0s autopkgtest [13:50:28]: starting date and time: 2024-11-14 13:50:28+0000 0s autopkgtest [13:50:28]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky 0s autopkgtest [13:50:28]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yg2d_np3/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 builder-cpu4-ram8-disk100 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-27.secgroup --name adt-plucky-amd64-python-pymbar-20241114-135028-juju-7f2275-prod-proposed-migration-environment-15-b8f87d65-3356-455f-acb9-3bbf66e141b1 --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-amd64 -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/ 58s autopkgtest [13:51:26]: testbed dpkg architecture: amd64 58s autopkgtest [13:51:26]: testbed apt version: 2.9.8 58s autopkgtest [13:51:26]: @@@@@@@@@@@@@@@@@@@@ test bed setup 60s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 60s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [983 kB] 60s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 60s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 60s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 60s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.9 kB] 60s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [138 kB] 60s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 60s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [291 kB] 60s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [749 kB] 60s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [1084 B] 60s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9252 B] 60s Fetched 2484 kB in 1s (3117 kB/s) 60s Reading package lists... 62s Reading package lists... 63s Building dependency tree... 63s Reading state information... 63s Calculating upgrade... 63s The following NEW packages will be installed: 63s python3.13-gdbm 63s The following packages will be upgraded: 63s libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal 63s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 63s Need to get 116 kB of archives. 63s After this operation, 100 kB of additional disk space will be used. 63s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 63s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 63s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 63s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 63s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 63s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 64s Fetched 116 kB in 0s (340 kB/s) 64s (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 ... 75542 files and directories currently installed.) 64s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 64s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 64s Setting up python3-minimal (3.12.7-1) ... 64s (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 ... 75542 files and directories currently installed.) 64s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 64s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 64s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 64s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 64s Selecting previously unselected package python3.13-gdbm. 64s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 64s Unpacking python3.13-gdbm (3.13.0-2) ... 64s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 64s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 64s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 64s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 64s Setting up python3.13-gdbm (3.13.0-2) ... 64s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 64s Setting up python3 (3.12.7-1) ... 65s Setting up python3-gdbm:amd64 (3.12.7-1) ... 65s Setting up pastebinit (1.7.1-1) ... 65s Processing triggers for man-db (2.12.1-3) ... 65s Reading package lists... 65s Building dependency tree... 65s Reading state information... 66s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 66s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 66s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 66s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 66s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 67s Reading package lists... 67s Reading package lists... 67s Building dependency tree... 67s Reading state information... 67s Calculating upgrade... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 68s Reading package lists... 68s Building dependency tree... 68s Reading state information... 68s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 71s autopkgtest [13:51:39]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 71s autopkgtest [13:51:39]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 74s Get:1 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (dsc) [2234 B] 74s Get:2 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (tar) [17.2 MB] 74s Get:3 http://ftpmaster.internal/ubuntu plucky/universe python-pymbar 4.0.3-2 (diff) [3444 B] 74s gpgv: Signature made Sat Jun 29 17:20:42 2024 UTC 74s gpgv: using RSA key 8F6DE104377F3B11E741748731F3144544A1741A 74s gpgv: issuer "tchet@debian.org" 74s gpgv: Can't check signature: No public key 74s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_4.0.3-2.dsc: no acceptable signature found 74s autopkgtest [13:51:42]: testing package python-pymbar version 4.0.3-2 75s autopkgtest [13:51:43]: build not needed 76s autopkgtest [13:51:44]: test command1: preparing testbed 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 80s Starting pkgProblemResolver with broken count: 0 80s Starting 2 pkgProblemResolver with broken count: 0 80s Done 80s The following additional packages will be installed: 80s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 80s python3-iniconfig python3-numexpr python3-numpy python3-packaging 80s python3-pluggy python3-pymbar python3-pytest python3-scipy 80s Suggested packages: 80s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 80s Recommended packages: 80s g++ | c++-compiler python3-pil 80s The following NEW packages will be installed: 80s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 80s python3-decorator python3-iniconfig python3-numexpr python3-numpy 80s python3-packaging python3-pluggy python3-pymbar python3-pytest python3-scipy 80s 0 upgraded, 14 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 27.0 MB/27.0 MB of archives. 80s After this operation, 111 MB of additional disk space will be used. 80s Get:1 /tmp/autopkgtest.fPoYD8/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 81s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 81s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 81s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 81s Get:5 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 81s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 81s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 81s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 82s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 82s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numexpr amd64 2.10.1-2 [117 kB] 82s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 82s Get:12 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 83s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymbar all 4.0.3-2 [80.7 kB] 83s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 83s Fetched 27.0 MB in 3s (9916 kB/s) 83s Selecting previously unselected package libblas3:amd64. 83s (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 ... 75549 files and directories currently installed.) 83s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 83s Unpacking libblas3:amd64 (3.12.0-3build2) ... 83s Selecting previously unselected package libgfortran5:amd64. 83s Preparing to unpack .../01-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 83s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 83s Selecting previously unselected package liblapack3:amd64. 83s Preparing to unpack .../02-liblapack3_3.12.0-3build2_amd64.deb ... 83s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 83s Selecting previously unselected package liblbfgsb0:amd64. 83s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 83s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 83s Selecting previously unselected package python3-decorator. 83s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 83s Unpacking python3-decorator (5.1.1-5) ... 83s Selecting previously unselected package python3-iniconfig. 83s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 83s Unpacking python3-iniconfig (1.1.1-2) ... 83s Selecting previously unselected package python3-numpy. 83s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 83s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 84s Selecting previously unselected package python3-packaging. 84s Preparing to unpack .../07-python3-packaging_24.1-1_all.deb ... 84s Unpacking python3-packaging (24.1-1) ... 84s Selecting previously unselected package python3-numexpr. 84s Preparing to unpack .../08-python3-numexpr_2.10.1-2_amd64.deb ... 84s Unpacking python3-numexpr (2.10.1-2) ... 84s Selecting previously unselected package python3-pluggy. 84s Preparing to unpack .../09-python3-pluggy_1.5.0-1_all.deb ... 84s Unpacking python3-pluggy (1.5.0-1) ... 84s Selecting previously unselected package python3-scipy. 84s Preparing to unpack .../10-python3-scipy_1.13.1-5_amd64.deb ... 84s Unpacking python3-scipy (1.13.1-5) ... 84s Selecting previously unselected package python3-pymbar. 84s Preparing to unpack .../11-python3-pymbar_4.0.3-2_all.deb ... 84s Unpacking python3-pymbar (4.0.3-2) ... 84s Selecting previously unselected package python3-pytest. 84s Preparing to unpack .../12-python3-pytest_8.3.3-1_all.deb ... 84s Unpacking python3-pytest (8.3.3-1) ... 84s Selecting previously unselected package autopkgtest-satdep. 84s Preparing to unpack .../13-1-autopkgtest-satdep.deb ... 84s Unpacking autopkgtest-satdep (0) ... 84s Setting up python3-iniconfig (1.1.1-2) ... 84s Setting up python3-decorator (5.1.1-5) ... 84s Setting up libblas3:amd64 (3.12.0-3build2) ... 84s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 84s Setting up python3-packaging (24.1-1) ... 85s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 85s Setting up python3-pluggy (1.5.0-1) ... 85s Setting up liblapack3:amd64 (3.12.0-3build2) ... 85s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 85s Setting up python3-pytest (8.3.3-1) ... 85s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 86s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 86s Setting up python3-scipy (1.13.1-5) ... 89s Setting up python3-numexpr (2.10.1-2) ... 89s Setting up python3-pymbar (4.0.3-2) ... 89s Setting up autopkgtest-satdep (0) ... 89s Processing triggers for man-db (2.12.1-3) ... 89s Processing triggers for libc-bin (2.40-1ubuntu3) ... 91s (Reading database ... 78135 files and directories currently installed.) 91s Removing autopkgtest-satdep (0) ... 92s autopkgtest [13:52:00]: test command1: rm pymbar/*.py && pytest-3 92s autopkgtest [13:52:00]: test command1: [----------------------- 93s ============================= test session starts ============================== 93s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 93s rootdir: /tmp/autopkgtest.fPoYD8/build.7XB/src 93s configfile: setup.cfg 93s plugins: typeguard-4.4.1 93s collected 150 items 93s 93s pymbar/tests/test_bar.py ..... [ 3%] 93s pymbar/tests/test_exp.py .... [ 6%] 97s pymbar/tests/test_fes.py ..xxsssssssss.....xxssssssss [ 24%] 99s pymbar/tests/test_mbar.py ...x..........x...............x..........xxxx. [ 55%] 100s ..x..................x [ 70%] 184s pymbar/tests/test_mbar_solvers.py ................ [ 80%] 187s pymbar/tests/test_timeseries.py ..ss.ss.. [ 86%] 187s pymbar/tests/test_utils.py ....xx..xx..xx..xx.. [100%] 187s 187s =============================== warnings summary =============================== 187s pymbar/tests/test_mbar_solvers.py:24 187s /tmp/autopkgtest.fPoYD8/build.7XB/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 187s @pytest.mark.flaky(max_runs=2) # Uses flaky plugin for pytest 187s 187s pymbar/tests/test_mbar_solvers.py:67 187s /tmp/autopkgtest.fPoYD8/build.7XB/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 187s pytest.param("TNC", marks=pytest.mark.flaky(max_runs=2)), # This one is flaky 187s 187s pymbar/tests/test_fes.py: 147 warnings 187s /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.) 187s g[i - 1] = N * np.dot(w_n, db_c[i](x_n)) 187s 187s pymbar/tests/test_mbar_solvers.py::test_protocols[trust-krylov] 187s /usr/lib/python3/dist-packages/scipy/optimize/_trustregion.py:225: RuntimeWarning: invalid value encountered in multiply 187s 187s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 187s ===== 108 passed, 21 skipped, 21 xfailed, 150 warnings in 94.61s (0:01:34) ===== 188s autopkgtest [13:53:36]: test command1: -----------------------] 188s autopkgtest [13:53:36]: test command1: - - - - - - - - - - results - - - - - - - - - - 188s command1 PASS 188s autopkgtest [13:53:36]: test autodep8-python3: preparing testbed 246s autopkgtest [13:54:34]: testbed dpkg architecture: amd64 246s autopkgtest [13:54:34]: testbed apt version: 2.9.8 246s autopkgtest [13:54:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 247s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 247s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [983 kB] 247s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 247s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 247s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [105 kB] 247s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [79.9 kB] 247s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [138 kB] 247s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 247s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [749 kB] 248s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [291 kB] 248s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [1084 B] 248s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [9252 B] 248s Fetched 2484 kB in 1s (3071 kB/s) 248s Reading package lists... 250s Reading package lists... 250s Building dependency tree... 250s Reading state information... 250s Calculating upgrade... 250s The following NEW packages will be installed: 250s python3.13-gdbm 250s The following packages will be upgraded: 250s libpython3-stdlib pastebinit python3 python3-gdbm python3-minimal 250s 5 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 250s Need to get 116 kB of archives. 250s After this operation, 100 kB of additional disk space will be used. 250s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-minimal amd64 3.12.7-1 [27.4 kB] 251s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3 amd64 3.12.7-1 [24.0 kB] 251s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libpython3-stdlib amd64 3.12.7-1 [10.0 kB] 251s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-gdbm amd64 3.13.0-2 [31.3 kB] 251s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-gdbm amd64 3.12.7-1 [8642 B] 251s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 pastebinit all 1.7.1-1 [14.9 kB] 251s Fetched 116 kB in 0s (345 kB/s) 251s (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 ... 75542 files and directories currently installed.) 251s Preparing to unpack .../python3-minimal_3.12.7-1_amd64.deb ... 251s Unpacking python3-minimal (3.12.7-1) over (3.12.6-0ubuntu1) ... 251s Setting up python3-minimal (3.12.7-1) ... 251s (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 ... 75542 files and directories currently installed.) 251s Preparing to unpack .../python3_3.12.7-1_amd64.deb ... 251s Unpacking python3 (3.12.7-1) over (3.12.6-0ubuntu1) ... 251s Preparing to unpack .../libpython3-stdlib_3.12.7-1_amd64.deb ... 251s Unpacking libpython3-stdlib:amd64 (3.12.7-1) over (3.12.6-0ubuntu1) ... 251s Selecting previously unselected package python3.13-gdbm. 251s Preparing to unpack .../python3.13-gdbm_3.13.0-2_amd64.deb ... 251s Unpacking python3.13-gdbm (3.13.0-2) ... 251s Preparing to unpack .../python3-gdbm_3.12.7-1_amd64.deb ... 251s Unpacking python3-gdbm:amd64 (3.12.7-1) over (3.12.6-1ubuntu1) ... 251s Preparing to unpack .../pastebinit_1.7.1-1_all.deb ... 251s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ... 252s Setting up python3.13-gdbm (3.13.0-2) ... 252s Setting up libpython3-stdlib:amd64 (3.12.7-1) ... 252s Setting up python3 (3.12.7-1) ... 252s Setting up python3-gdbm:amd64 (3.12.7-1) ... 252s Setting up pastebinit (1.7.1-1) ... 252s Processing triggers for man-db (2.12.1-3) ... 252s Reading package lists... 253s Building dependency tree... 253s Reading state information... 253s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 253s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 253s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 253s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 253s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 254s Reading package lists... 254s Reading package lists... 254s Building dependency tree... 254s Reading state information... 255s Calculating upgrade... 255s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 255s Reading package lists... 255s Building dependency tree... 255s Reading state information... 255s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 259s Reading package lists... 260s Building dependency tree... 260s Reading state information... 260s Starting pkgProblemResolver with broken count: 0 260s Starting 2 pkgProblemResolver with broken count: 0 260s Done 260s The following additional packages will be installed: 260s libblas3 libgfortran5 liblapack3 liblbfgsb0 libpython3.13-minimal 260s libpython3.13-stdlib python3-all python3-decorator python3-numexpr 260s python3-numpy python3-packaging python3-pymbar python3-scipy python3.13 260s python3.13-minimal 260s Suggested packages: 260s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 260s python3.13-venv python3.13-doc binfmt-support 260s Recommended packages: 260s g++ | c++-compiler python3-pil 260s The following NEW packages will be installed: 260s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 260s libpython3.13-minimal libpython3.13-stdlib python3-all python3-decorator 260s python3-numexpr python3-numpy python3-packaging python3-pymbar python3-scipy 260s python3.13 python3.13-minimal 260s 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. 260s Need to get 32.7 MB/32.7 MB of archives. 260s After this operation, 132 MB of additional disk space will be used. 260s Get:1 /tmp/autopkgtest.fPoYD8/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [712 B] 260s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-minimal amd64 3.13.0-2 [879 kB] 261s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13-minimal amd64 3.13.0-2 [2188 kB] 261s Get:4 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 261s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-8ubuntu1 [909 kB] 261s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 261s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 261s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 libpython3.13-stdlib amd64 3.13.0-2 [2107 kB] 261s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3.13 amd64 3.13.0-2 [719 kB] 261s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 python3-all amd64 3.12.7-1 [890 B] 261s Get:11 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 261s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 261s Get:13 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 261s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-numexpr amd64 2.10.1-2 [117 kB] 261s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 262s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pymbar all 4.0.3-2 [80.7 kB] 262s Fetched 32.7 MB in 2s (17.4 MB/s) 262s Selecting previously unselected package libpython3.13-minimal:amd64. 262s (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 ... 75549 files and directories currently installed.) 262s Preparing to unpack .../00-libpython3.13-minimal_3.13.0-2_amd64.deb ... 262s Unpacking libpython3.13-minimal:amd64 (3.13.0-2) ... 262s Selecting previously unselected package python3.13-minimal. 262s Preparing to unpack .../01-python3.13-minimal_3.13.0-2_amd64.deb ... 262s Unpacking python3.13-minimal (3.13.0-2) ... 262s Selecting previously unselected package libblas3:amd64. 262s Preparing to unpack .../02-libblas3_3.12.0-3build2_amd64.deb ... 262s Unpacking libblas3:amd64 (3.12.0-3build2) ... 262s Selecting previously unselected package libgfortran5:amd64. 262s Preparing to unpack .../03-libgfortran5_14.2.0-8ubuntu1_amd64.deb ... 262s Unpacking libgfortran5:amd64 (14.2.0-8ubuntu1) ... 262s Selecting previously unselected package liblapack3:amd64. 262s Preparing to unpack .../04-liblapack3_3.12.0-3build2_amd64.deb ... 262s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 263s Selecting previously unselected package liblbfgsb0:amd64. 263s Preparing to unpack .../05-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 263s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 263s Selecting previously unselected package libpython3.13-stdlib:amd64. 263s Preparing to unpack .../06-libpython3.13-stdlib_3.13.0-2_amd64.deb ... 263s Unpacking libpython3.13-stdlib:amd64 (3.13.0-2) ... 263s Selecting previously unselected package python3.13. 263s Preparing to unpack .../07-python3.13_3.13.0-2_amd64.deb ... 263s Unpacking python3.13 (3.13.0-2) ... 263s Selecting previously unselected package python3-all. 263s Preparing to unpack .../08-python3-all_3.12.7-1_amd64.deb ... 263s Unpacking python3-all (3.12.7-1) ... 263s Selecting previously unselected package python3-decorator. 263s Preparing to unpack .../09-python3-decorator_5.1.1-5_all.deb ... 263s Unpacking python3-decorator (5.1.1-5) ... 263s Selecting previously unselected package python3-numpy. 263s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 263s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 263s Selecting previously unselected package python3-packaging. 263s Preparing to unpack .../11-python3-packaging_24.1-1_all.deb ... 263s Unpacking python3-packaging (24.1-1) ... 263s Selecting previously unselected package python3-numexpr. 263s Preparing to unpack .../12-python3-numexpr_2.10.1-2_amd64.deb ... 263s Unpacking python3-numexpr (2.10.1-2) ... 263s Selecting previously unselected package python3-scipy. 263s Preparing to unpack .../13-python3-scipy_1.13.1-5_amd64.deb ... 263s Unpacking python3-scipy (1.13.1-5) ... 263s Selecting previously unselected package python3-pymbar. 263s Preparing to unpack .../14-python3-pymbar_4.0.3-2_all.deb ... 263s Unpacking python3-pymbar (4.0.3-2) ... 263s Selecting previously unselected package autopkgtest-satdep. 263s Preparing to unpack .../15-2-autopkgtest-satdep.deb ... 263s Unpacking autopkgtest-satdep (0) ... 263s Setting up libpython3.13-minimal:amd64 (3.13.0-2) ... 263s Setting up python3-decorator (5.1.1-5) ... 264s Setting up libblas3:amd64 (3.12.0-3build2) ... 264s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 264s Setting up python3-packaging (24.1-1) ... 264s Setting up libgfortran5:amd64 (14.2.0-8ubuntu1) ... 264s Setting up python3.13-minimal (3.13.0-2) ... 264s Setting up libpython3.13-stdlib:amd64 (3.13.0-2) ... 264s Setting up liblapack3:amd64 (3.12.0-3build2) ... 264s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 264s Setting up python3.13 (3.13.0-2) ... 265s Setting up python3-all (3.12.7-1) ... 265s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 268s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 268s Setting up python3-scipy (1.13.1-5) ... 273s Setting up python3-numexpr (2.10.1-2) ... 273s Setting up python3-pymbar (4.0.3-2) ... 273s Setting up autopkgtest-satdep (0) ... 273s Processing triggers for systemd (256.5-2ubuntu4) ... 273s Processing triggers for man-db (2.12.1-3) ... 273s Processing triggers for libc-bin (2.40-1ubuntu3) ... 276s (Reading database ... 78729 files and directories currently installed.) 276s Removing autopkgtest-satdep (0) ... 280s autopkgtest [13:55:08]: test autodep8-python3: set -e ; for py in $(py3versions -r 2>/dev/null) ; do cd "$AUTOPKGTEST_TMP" ; echo "Testing with $py:" ; $py -c "import pymbar; print(pymbar)" ; done 280s autopkgtest [13:55:08]: test autodep8-python3: [----------------------- 280s Testing with python3.13: 280s Traceback (most recent call last): 280s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 24, in 280s from . import multiarray 280s File "/usr/lib/python3/dist-packages/numpy/core/multiarray.py", line 10, in 280s from . import overrides 280s File "/usr/lib/python3/dist-packages/numpy/core/overrides.py", line 8, in 280s from numpy.core._multiarray_umath import ( 280s add_docstring, _get_implementing_args, _ArrayFunctionDispatcher) 280s ModuleNotFoundError: No module named 'numpy.core._multiarray_umath' 280s 280s During handling of the above exception, another exception occurred: 280s 280s Traceback (most recent call last): 280s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 130, in 280s from numpy.__config__ import show as show_config 280s File "/usr/lib/python3/dist-packages/numpy/__config__.py", line 4, in 280s from numpy.core._multiarray_umath import ( 280s ...<3 lines>... 280s ) 280s File "/usr/lib/python3/dist-packages/numpy/core/__init__.py", line 50, in 280s raise ImportError(msg) 280s ImportError: 280s 280s IMPORTANT: PLEASE READ THIS FOR ADVICE ON HOW TO SOLVE THIS ISSUE! 280s 280s Importing the numpy C-extensions failed. This error can happen for 280s many reasons, often due to issues with your setup or how NumPy was 280s installed. 280s 280s We have compiled some common reasons and troubleshooting tips at: 280s 280s https://numpy.org/devdocs/user/troubleshooting-importerror.html 280s 280s Please note and check the following: 280s 280s * The Python version is: Python3.13 from "/usr/bin/python3.13" 280s * The NumPy version is: "1.26.4" 280s 280s and make sure that they are the versions you expect. 280s Please carefully study the documentation linked above for further help. 280s 280s Original error was: No module named 'numpy.core._multiarray_umath' 280s 280s 280s The above exception was the direct cause of the following exception: 280s 280s Traceback (most recent call last): 280s File "", line 1, in 280s import pymbar; print(pymbar) 280s ^^^^^^^^^^^^^ 280s File "/usr/lib/python3/dist-packages/pymbar/__init__.py", line 31, in 280s from . import timeseries, testsystems, confidenceintervals 280s File "/usr/lib/python3/dist-packages/pymbar/timeseries.py", line 60, in 280s import numpy as np 280s File "/usr/lib/python3/dist-packages/numpy/__init__.py", line 135, in 280s raise ImportError(msg) from e 280s ImportError: Error importing numpy: you should not try to import numpy from 280s its source directory; please exit the numpy source tree, and relaunch 280s your python interpreter from there. 280s autopkgtest [13:55:08]: test autodep8-python3: -----------------------] 281s autopkgtest [13:55:09]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 281s autodep8-python3 FAIL non-zero exit status 1 281s autopkgtest [13:55:09]: @@@@@@@@@@@@@@@@@@@@ summary 281s command1 PASS 281s autodep8-python3 FAIL non-zero exit status 1 295s nova [W] Skipping flock for amd64 295s Creating nova instance adt-plucky-amd64-python-pymbar-20241114-135028-juju-7f2275-prod-proposed-migration-environment-15-b8f87d65-3356-455f-acb9-3bbf66e141b1 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)... 295s nova [W] Skipping flock for amd64 295s Creating nova instance adt-plucky-amd64-python-pymbar-20241114-135028-juju-7f2275-prod-proposed-migration-environment-15-b8f87d65-3356-455f-acb9-3bbf66e141b1 from image adt/ubuntu-plucky-amd64-server-20241114.img (UUID 79d80331-8736-463c-82c6-8c9e13c0a4ca)...