0s autopkgtest [15:29:01]: starting date and time: 2024-11-13 15:29:01+0000 0s autopkgtest [15:29:01]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [15:29:01]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.eezuhmmu/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-s390x --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-s390x-6.secgroup --name adt-plucky-s390x-python-pymbar-20241113-152901-juju-7f2275-prod-proposed-migration-environment-15-f25ccf95-5207-4783-83de-d88b2b9c727b --image adt/ubuntu-plucky-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-s390x -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/ 108s autopkgtest [15:30:49]: testbed dpkg architecture: s390x 108s autopkgtest [15:30:49]: testbed apt version: 2.9.8 108s autopkgtest [15:30:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 109s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 109s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 109s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [962 kB] 110s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 110s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 110s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [110 kB] 110s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [639 kB] 110s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 110s Fetched 1931 kB in 1s (1969 kB/s) 110s Reading package lists... 112s Reading package lists... 112s Building dependency tree... 112s Reading state information... 112s Calculating upgrade... 112s The following NEW packages will be installed: 112s python3.13-gdbm 112s The following packages will be upgraded: 112s libgnutls30t64 libgpgme11t64 libjson-glib-1.0-0 libjson-glib-1.0-common 112s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 113s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 113s Need to get 1285 kB of archives. 113s After this operation, 103 kB of additional disk space will be used. 113s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 113s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 113s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 113s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgnutls30t64 s390x 3.8.8-2ubuntu1 [950 kB] 113s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 113s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 113s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 113s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 113s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-0 s390x 1.10.0+ds-3 [67.5 kB] 113s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libutempter0 s390x 1.2.1-4 [9708 B] 113s Fetched 1285 kB in 1s (1683 kB/s) 114s (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 ... 55510 files and directories currently installed.) 114s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 114s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 114s Setting up python3-minimal (3.12.7-1) ... 114s (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 ... 55510 files and directories currently installed.) 114s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 114s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 114s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 114s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 114s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_s390x.deb ... 114s Unpacking libgnutls30t64:s390x (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 114s Setting up libgnutls30t64:s390x (3.8.8-2ubuntu1) ... 114s Selecting previously unselected package python3.13-gdbm. 114s (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 ... 55510 files and directories currently installed.) 114s Preparing to unpack .../0-python3.13-gdbm_3.13.0-2_s390x.deb ... 114s Unpacking python3.13-gdbm (3.13.0-2) ... 114s Preparing to unpack .../1-python3-gdbm_3.12.7-1_s390x.deb ... 114s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 114s Preparing to unpack .../2-libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 114s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 114s Preparing to unpack .../3-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 114s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 114s Preparing to unpack .../4-libjson-glib-1.0-0_1.10.0+ds-3_s390x.deb ... 114s Unpacking libjson-glib-1.0-0:s390x (1.10.0+ds-3) over (1.10.0+ds-2) ... 114s Preparing to unpack .../5-libutempter0_1.2.1-4_s390x.deb ... 114s Unpacking libutempter0:s390x (1.2.1-4) over (1.2.1-3build1) ... 114s Setting up libutempter0:s390x (1.2.1-4) ... 114s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 114s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 114s Setting up python3.13-gdbm (3.13.0-2) ... 114s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 114s Setting up python3 (3.12.7-1) ... 114s Setting up libjson-glib-1.0-0:s390x (1.10.0+ds-3) ... 114s Setting up python3-gdbm:s390x (3.12.7-1) ... 114s Processing triggers for man-db (2.12.1-3) ... 115s Processing triggers for libc-bin (2.40-1ubuntu3) ... 115s Reading package lists... 115s Building dependency tree... 115s Reading state information... 115s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 115s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 116s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 116s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 116s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 116s Reading package lists... 116s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s Calculating upgrade... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 117s Reading package lists... 117s Building dependency tree... 117s Reading state information... 117s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 119s autopkgtest [15:31:00]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 12:49:35 UTC 2024 120s autopkgtest [15:31:01]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 123s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (dsc) [2234 B] 123s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (tar) [17.2 MB] 123s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (diff) [3444 B] 123s gpgv: Signature made Sat Jun 29 17:20:42 2024 UTC 123s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 123s gpgv: issuer "tchet@debian.org" 123s gpgv: Can't check signature: No public key 123s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_4.0.3-2.dsc: no acceptable signature found 124s autopkgtest [15:31:05]: testing package python-pymbar version 4.0.3-2 124s autopkgtest [15:31:05]: build not needed 126s autopkgtest [15:31:07]: test command1: preparing testbed 127s Reading package lists... 127s Building dependency tree... 127s Reading state information... 127s Starting pkgProblemResolver with broken count: 0 127s Starting 2 pkgProblemResolver with broken count: 0 127s Done 127s The following additional packages will be installed: 127s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 127s python3-iniconfig python3-numexpr python3-numpy python3-packaging 127s python3-pluggy python3-pymbar python3-pytest python3-scipy 127s Suggested packages: 127s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 127s Recommended packages: 127s g++ | c++-compiler python3-pil 127s The following NEW packages will be installed: 127s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 127s python3-decorator python3-iniconfig python3-numexpr python3-numpy 127s python3-packaging python3-pluggy python3-pymbar python3-pytest python3-scipy 127s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 127s Need to get 26.0 MB/26.0 MB of archives. 127s After this operation, 104 MB of additional disk space will be used. 127s Get:1 /tmp/autopkgtest.MPTwLu/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 128s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 128s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 128s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 128s Get:5 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 128s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 128s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 128s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 129s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 129s Get:10 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-numexpr s390x 2.10.1-2 [138 kB] 129s Get:11 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 129s Get:12 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB] 130s Get:13 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pymbar all 4.0.3-2 [80.7 kB] 130s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pytest all 8.3.3-1 [251 kB] 130s Fetched 26.0 MB in 2s (12.1 MB/s) 130s Selecting previously unselected package libblas3:s390x. 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 ... 55517 files and directories currently installed.) 130s Preparing to unpack .../00-libblas3_3.12.0-3build2_s390x.deb ... 130s Unpacking libblas3:s390x (3.12.0-3build2) ... 130s Selecting previously unselected package libgfortran5:s390x. 130s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 130s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 130s Selecting previously unselected package liblapack3:s390x. 130s Preparing to unpack .../02-liblapack3_3.12.0-3build2_s390x.deb ... 130s Unpacking liblapack3:s390x (3.12.0-3build2) ... 130s Selecting previously unselected package liblbfgsb0:s390x. 130s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 130s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 130s Selecting previously unselected package python3-decorator. 130s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 130s Unpacking python3-decorator (5.1.1-5) ... 130s Selecting previously unselected package python3-iniconfig. 130s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 130s Unpacking python3-iniconfig (1.1.1-2) ... 130s Selecting previously unselected package python3-numpy. 130s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 130s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 130s Selecting previously unselected package python3-packaging. 130s Preparing to unpack .../07-python3-packaging_24.1-1_all.deb ... 130s Unpacking python3-packaging (24.1-1) ... 130s Selecting previously unselected package python3-numexpr. 130s Preparing to unpack .../08-python3-numexpr_2.10.1-2_s390x.deb ... 130s Unpacking python3-numexpr (2.10.1-2) ... 130s Selecting previously unselected package python3-pluggy. 130s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 130s Unpacking python3-pluggy (1.5.0-1) ... 130s Selecting previously unselected package python3-scipy. 130s Preparing to unpack .../10-python3-scipy_1.13.1-5_s390x.deb ... 130s Unpacking python3-scipy (1.13.1-5) ... 130s Selecting previously unselected package python3-pymbar. 131s Preparing to unpack .../11-python3-pymbar_4.0.3-2_all.deb ... 131s Unpacking python3-pymbar (4.0.3-2) ... 131s Selecting previously unselected package python3-pytest. 131s Preparing to unpack .../12-python3-pytest_8.3.3-1_all.deb ... 131s Unpacking python3-pytest (8.3.3-1) ... 131s Selecting previously unselected package autopkgtest-satdep. 131s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 131s Unpacking autopkgtest-satdep (0) ... 131s Setting up python3-iniconfig (1.1.1-2) ... 131s Setting up python3-decorator (5.1.1-5) ... 131s Setting up libblas3:s390x (3.12.0-3build2) ... 131s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 131s Setting up python3-packaging (24.1-1) ... 131s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 131s Setting up python3-pluggy (1.5.0-1) ... 131s Setting up liblapack3:s390x (3.12.0-3build2) ... 131s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 131s Setting up python3-pytest (8.3.3-1) ... 131s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 133s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 133s Setting up python3-scipy (1.13.1-5) ... 137s Setting up python3-numexpr (2.10.1-2) ... 137s Setting up python3-pymbar (4.0.3-2) ... 137s Setting up autopkgtest-satdep (0) ... 137s Processing triggers for man-db (2.12.1-3) ... 137s Processing triggers for libc-bin (2.40-1ubuntu3) ... 139s (Reading database ... 58103 files and directories currently installed.) 139s Removing autopkgtest-satdep (0) ... 140s autopkgtest [15:31:21]: test command1: rm pymbar/*.py && pytest-3 140s autopkgtest [15:31:21]: test command1: [----------------------- 141s ============================= test session starts ============================== 141s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 141s rootdir: /tmp/autopkgtest.MPTwLu/build.Qux/src 141s configfile: setup.cfg 141s plugins: typeguard-4.4.1 141s collected 150 items 141s 141s pymbar/tests/test_bar.py ..... [ 3%] 141s pymbar/tests/test_exp.py .... [ 6%] 146s pymbar/tests/test_fes.py ..xxsssssssss.....xxssssssss [ 24%] 148s pymbar/tests/test_mbar.py ...x..........x...............x..........xxxx. [ 55%] 148s ..x..................x [ 70%] 158s pymbar/tests/test_mbar_solvers.py ................ [ 80%] 161s pymbar/tests/test_timeseries.py ..ss.ss.. [ 86%] 162s pymbar/tests/test_utils.py ....xx..xx..xx..xx.. [100%] 162s 162s =============================== warnings summary =============================== 162s pymbar/tests/test_mbar_solvers.py:24 162s /tmp/autopkgtest.MPTwLu/build.Qux/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 162s @pytest.mark.flaky(max_runs=2) # Uses flaky plugin for pytest 162s 162s pymbar/tests/test_mbar_solvers.py:67 162s /tmp/autopkgtest.MPTwLu/build.Qux/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 162s pytest.param("TNC", marks=pytest.mark.flaky(max_runs=2)), # This one is flaky 162s 162s pymbar/tests/test_fes.py: 243 warnings 162s /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.) 162s g[i - 1] = N * np.dot(w_n, db_c[i](x_n)) 162s 162s pymbar/tests/test_fes.py::test_1d_fes_spline[from-lowest-gen_kwargs0] 162s pymbar/tests/test_fes.py::test_1d_fes_spline[from-lowest-gen_kwargs1] 162s pymbar/tests/test_fes.py::test_1d_fes_spline_bootstraped 162s /usr/lib/python3/dist-packages/scipy/optimize/_optimize.py:2116: OptimizeWarning: Warning: Desired error not necessarily achieved due to precision loss. 162s return terminate(2, msg) 162s 162s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 162s ========== 108 passed, 21 skipped, 21 xfailed, 248 warnings in 21.39s ========== 162s autopkgtest [15:31:43]: test command1: -----------------------] 162s autopkgtest [15:31:43]: test command1: - - - - - - - - - - results - - - - - - - - - - 162s command1 PASS 163s autopkgtest [15:31:44]: test autodep8-python3: preparing testbed 282s autopkgtest [15:33:43]: testbed dpkg architecture: s390x 282s autopkgtest [15:33:43]: testbed apt version: 2.9.8 282s autopkgtest [15:33:43]: @@@@@@@@@@@@@@@@@@@@ test bed setup 283s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 283s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 283s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [16.5 kB] 283s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [962 kB] 284s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 284s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x Packages [110 kB] 284s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe s390x Packages [639 kB] 284s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse s390x Packages [17.4 kB] 284s Fetched 1931 kB in 1s (2238 kB/s) 284s Reading package lists... 286s Reading package lists... 286s Building dependency tree... 286s Reading state information... 286s Calculating upgrade... 286s The following NEW packages will be installed: 286s python3.13-gdbm 286s The following packages will be upgraded: 286s libgnutls30t64 libgpgme11t64 libjson-glib-1.0-0 libjson-glib-1.0-common 286s libpython3-stdlib libutempter0 python3 python3-gdbm python3-minimal 286s 9 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 286s Need to get 1285 kB of archives. 286s After this operation, 103 kB of additional disk space will be used. 286s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-minimal s390x 3.12.7-1 [27.4 kB] 286s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3 s390x 3.12.7-1 [24.0 kB] 286s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x libpython3-stdlib s390x 3.12.7-1 [10.0 kB] 286s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libgnutls30t64 s390x 3.8.8-2ubuntu1 [950 kB] 287s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-gdbm s390x 3.13.0-2 [31.0 kB] 287s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-gdbm s390x 3.12.7-1 [8642 B] 287s Get:7 http://ftpmaster.internal/ubuntu plucky/main s390x libgpgme11t64 s390x 1.23.2-5ubuntu4 [151 kB] 287s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B] 287s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x libjson-glib-1.0-0 s390x 1.10.0+ds-3 [67.5 kB] 287s Get:10 http://ftpmaster.internal/ubuntu plucky/main s390x libutempter0 s390x 1.2.1-4 [9708 B] 287s Fetched 1285 kB in 1s (2416 kB/s) 287s (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 ... 55510 files and directories currently installed.) 287s Preparing to unpack .../python3-minimal_3.12.7-1_s390x.deb ... 287s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 287s Setting up python3-minimal (3.12.7-1) ... 287s (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 ... 55510 files and directories currently installed.) 287s Preparing to unpack .../python3_3.12.7-1_s390x.deb ... 287s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 287s Preparing to unpack .../libpython3-stdlib_3.12.7-1_s390x.deb ... 287s Unpacking libpython3-stdlib:s390x (3.12.7-1) over (3.12.6-0ubuntu1) ... 287s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_s390x.deb ... 287s Unpacking libgnutls30t64:s390x (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ... 287s Setting up libgnutls30t64:s390x (3.8.8-2ubuntu1) ... 287s Selecting previously unselected package python3.13-gdbm. 287s (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 ... 55510 files and directories currently installed.) 287s Preparing to unpack .../0-python3.13-gdbm_3.13.0-2_s390x.deb ... 287s Unpacking python3.13-gdbm (3.13.0-2) ... 287s Preparing to unpack .../1-python3-gdbm_3.12.7-1_s390x.deb ... 287s Unpacking python3-gdbm:s390x (3.12.7-1) over (3.12.6-1ubuntu1) ... 287s Preparing to unpack .../2-libgpgme11t64_1.23.2-5ubuntu4_s390x.deb ... 287s Unpacking libgpgme11t64:s390x (1.23.2-5ubuntu4) over (1.18.0-4.1ubuntu4) ... 287s Preparing to unpack .../3-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ... 287s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ... 287s Preparing to unpack .../4-libjson-glib-1.0-0_1.10.0+ds-3_s390x.deb ... 287s Unpacking libjson-glib-1.0-0:s390x (1.10.0+ds-3) over (1.10.0+ds-2) ... 287s Preparing to unpack .../5-libutempter0_1.2.1-4_s390x.deb ... 287s Unpacking libutempter0:s390x (1.2.1-4) over (1.2.1-3build1) ... 287s Setting up libutempter0:s390x (1.2.1-4) ... 287s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ... 287s Setting up libgpgme11t64:s390x (1.23.2-5ubuntu4) ... 287s Setting up python3.13-gdbm (3.13.0-2) ... 287s Setting up libpython3-stdlib:s390x (3.12.7-1) ... 287s Setting up python3 (3.12.7-1) ... 288s Setting up libjson-glib-1.0-0:s390x (1.10.0+ds-3) ... 288s Setting up python3-gdbm:s390x (3.12.7-1) ... 288s Processing triggers for man-db (2.12.1-3) ... 288s Processing triggers for libc-bin (2.40-1ubuntu3) ... 288s Reading package lists... 288s Building dependency tree... 288s Reading state information... 288s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 289s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 289s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 289s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 289s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 290s Reading package lists... 290s Reading package lists... 290s Building dependency tree... 290s Reading state information... 290s Calculating upgrade... 290s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 290s Reading package lists... 290s Building dependency tree... 290s Reading state information... 290s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 299s Reading package lists... 299s Building dependency tree... 299s Reading state information... 299s Starting pkgProblemResolver with broken count: 0 299s Starting 2 pkgProblemResolver with broken count: 0 299s Done 300s The following additional packages will be installed: 300s libblas3 libgfortran5 liblapack3 liblbfgsb0 libpython3.13-minimal 300s libpython3.13-stdlib python3-all python3-decorator python3-numexpr 300s python3-numpy python3-packaging python3-pymbar python3-scipy python3.13 300s python3.13-minimal 300s Suggested packages: 300s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 300s python3.13-venv python3.13-doc binfmt-support 300s Recommended packages: 300s g++ | c++-compiler python3-pil 300s The following NEW packages will be installed: 300s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 300s libpython3.13-minimal libpython3.13-stdlib python3-all python3-decorator 300s python3-numexpr python3-numpy python3-packaging python3-pymbar python3-scipy 300s python3.13 python3.13-minimal 300s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 300s Need to get 31.6 MB/31.6 MB of archives. 300s After this operation, 125 MB of additional disk space will be used. 300s Get:1 /tmp/autopkgtest.MPTwLu/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 300s Get:2 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-minimal s390x 3.13.0-2 [877 kB] 301s Get:3 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13-minimal s390x 3.13.0-2 [2172 kB] 301s Get:4 http://ftpmaster.internal/ubuntu plucky/main s390x libblas3 s390x 3.12.0-3build2 [238 kB] 302s Get:5 http://ftpmaster.internal/ubuntu plucky/main s390x libgfortran5 s390x 14.2.0-8ubuntu1 [587 kB] 302s Get:6 http://ftpmaster.internal/ubuntu plucky/main s390x liblapack3 s390x 3.12.0-3build2 [2953 kB] 302s Get:7 http://ftpmaster.internal/ubuntu plucky/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 302s Get:8 http://ftpmaster.internal/ubuntu plucky/main s390x libpython3.13-stdlib s390x 3.13.0-2 [2086 kB] 303s Get:9 http://ftpmaster.internal/ubuntu plucky/main s390x python3.13 s390x 3.13.0-2 [719 kB] 303s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main s390x python3-all s390x 3.12.7-1 [890 B] 303s Get:11 http://ftpmaster.internal/ubuntu plucky/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 303s Get:12 http://ftpmaster.internal/ubuntu plucky/main s390x python3-numpy s390x 1:1.26.4+ds-11build1 [4113 kB] 303s Get:13 http://ftpmaster.internal/ubuntu plucky/main s390x python3-packaging all 24.1-1 [41.4 kB] 303s Get:14 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-numexpr s390x 2.10.1-2 [138 kB] 303s Get:15 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-scipy s390x 1.13.1-5 [17.5 MB] 305s Get:16 http://ftpmaster.internal/ubuntu plucky/universe s390x python3-pymbar all 4.0.3-2 [80.7 kB] 305s Fetched 31.6 MB in 5s (6078 kB/s) 305s Selecting previously unselected package libpython3.13-minimal:s390x. 305s (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 ... 55517 files and directories currently installed.) 305s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_s390x.deb ... 305s Unpacking libpython3.13-minimal:s390x (3.13.0-2) ... 305s Selecting previously unselected package python3.13-minimal. 305s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_s390x.deb ... 305s Unpacking python3.13-minimal (3.13.0-2) ... 305s Selecting previously unselected package libblas3:s390x. 305s Preparing to unpack .../02-libblas3_3.12.0-3build2_s390x.deb ... 305s Unpacking libblas3:s390x (3.12.0-3build2) ... 305s Selecting previously unselected package libgfortran5:s390x. 305s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_s390x.deb ... 305s Unpacking libgfortran5:s390x (14.2.0-8ubuntu1) ... 305s Selecting previously unselected package liblapack3:s390x. 305s Preparing to unpack .../04-liblapack3_3.12.0-3build2_s390x.deb ... 305s Unpacking liblapack3:s390x (3.12.0-3build2) ... 305s Selecting previously unselected package liblbfgsb0:s390x. 305s Preparing to unpack .../05-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 305s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 305s Selecting previously unselected package libpython3.13-stdlib:s390x. 305s Preparing to unpack .../06-libpython3.13-stdlib_3.13.0-2_s390x.deb ... 305s Unpacking libpython3.13-stdlib:s390x (3.13.0-2) ... 305s Selecting previously unselected package python3.13. 305s Preparing to unpack .../07-python3.13_3.13.0-2_s390x.deb ... 305s Unpacking python3.13 (3.13.0-2) ... 305s Selecting previously unselected package python3-all. 305s Preparing to unpack .../08-python3-all_3.12.7-1_s390x.deb ... 305s Unpacking python3-all (3.12.7-1) ... 305s Selecting previously unselected package python3-decorator. 305s Preparing to unpack .../09-python3-decorator_5.1.1-5_all.deb ... 305s Unpacking python3-decorator (5.1.1-5) ... 305s Selecting previously unselected package python3-numpy. 305s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_s390x.deb ... 305s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 305s Selecting previously unselected package python3-packaging. 305s Preparing to unpack .../11-python3-packaging_24.1-1_all.deb ... 305s Unpacking python3-packaging (24.1-1) ... 305s Selecting previously unselected package python3-numexpr. 305s Preparing to unpack .../12-python3-numexpr_2.10.1-2_s390x.deb ... 305s Unpacking python3-numexpr (2.10.1-2) ... 306s Selecting previously unselected package python3-scipy. 306s Preparing to unpack .../13-python3-scipy_1.13.1-5_s390x.deb ... 306s Unpacking python3-scipy (1.13.1-5) ... 306s Selecting previously unselected package python3-pymbar. 306s Preparing to unpack .../14-python3-pymbar_4.0.3-2_all.deb ... 306s Unpacking python3-pymbar (4.0.3-2) ... 306s Selecting previously unselected package autopkgtest-satdep. 306s Preparing to unpack .../15-2-autopkgtest-satdep.deb ... 306s Unpacking autopkgtest-satdep (0) ... 306s Setting up libpython3.13-minimal:s390x (3.13.0-2) ... 306s Setting up python3-decorator (5.1.1-5) ... 306s Setting up libblas3:s390x (3.12.0-3build2) ... 306s update-alternatives: using /usr/lib/s390x-linux-gnu/blas/libblas.so.3 to provide /usr/lib/s390x-linux-gnu/libblas.so.3 (libblas.so.3-s390x-linux-gnu) in auto mode 306s Setting up python3-packaging (24.1-1) ... 306s Setting up libgfortran5:s390x (14.2.0-8ubuntu1) ... 306s Setting up python3.13-minimal (3.13.0-2) ... 307s Setting up libpython3.13-stdlib:s390x (3.13.0-2) ... 307s Setting up liblapack3:s390x (3.12.0-3build2) ... 307s update-alternatives: using /usr/lib/s390x-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/s390x-linux-gnu/liblapack.so.3 (liblapack.so.3-s390x-linux-gnu) in auto mode 307s Setting up python3.13 (3.13.0-2) ... 308s Setting up python3-all (3.12.7-1) ... 308s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 312s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 312s Setting up python3-scipy (1.13.1-5) ... 319s Setting up python3-numexpr (2.10.1-2) ... 319s Setting up python3-pymbar (4.0.3-2) ... 319s Setting up autopkgtest-satdep (0) ... 319s Processing triggers for systemd (256.5-2ubuntu4) ... 319s Processing triggers for man-db (2.12.1-3) ... 319s Processing triggers for libc-bin (2.40-1ubuntu3) ... 321s (Reading database ... 58697 files and directories currently installed.) 321s Removing autopkgtest-satdep (0) ... 324s autopkgtest [15:34:25]: 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 324s autopkgtest [15:34:25]: test autodep8-python3: [----------------------- 324s Testing with python3.13: 324s Traceback (most recent call last): 324s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 324s from . import multiarray 324s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 324s from . import overrides 324s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 324s from numpy.core._multiarray_umath import ( 324s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 324s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 324s 324s During handling of the above exception, another exception occurred: 324s 324s Traceback (most recent call last): 324s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 324s from numpy.__config__ import show as show_config 324s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 324s from numpy.core._multiarray_umath import ( 324s ...<3 lines>... 324s ) 324s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 324s raise ImportError(msg) 324s ImportError: 324s 324s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 324s 324s Importing the numpy C-extensions failed. This error can happen for 324s many reasons, often due to issues with your setup or how NumPy was 324s installed. 324s 324s We have compiled some common reasons and troubleshooting tips at: 324s 324s https://numpy.org/devdocs/user/troubleshooting-importerror.html 324s 324s Please note and check the following: 324s 324s * The Python version is: Python3.13 from "/usr/bin/python3.13" 324s * The NumPy version is: "1.26.4" 324s 324s and make sure that they are the versions you expect. 324s Please carefully study the documentation linked above for further help. 324s 324s Original error was: No module named 'numpy.core._multiarray_umath' 324s 324s 324s The above exception was the direct cause of the following exception: 324s 324s Traceback (most recent call last): 324s File "", line 1, in 324s import pymbar; print(pymbar) 324s ^^^^^^^^^^^^^ 324s File "/usr/lib/python3/dist-packages/pymbar/__init__.py", line 31, in 324s from . import timeseries, testsystems, confidenceintervals 324s File "/usr/lib/python3/dist-packages/pymbar/timeseries.py", line 60, in 324s import numpy as np 324s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 324s raise ImportError(msg) from e 324s ImportError: Error importing numpy: you should not try to import numpy from 324s its source directory; please exit the numpy source tree, and relaunch 324s your python interpreter from there. 325s autopkgtest [15:34:26]: test autodep8-python3: -----------------------] 325s autopkgtest [15:34:26]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 325s autodep8-python3 FAIL non-zero exit status 1 325s autopkgtest [15:34:26]: @@@@@@@@@@@@@@@@@@@@ summary 325s command1 PASS 325s autodep8-python3 FAIL non-zero exit status 1 337s nova [W] Using flock in prodstack6-s390x 337s flock: timeout while waiting to get lock 337s Creating nova instance adt-plucky-s390x-python-pymbar-20241113-152901-juju-7f2275-prod-proposed-migration-environment-15-f25ccf95-5207-4783-83de-d88b2b9c727b from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)... 337s nova [W] Using flock in prodstack6-s390x 337s Creating nova instance adt-plucky-s390x-python-pymbar-20241113-152901-juju-7f2275-prod-proposed-migration-environment-15-f25ccf95-5207-4783-83de-d88b2b9c727b from image adt/ubuntu-plucky-s390x-server-20241113.img (UUID e740277e-1f72-40ae-bfbe-46030537c71c)...