12.1-3) ... 155s Processing triggers for libc-bin (2.40-1ubuntu3) ... 161s (Reading database ... 82517 files and directories currently installed.) 161s Removing autopkgtest-satdep (0) ... 162s autopkgtest [10:13:01]: test command1: rm pymbar/*.py && pytest-3 162s autopkgtest [10:13:01]: test command1: [----------------------- 164s ============================= test session starts ============================== 164s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 164s rootdir: /tmp/autopkgtest.L5WCnl/build.WUz/src 164s configfile: setup.cfg 164s plugins: typeguard-4.4.1 164s collected 150 items 164s 164s pymbar/tests/test_bar.py ..... [ 3%] 165s pymbar/tests/test_exp.py .... [ 6%] 172s pymbar/tests/test_fes.py ..xxsssssssss.....xxssssssss [ 24%] 176s pymbar/tests/test_mbar.py ...x..........x...............x..........xxxx. [ 55%] 176s ..x..................x [ 70%] 318s pymbar/tests/test_mbar_solvers.py ................ [ 80%] 323s pymbar/tests/test_timeseries.py ..ss.ss.. [ 86%] 324s pymbar/tests/test_utils.py ....xx..xx..xx..xx.. [100%] 324s 324s =============================== warnings summary =============================== 324s pymbar/tests/test_mbar_solvers.py:24 324s /tmp/autopkgtest.L5WCnl/build.WUz/src/pymbar/tests/test_mbar_solvers.py:24: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 324s @pytest.mark.flaky(max_runs=2) # Uses flaky plugin for pytest 324s 324s pymbar/tests/test_mbar_solvers.py:67 324s /tmp/autopkgtest.L5WCnl/build.WUz/src/pymbar/tests/test_mbar_solvers.py:67: PytestUnknownMarkWarning: Unknown pytest.mark.flaky - is this a typo? You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/how-to/mark.html 324s pytest.param("TNC", marks=pytest.mark.flaky(max_runs=2)), # This one is flaky 324s 324s pymbar/tests/test_fes.py: 189 warnings 324s /usr/lib/python3/dist-packages/pymbar/fes.py:2246: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) 324s g[i - 1] = N * np.dot(w_n, db_c[i](x_n)) 324s 324s pymbar/tests/test_mbar_solvers.py::test_protocols[trust-krylov] 324s pymbar/tests/test_mbar_solvers.py::test_protocols[trust-krylov] 324s /usr/lib/python3/dist-packages/scipy/optimize/_trustregion.py:225: RuntimeWarning: invalid value encountered in multiply 324s 324s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 324s ==== 108 passed, 21 skipped, 21 xfailed, 193 warnings in 160.58s (0:02:40) ===== 324s autopkgtest [10:15:43]: test command1: -----------------------] 325s command1 PASS 325s autopkgtest [10:15:44]: test command1: - - - - - - - - - - results - - - - - - - - - - 326s autopkgtest [10:15:45]: test autodep8-python3: preparing testbed 411s autopkgtest [10:17:10]: testbed dpkg architecture: arm64 411s autopkgtest [10:17:10]: testbed apt version: 2.9.8 411s autopkgtest [10:17:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 412s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 412s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [849 kB] 413s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 413s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [76.4 kB] 413s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 413s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [104 kB] 413s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 413s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [601 kB] 413s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 413s Fetched 1794 kB in 1s (1972 kB/s) 413s Reading package lists... 416s Reading package lists... 416s Building dependency tree... 416s Reading state information... 418s Calculating upgrade... 419s The following NEW packages will be installed: 419s python3.13-gdbm 419s The following packages will be upgraded: 419s libpython3-stdlib python3 python3-gdbm python3-minimal 419s 4 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 419s Need to get 101 kB of archives. 419s After this operation, 141 kB of additional disk space will be used. 419s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-minimal arm64 3.12.7-1 [27.4 kB] 419s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3 arm64 3.12.7-1 [24.0 kB] 419s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libpython3-stdlib arm64 3.12.7-1 [10.0 kB] 419s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-gdbm arm64 3.13.0-2 [30.7 kB] 419s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-gdbm arm64 3.12.7-1 [8642 B] 420s Fetched 101 kB in 0s (288 kB/s) 420s (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.) 420s Preparing to unpack .../python3-minimal_3.12.7-1_arm64.deb ... 420s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 420s Setting up python3-minimal (3.12.7-1) ... 420s (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.) 420s Preparing to unpack .../python3_3.12.7-1_arm64.deb ... 420s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 420s Preparing to unpack .../libpython3-stdlib_3.12.7-1_arm64.deb ... 420s Unpacking libpython3-stdlib:arm64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 420s Selecting previously unselected package python3.13-gdbm. 420s Preparing to unpack .../python3.13-gdbm_3.13.0-2_arm64.deb ... 420s Unpacking python3.13-gdbm (3.13.0-2) ... 421s Preparing to unpack .../python3-gdbm_3.12.7-1_arm64.deb ... 421s Unpacking python3-gdbm:arm64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 421s Setting up python3.13-gdbm (3.13.0-2) ... 421s Setting up libpython3-stdlib:arm64 (3.12.7-1) ... 421s Setting up python3 (3.12.7-1) ... 421s Setting up python3-gdbm:arm64 (3.12.7-1) ... 421s Processing triggers for man-db (2.12.1-3) ... 422s Reading package lists... 423s Building dependency tree... 423s Reading state information... 424s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 424s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 424s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 424s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 424s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 426s Reading package lists... 426s Reading package lists... 427s Building dependency tree... 427s Reading state information... 427s Calculating upgrade... 428s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 428s Reading package lists... 428s Building dependency tree... 428s Reading state information... 429s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 449s Reading package lists... 449s Building dependency tree... 449s Reading state information... 450s Starting pkgProblemResolver with broken count: 0 450s Starting 2 pkgProblemResolver with broken count: 0 450s Done 451s The following additional packages will be installed: 451s libblas3 libgfortran5 liblapack3 liblbfgsb0 libpython3.13-minimal 451s libpython3.13-stdlib python3-all python3-decorator python3-numexpr 452s python3-numpy python3-packaging python3-pymbar python3-scipy python3.13 452s python3.13-minimal 452s Suggested packages: 452s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 452s python3.13-venv python3.13-doc binfmt-support 452s Recommended packages: 452s g++ | c++-compiler python3-pil 452s The following NEW packages will be installed: 452s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 452s libpython3.13-minimal libpython3.13-stdlib python3-all python3-decorator 452s python3-numexpr python3-numpy python3-packaging python3-pymbar python3-scipy 452s python3.13 python3.13-minimal 452s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 452s Need to get 28.9 MB/28.9 MB of archives. 452s After this operation, 120 MB of additional disk space will be used. 452s Get:1 /tmp/autopkgtest.L5WCnl/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [720 B] 452s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-minimal arm64 3.13.0-2 [877 kB] 452s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13-minimal arm64 3.13.0-2 [2100 kB] 452s Get:4 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 452s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-8ubuntu1 [438 kB] 452s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 452s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 452s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 libpython3.13-stdlib arm64 3.13.0-2 [2073 kB] 453s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3.13 arm64 3.13.0-2 [719 kB] 453s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 python3-all arm64 3.12.7-1 [890 B] 453s Get:11 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 453s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 453s Get:13 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 453s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-numexpr arm64 2.10.1-2 [114 kB] 453s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-5 [16.3 MB] 453s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pymbar all 4.0.3-2 [80.7 kB] 454s Fetched 28.9 MB in 1s (20.8 MB/s) 454s Selecting previously unselected package libpython3.13-minimal:arm64. 454s (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.) 454s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_arm64.deb ... 454s Unpacking libpython3.13-minimal:arm64 (3.13.0-2) ... 454s Selecting previously unselected package python3.13-minimal. 454s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_arm64.deb ... 454s Unpacking python3.13-minimal (3.13.0-2) ... 454s Selecting previously unselected package libblas3:arm64. 454s Preparing to unpack .../02-libblas3_3.12.0-3build2_arm64.deb ... 454s Unpacking libblas3:arm64 (3.12.0-3build2) ... 454s Selecting previously unselected package libgfortran5:arm64. 454s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_arm64.deb ... 454s Unpacking libgfortran5:arm64 (14.2.0-8ubuntu1) ... 454s Selecting previously unselected package liblapack3:arm64. 454s Preparing to unpack .../04-liblapack3_3.12.0-3build2_arm64.deb ... 454s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 454s Selecting previously unselected package liblbfgsb0:arm64. 454s Preparing to unpack .../05-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 454s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 454s Selecting previously unselected package libpython3.13-stdlib:arm64. 454s Preparing to unpack .../06-libpython3.13-stdlib_3.13.0-2_arm64.deb ... 454s Unpacking libpython3.13-stdlib:arm64 (3.13.0-2) ... 455s Selecting previously unselected package python3.13. 455s Preparing to unpack .../07-python3.13_3.13.0-2_arm64.deb ... 455s Unpacking python3.13 (3.13.0-2) ... 455s Selecting previously unselected package python3-all. 455s Preparing to unpack .../08-python3-all_3.12.7-1_arm64.deb ... 455s Unpacking python3-all (3.12.7-1) ... 455s Selecting previously unselected package python3-decorator. 455s Preparing to unpack .../09-python3-decorator_5.1.1-5_all.deb ... 455s Unpacking python3-decorator (5.1.1-5) ... 455s Selecting previously unselected package python3-numpy. 455s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 455s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 455s Selecting previously unselected package python3-packaging. 455s Preparing to unpack .../11-python3-packaging_24.1-1_all.deb ... 455s Unpacking python3-packaging (24.1-1) ... 455s Selecting previously unselected package python3-numexpr. 455s Preparing to unpack .../12-python3-numexpr_2.10.1-2_arm64.deb ... 455s Unpacking python3-numexpr (2.10.1-2) ... 455s Selecting previously unselected package python3-scipy. 455s Preparing to unpack .../13-python3-scipy_1.13.1-5_arm64.deb ... 455s Unpacking python3-scipy (1.13.1-5) ... 456s Selecting previously unselected package python3-pymbar. 456s Preparing to unpack .../14-python3-pymbar_4.0.3-2_all.deb ... 456s Unpacking python3-pymbar (4.0.3-2) ... 456s Selecting previously unselected package autopkgtest-satdep. 456s Preparing to unpack .../15-2-autopkgtest-satdep.deb ... 456s Unpacking autopkgtest-satdep (0) ... 456s Setting up libpython3.13-minimal:arm64 (3.13.0-2) ... 456s Setting up python3-decorator (5.1.1-5) ... 457s Setting up libblas3:arm64 (3.12.0-3build2) ... 457s 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 457s Setting up python3-packaging (24.1-1) ... 457s Setting up libgfortran5:arm64 (14.2.0-8ubuntu1) ... 457s Setting up python3.13-minimal (3.13.0-2) ... 458s Setting up libpython3.13-stdlib:arm64 (3.13.0-2) ... 458s Setting up liblapack3:arm64 (3.12.0-3build2) ... 458s 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 458s Setting up python3.13 (3.13.0-2) ... 460s Setting up python3-all (3.12.7-1) ... 460s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 465s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 465s Setting up python3-scipy (1.13.1-5) ... 473s Setting up python3-numexpr (2.10.1-2) ... 473s Setting up python3-pymbar (4.0.3-2) ... 473s Setting up autopkgtest-satdep (0) ... 473s Processing triggers for systemd (256.5-2ubuntu4) ... 474s Processing triggers for man-db (2.12.1-3) ... 474s Processing triggers for libc-bin (2.40-1ubuntu3) ... 482s (Reading database ... 83111 files and directories currently installed.) 482s Removing autopkgtest-satdep (0) ... 541s autopkgtest [10:19:20]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pymbar; print(pymbar)" ; done 541s autopkgtest [10:19:20]: test autodep8-python3: [----------------------- 550s Testing with python3.13: 550s Traceback (most recent call last): 550s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 550s from . import multiarray 550s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 550s from . import overrides 550s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 550s from numpy.core._multiarray_umath import ( 550s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 550s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 550s 550s During handling of the above exception, another exception occurred: 550s 550s Traceback (most recent call last): 550s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 550s from numpy.__config__ import show as show_config 550s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 550s from numpy.core._multiarray_umath import ( 550s ...<3 lines>... 550s ) 550s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 550s raise ImportError(msg) 550s ImportError: 550s 550s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 550s 550s Importing the numpy C-extensions failed. This error can happen for 550s many reasons, often due to issues with your setup or how NumPy was 550s installed. 550s 550s We have compiled some common reasons and troubleshooting tips at: 550s 550s https://numpy.org/devdocs/user/troubleshooting-importerror.html 550s 550s Please note and check the following: 550s 550s * The Python version is: Python3.13 from "/usr/bin/python3.13" 550s * The NumPy version is: "1.26.4" 550s 550s and make sure that they are the versions you expect. 550s Please carefully study the documentation linked above for further help. 550s 550s Original error was: No module named 'numpy.core._multiarray_umath' 550s 550s 550s The above exception was the direct cause of the following exception: 550s 550s Traceback (most recent call last): 550s File "", line 1, in 550s import pymbar; print(pymbar) 550s ^^^^^^^^^^^^^ 550s File "/usr/lib/python3/dist-packages/pymbar/__init__.py", line 31, in 550s from . import timeseries, testsystems, confidenceintervals 550s File "/usr/lib/python3/dist-packages/pymbar/timeseries.py", line 60, in 550s import numpy as np 550s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 550s raise ImportError(msg) from e 550s ImportError: Error importing numpy: you should not try to import numpy from 550s its source directory; please exit the numpy source tree, and relaunch 550s your python interpreter from there. 550s autopkgtest [10:19:29]: test autodep8-python3: -----------------------] 564s autopkgtest [10:19:43]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 564s autodep8-python3 FAIL non-zero exit status 1 567s autopkgtest [10:19:46]: @@@@@@@@@@@@@@@@@@@@ summary 567s command1 PASS 567s autodep8-python3 FAIL non-zero exit status 1 595s nova [W] Skipping flock in bos03-arm64 595s Creating nova instance adt-plucky-arm64-python-pymbar-20241113-101019-juju-7f2275-prod-proposed-migration-environment-15-64b1fb99-4b5c-46b7-9f25-a8eecc1a267f from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)... 595s nova [W] Skipping flock in bos03-arm64 595s Creating nova instance adt-plucky-arm64-python-pymbar-20241113-101019-juju-7f2275-prod-proposed-migration-environment-15-64b1fb99-4b5c-46b7-9f25-a8eecc1a267f from image adt/ubuntu-plucky-arm64-server-20241113.img (UUID 2d7760e6-2439-4200-89d6-5ed33e5c6330)...