0s autopkgtest [02:35:11]: starting date and time: 2024-06-08 02:35:11+0000 0s autopkgtest [02:35:11]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [02:35:11]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work._itnbwed/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:pytest,src:astropy --apt-upgrade python-pymbar --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=pytest/8.2.2-1ubuntu1 astropy/6.0.1-4' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-3@bos01-s390x-4.secgroup --name adt-oracular-s390x-python-pymbar-20240608-023511-juju-7f2275-prod-proposed-migration-environment-3-bf1275f7-70ef-411d-a376-33a78f98eb0b --image adt/ubuntu-oracular-s390x-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-3 --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://us.ports.ubuntu.com/ubuntu-ports/ 142s autopkgtest [02:37:33]: testbed dpkg architecture: s390x 142s autopkgtest [02:37:33]: testbed apt version: 2.9.3 142s autopkgtest [02:37:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 143s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 143s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 144s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 144s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 144s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [333 kB] 144s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [47.8 kB] 144s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x Packages [1860 B] 144s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [258 kB] 144s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x Packages [1768 B] 144s Fetched 808 kB in 1s (994 kB/s) 144s Reading package lists... 146s Reading package lists... 146s Building dependency tree... 146s Reading state information... 147s Calculating upgrade... 147s The following packages will be upgraded: 147s debianutils libheif-plugin-aomdec libheif-plugin-aomenc 147s libheif-plugin-libde265 libheif1 libnetplan1 liburcu8t64 netplan-generator 147s netplan.io python3-netplan 147s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 147s Need to get 758 kB of archives. 147s After this operation, 48.1 kB disk space will be freed. 147s Get:1 http://ftpmaster.internal/ubuntu oracular/main s390x debianutils s390x 5.18 [90.2 kB] 147s Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x netplan-generator s390x 1.0-3ubuntu1 [59.2 kB] 147s Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x python3-netplan s390x 1.0-3ubuntu1 [22.9 kB] 147s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x netplan.io s390x 1.0-3ubuntu1 [65.8 kB] 147s Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x libnetplan1 s390x 1.0-3ubuntu1 [125 kB] 147s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-aomdec s390x 1.17.6-3 [10.1 kB] 147s Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-aomenc s390x 1.17.6-3 [15.1 kB] 147s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x libheif1 s390x 1.17.6-3 [295 kB] 147s Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-libde265 s390x 1.17.6-3 [8172 B] 147s Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x liburcu8t64 s390x 0.14.0-4 [66.5 kB] 148s Fetched 758 kB in 1s (1314 kB/s) 148s (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 ... 54607 files and directories currently installed.) 148s Preparing to unpack .../debianutils_5.18_s390x.deb ... 148s Unpacking debianutils (5.18) over (5.17build1) ... 148s Setting up debianutils (5.18) ... 148s (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 ... 54607 files and directories currently installed.) 148s Preparing to unpack .../0-netplan-generator_1.0-3ubuntu1_s390x.deb ... 148s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 148s Unpacking netplan-generator (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 148s Preparing to unpack .../1-python3-netplan_1.0-3ubuntu1_s390x.deb ... 148s Unpacking python3-netplan (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 148s Preparing to unpack .../2-netplan.io_1.0-3ubuntu1_s390x.deb ... 148s Unpacking netplan.io (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 148s Preparing to unpack .../3-libnetplan1_1.0-3ubuntu1_s390x.deb ... 148s Unpacking libnetplan1:s390x (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 148s Preparing to unpack .../4-libheif-plugin-aomdec_1.17.6-3_s390x.deb ... 148s Unpacking libheif-plugin-aomdec:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 148s Preparing to unpack .../5-libheif-plugin-aomenc_1.17.6-3_s390x.deb ... 148s Unpacking libheif-plugin-aomenc:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 148s Preparing to unpack .../6-libheif1_1.17.6-3_s390x.deb ... 148s Unpacking libheif1:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 148s Preparing to unpack .../7-libheif-plugin-libde265_1.17.6-3_s390x.deb ... 148s Unpacking libheif-plugin-libde265:s390x (1.17.6-3) over (1.17.6-1ubuntu4) ... 148s Preparing to unpack .../8-liburcu8t64_0.14.0-4_s390x.deb ... 148s Unpacking liburcu8t64:s390x (0.14.0-4) over (0.14.0-3.1build1) ... 148s Setting up liburcu8t64:s390x (0.14.0-4) ... 148s Setting up libnetplan1:s390x (1.0-3ubuntu1) ... 148s Setting up python3-netplan (1.0-3ubuntu1) ... 148s Setting up netplan-generator (1.0-3ubuntu1) ... 148s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 148s Setting up netplan.io (1.0-3ubuntu1) ... 148s Setting up libheif-plugin-aomdec:s390x (1.17.6-3) ... 148s Setting up libheif-plugin-libde265:s390x (1.17.6-3) ... 148s Setting up libheif1:s390x (1.17.6-3) ... 148s Setting up libheif-plugin-aomenc:s390x (1.17.6-3) ... 148s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 148s Processing triggers for man-db (2.12.1-1) ... 150s Processing triggers for dbus (1.14.10-4ubuntu4) ... 150s Reading package lists... 151s Building dependency tree... 151s Reading state information... 151s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 151s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 151s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 151s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 152s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 153s Reading package lists... 153s Reading package lists... 153s Building dependency tree... 153s Reading state information... 154s Calculating upgrade... 154s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 154s Reading package lists... 154s Building dependency tree... 154s Reading state information... 155s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 158s autopkgtest [02:37:49]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:14:26 UTC 2024 158s autopkgtest [02:37:49]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 161s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (dsc) [2363 B] 161s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (tar) [17.1 MB] 161s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (diff) [3916 B] 162s gpgv: Signature made Wed Feb 1 21:01:41 2023 UTC 162s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 162s gpgv: issuer "emollier@debian.org" 162s gpgv: Can't check signature: No public key 162s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found 162s autopkgtest [02:37:53]: testing package python-pymbar version 3.1.0-4 163s autopkgtest [02:37:54]: build not needed 208s autopkgtest [02:38:39]: test command1: preparing testbed 209s Reading package lists... 210s Building dependency tree... 210s Reading state information... 210s Starting pkgProblemResolver with broken count: 0 210s Starting 2 pkgProblemResolver with broken count: 0 210s Done 210s The following additional packages will be installed: 210s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 210s python3-iniconfig python3-numpy python3-packaging python3-pluggy 210s python3-pymbar python3-pytest python3-scipy 210s Suggested packages: 210s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 210s Recommended packages: 210s g++ | c++-compiler python3-pil 210s The following NEW packages will be installed: 210s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 210s python3-decorator python3-iniconfig python3-numpy python3-packaging 210s python3-pluggy python3-pymbar python3-pytest python3-scipy 211s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 211s Need to get 24.6 MB/24.6 MB of archives. 211s After this operation, 97.2 MB of additional disk space will be used. 211s Get:1 /tmp/autopkgtest.7RqYDx/1-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 211s Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] 211s Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x libgfortran5 s390x 14.1.0-1ubuntu1 [600 kB] 211s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] 211s Get:5 http://ftpmaster.internal/ubuntu oracular/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 211s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 211s Get:7 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-iniconfig all 1.1.1-2 [6024 B] 211s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x python3-numpy s390x 1:1.26.4+ds-10 [4090 kB] 212s Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x python3-packaging all 24.0-1 [41.1 kB] 212s Get:10 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-pluggy all 1.5.0-1 [21.0 kB] 212s Get:11 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-scipy s390x 1.11.4-10 [16.2 MB] 212s Get:12 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-pymbar all 3.1.0-4 [67.8 kB] 212s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x python3-pytest all 8.2.2-1ubuntu1 [250 kB] 213s Fetched 24.6 MB in 2s (12.9 MB/s) 213s Selecting previously unselected package libblas3:s390x. 213s (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 ... 54607 files and directories currently installed.) 213s Preparing to unpack .../00-libblas3_3.12.0-3build1_s390x.deb ... 213s Unpacking libblas3:s390x (3.12.0-3build1) ... 213s Selecting previously unselected package libgfortran5:s390x. 213s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_s390x.deb ... 213s Unpacking libgfortran5:s390x (14.1.0-1ubuntu1) ... 213s Selecting previously unselected package liblapack3:s390x. 213s Preparing to unpack .../02-liblapack3_3.12.0-3build1_s390x.deb ... 213s Unpacking liblapack3:s390x (3.12.0-3build1) ... 213s Selecting previously unselected package liblbfgsb0:s390x. 213s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 213s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 213s Selecting previously unselected package python3-decorator. 213s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 213s Unpacking python3-decorator (5.1.1-5) ... 213s Selecting previously unselected package python3-iniconfig. 213s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 213s Unpacking python3-iniconfig (1.1.1-2) ... 213s Selecting previously unselected package python3-numpy. 213s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-10_s390x.deb ... 213s Unpacking python3-numpy (1:1.26.4+ds-10) ... 214s Selecting previously unselected package python3-packaging. 214s Preparing to unpack .../07-python3-packaging_24.0-1_all.deb ... 214s Unpacking python3-packaging (24.0-1) ... 214s Selecting previously unselected package python3-pluggy. 214s Preparing to unpack .../08-python3-pluggy_1.5.0-1_all.deb ... 214s Unpacking python3-pluggy (1.5.0-1) ... 214s Selecting previously unselected package python3-scipy. 214s Preparing to unpack .../09-python3-scipy_1.11.4-10_s390x.deb ... 214s Unpacking python3-scipy (1.11.4-10) ... 215s Selecting previously unselected package python3-pymbar. 215s Preparing to unpack .../10-python3-pymbar_3.1.0-4_all.deb ... 215s Unpacking python3-pymbar (3.1.0-4) ... 215s Selecting previously unselected package python3-pytest. 215s Preparing to unpack .../11-python3-pytest_8.2.2-1ubuntu1_all.deb ... 215s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 215s Selecting previously unselected package autopkgtest-satdep. 215s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 215s Unpacking autopkgtest-satdep (0) ... 215s Setting up python3-iniconfig (1.1.1-2) ... 215s Setting up python3-decorator (5.1.1-5) ... 215s Setting up libblas3:s390x (3.12.0-3build1) ... 215s 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 215s Setting up python3-packaging (24.0-1) ... 216s Setting up libgfortran5:s390x (14.1.0-1ubuntu1) ... 216s Setting up python3-pluggy (1.5.0-1) ... 216s Setting up liblapack3:s390x (3.12.0-3build1) ... 216s 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 216s Setting up python3-pytest (8.2.2-1ubuntu1) ... 217s Setting up python3-numpy (1:1.26.4+ds-10) ... 220s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 220s Setting up python3-scipy (1.11.4-10) ... 226s Setting up python3-pymbar (3.1.0-4) ... 226s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 226s """A function that when zeroed is equivalent to the solution of 226s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 226s """ 226s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 226s """ 226s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 226s """ 226s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 226s """ 226s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 226s """ 226s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 226s """Compute estimate of overlap matrix between the states. 226s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 226s """Compute the free energy of occupying a number of bins. 226s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 226s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 227s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 227s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 227s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 227s """ 227s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 227s """Generate samples from forward and reverse Gaussian work distributions. 227s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 227s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 227s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 227s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 227s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 227s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 227s Setting up autopkgtest-satdep (0) ... 227s Processing triggers for man-db (2.12.1-1) ... 227s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 230s (Reading database ... 57081 files and directories currently installed.) 230s Removing autopkgtest-satdep (0) ... 231s autopkgtest [02:39:02]: test command1: rm pymbar/*.py && pytest-3 231s autopkgtest [02:39:02]: test command1: [----------------------- 232s ============================= test session starts ============================== 232s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 232s rootdir: /tmp/autopkgtest.7RqYDx/build.3N5/src 232s collected 37 items 232s 232s pymbar/tests/test_bar.py .. [ 5%] 724s pymbar/tests/test_covariance.py ... [ 13%] 761s pymbar/tests/test_mbar.py ................ [ 56%] 802s pymbar/tests/test_mbar_solvers.py .... [ 67%] 809s pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] 809s pymbar/tests/test_utils.py ... [100%] 809s 809s =============================== warnings summary =============================== 809s ../../../../usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29 809s /usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html 809s from pkg_resources import resource_filename 809s 809s pymbar/tests/test_bar.py: 4 warnings 809s pymbar/tests/test_covariance.py: 9 warnings 809s pymbar/tests/test_mbar.py: 8 warnings 809s pymbar/tests/test_mbar_solvers.py: 11 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:561: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s f_i = np.matrix(self.f_k) 809s 809s pymbar/tests/test_bar.py: 4 warnings 809s pymbar/tests/test_covariance.py: 3 warnings 809s pymbar/tests/test_mbar.py: 29 warnings 809s pymbar/tests/test_mbar_solvers.py: 11 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1772: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 809s 809s pymbar/tests/test_bar.py: 4 warnings 809s pymbar/tests/test_covariance.py: 3 warnings 809s pymbar/tests/test_mbar.py: 29 warnings 809s pymbar/tests/test_mbar_solvers.py: 11 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1773: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s W = np.matrix(W, dtype=np.float64) 809s 809s pymbar/tests/test_bar.py: 40 warnings 809s pymbar/tests/test_covariance.py: 78 warnings 809s pymbar/tests/test_mbar.py: 287 warnings 809s pymbar/tests/test_mbar_solvers.py: 99 warnings 809s /usr/lib/python3/dist-packages/numpy/matrixlib/defmatrix.py:70: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s return matrix(data, dtype=dtype, copy=False) 809s 809s pymbar/tests/test_bar.py: 4 warnings 809s pymbar/tests/test_covariance.py: 3 warnings 809s pymbar/tests/test_mbar.py: 29 warnings 809s pymbar/tests/test_mbar_solvers.py: 11 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1783: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Sigma = np.matrix(np.diag(np.sqrt(S2))) 809s 809s pymbar/tests/test_bar.py: 4 warnings 809s pymbar/tests/test_covariance.py: 3 warnings 809s pymbar/tests/test_mbar.py: 29 warnings 809s pymbar/tests/test_mbar_solvers.py: 11 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1784: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s V = np.matrix(V) 809s 809s pymbar/tests/test_bar.py: 4 warnings 809s pymbar/tests/test_covariance.py: 9 warnings 809s pymbar/tests/test_mbar.py: 23 warnings 809s pymbar/tests/test_mbar_solvers.py: 11 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1636: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s diag = np.matrix(cov.diagonal()) 809s 809s pymbar/tests/test_bar.py::test_bar_computeOverlap 809s pymbar/tests/test_bar.py::test_bar_computeOverlap 809s /usr/lib/python3/dist-packages/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases 809s warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) 809s 809s pymbar/tests/test_bar.py::test_bar_computeOverlap 809s pymbar/tests/test_bar.py::test_bar_computeOverlap 809s pymbar/tests/test_bar.py::test_bar_computeOverlap 809s pymbar/tests/test_bar.py::test_bar_computeOverlap 809s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 809s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 809s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 809s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:485: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s W = np.matrix(self.getWeights(), np.float64) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1753: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1754: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s W = np.matrix(W, dtype=np.float64) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1759: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Sigma = np.matrix(np.diag(S)) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1760: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s V = np.matrix(Vt).T 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:385: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s f_i = np.matrix(self.f_k) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1925: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1926: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s W = np.matrix(W, dtype=np.float64) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1931: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Sigma = np.matrix(np.diag(S)) 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1932: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s V = np.matrix(Vt).T 809s 809s pymbar/tests/test_covariance.py::test_100x100_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_oscillators 809s pymbar/tests/test_covariance.py::test_200x50_exponentials 809s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1784: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) 809s 809s pymbar/tests/test_mbar.py: 560 warnings 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:579: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 809s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1088: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s A_im = np.matrix(inner_results['observables']) 809s 809s pymbar/tests/test_mbar.py: 16 warnings 809s /tmp/autopkgtest.7RqYDx/build.3N5/src/pymbar/tests/test_mbar.py:23: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1377: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1382: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s f_k = np.matrix(inner_results['f']) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1389: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s u_k = np.matrix(inner_results['observables']) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s /tmp/autopkgtest.7RqYDx/build.3N5/src/pymbar/tests/test_mbar.py:253: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s /tmp/autopkgtest.7RqYDx/build.3N5/src/pymbar/tests/test_mbar.py:254: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 809s /tmp/autopkgtest.7RqYDx/build.3N5/src/pymbar/tests/test_mbar.py:255: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 809s /tmp/autopkgtest.7RqYDx/build.3N5/src/pymbar/tests/test_mbar.py:301: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) 809s 809s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 809s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 809s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 809s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 809s /usr/lib/python3/dist-packages/pymbar/mbar.py:1280: PendingDeprecationWarning: the matrix subclass is not the recommended way to represent matrices or deal with linear algebra (see https://docs.scipy.org/doc/numpy/user/numpy-for-matlab-users.html). Please adjust your code to use regular ndarray. 809s f_k = np.matrix(inner_results['f']) 809s 809s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 809s =========== 33 passed, 4 skipped, 1431 warnings in 577.80s (0:09:37) =========== 810s autopkgtest [02:48:41]: test command1: -----------------------] 810s command1 PASS 810s autopkgtest [02:48:41]: test command1: - - - - - - - - - - results - - - - - - - - - - 811s autopkgtest [02:48:42]: test autodep8-python3: preparing testbed 1038s autopkgtest [02:52:29]: testbed dpkg architecture: s390x 1038s autopkgtest [02:52:29]: testbed apt version: 2.9.3 1038s autopkgtest [02:52:29]: @@@@@@@@@@@@@@@@@@@@ test bed setup 1039s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 1040s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [333 kB] 1040s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 1040s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 1040s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 1040s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main s390x Packages [47.8 kB] 1040s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted s390x Packages [1860 B] 1040s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe s390x Packages [258 kB] 1040s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse s390x Packages [1768 B] 1040s Fetched 808 kB in 1s (919 kB/s) 1040s Reading package lists... 1043s Reading package lists... 1043s Building dependency tree... 1043s Reading state information... 1043s Calculating upgrade... 1044s The following packages will be upgraded: 1044s debianutils libheif-plugin-aomdec libheif-plugin-aomenc 1044s libheif-plugin-libde265 libheif1 libnetplan1 liburcu8t64 netplan-generator 1044s netplan.io python3-netplan 1044s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1044s Need to get 758 kB of archives. 1044s After this operation, 48.1 kB disk space will be freed. 1044s Get:1 http://ftpmaster.internal/ubuntu oracular/main s390x debianutils s390x 5.18 [90.2 kB] 1044s Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x netplan-generator s390x 1.0-3ubuntu1 [59.2 kB] 1044s Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x python3-netplan s390x 1.0-3ubuntu1 [22.9 kB] 1044s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x netplan.io s390x 1.0-3ubuntu1 [65.8 kB] 1044s Get:5 http://ftpmaster.internal/ubuntu oracular/main s390x libnetplan1 s390x 1.0-3ubuntu1 [125 kB] 1044s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-aomdec s390x 1.17.6-3 [10.1 kB] 1044s Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-aomenc s390x 1.17.6-3 [15.1 kB] 1044s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x libheif1 s390x 1.17.6-3 [295 kB] 1044s Get:9 http://ftpmaster.internal/ubuntu oracular/main s390x libheif-plugin-libde265 s390x 1.17.6-3 [8172 B] 1044s Get:10 http://ftpmaster.internal/ubuntu oracular/main s390x liburcu8t64 s390x 0.14.0-4 [66.5 kB] 1045s Fetched 758 kB in 1s (1032 kB/s) 1045s (Reading database ... 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(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 ... 54607 files and directories currently installed.) 1045s Preparing to unpack .../0-netplan-generator_1.0-3ubuntu1_s390x.deb ... 1045s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 1045s Unpacking netplan-generator (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 1045s Preparing to unpack .../1-python3-netplan_1.0-3ubuntu1_s390x.deb ... 1045s Unpacking python3-netplan 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1046s Unpacking liburcu8t64:s390x (0.14.0-4) over (0.14.0-3.1build1) ... 1046s Setting up liburcu8t64:s390x (0.14.0-4) ... 1046s Setting up libnetplan1:s390x (1.0-3ubuntu1) ... 1046s Setting up python3-netplan (1.0-3ubuntu1) ... 1046s Setting up netplan-generator (1.0-3ubuntu1) ... 1046s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 1046s Setting up netplan.io (1.0-3ubuntu1) ... 1046s Setting up libheif-plugin-aomdec:s390x (1.17.6-3) ... 1046s Setting up libheif-plugin-libde265:s390x (1.17.6-3) ... 1046s Setting up libheif1:s390x (1.17.6-3) ... 1046s Setting up libheif-plugin-aomenc:s390x (1.17.6-3) ... 1046s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 1046s Processing triggers for man-db (2.12.1-1) ... 1047s Processing triggers for dbus (1.14.10-4ubuntu4) ... 1048s Reading package lists... 1048s Building dependency tree... 1048s Reading state information... 1049s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1049s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 1049s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 1049s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 1049s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 1051s Reading package lists... 1051s Reading package lists... 1051s Building dependency tree... 1051s Reading state information... 1051s Calculating upgrade... 1052s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1052s Reading package lists... 1052s Building dependency tree... 1052s Reading state information... 1052s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1057s Reading package lists... 1057s Building dependency tree... 1057s Reading state information... 1057s Starting pkgProblemResolver with broken count: 0 1057s Starting 2 pkgProblemResolver with broken count: 0 1057s Done 1058s The following additional packages will be installed: 1058s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all python3-decorator 1058s python3-numpy python3-pymbar python3-scipy 1058s Suggested packages: 1058s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 1058s Recommended packages: 1058s g++ | c++-compiler python3-pil 1058s The following NEW packages will be installed: 1058s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all 1058s python3-decorator python3-numpy python3-pymbar python3-scipy 1058s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 1058s Need to get 24.2 MB/24.2 MB of archives. 1058s After this operation, 95.7 MB of additional disk space will be used. 1058s Get:1 /tmp/autopkgtest.7RqYDx/2-autopkgtest-satdep.deb autopkgtest-satdep s390x 0 [720 B] 1058s Get:2 http://ftpmaster.internal/ubuntu oracular/main s390x libblas3 s390x 3.12.0-3build1 [245 kB] 1058s Get:3 http://ftpmaster.internal/ubuntu oracular/main s390x libgfortran5 s390x 14.1.0-1ubuntu1 [600 kB] 1058s Get:4 http://ftpmaster.internal/ubuntu oracular/main s390x liblapack3 s390x 3.12.0-3build1 [2976 kB] 1059s Get:5 http://ftpmaster.internal/ubuntu oracular/universe s390x liblbfgsb0 s390x 3.0+dfsg.4-1build1 [32.4 kB] 1059s Get:6 http://ftpmaster.internal/ubuntu oracular/main s390x python3-all s390x 3.12.3-0ubuntu1 [890 B] 1059s Get:7 http://ftpmaster.internal/ubuntu oracular/main s390x python3-decorator all 5.1.1-5 [10.1 kB] 1059s Get:8 http://ftpmaster.internal/ubuntu oracular/main s390x python3-numpy s390x 1:1.26.4+ds-10 [4090 kB] 1060s Get:9 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-scipy s390x 1.11.4-10 [16.2 MB] 1062s Get:10 http://ftpmaster.internal/ubuntu oracular/universe s390x python3-pymbar all 3.1.0-4 [67.8 kB] 1062s Fetched 24.2 MB in 4s (6089 kB/s) 1062s Selecting previously unselected package libblas3:s390x. 1062s (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 ... 54607 files and directories currently installed.) 1062s Preparing to unpack .../0-libblas3_3.12.0-3build1_s390x.deb ... 1062s Unpacking libblas3:s390x (3.12.0-3build1) ... 1062s Selecting previously unselected package libgfortran5:s390x. 1062s Preparing to unpack .../1-libgfortran5_14.1.0-1ubuntu1_s390x.deb ... 1062s Unpacking libgfortran5:s390x (14.1.0-1ubuntu1) ... 1062s Selecting previously unselected package liblapack3:s390x. 1062s Preparing to unpack .../2-liblapack3_3.12.0-3build1_s390x.deb ... 1062s Unpacking liblapack3:s390x (3.12.0-3build1) ... 1062s Selecting previously unselected package liblbfgsb0:s390x. 1062s Preparing to unpack .../3-liblbfgsb0_3.0+dfsg.4-1build1_s390x.deb ... 1062s Unpacking liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 1062s Selecting previously unselected package python3-all. 1062s Preparing to unpack .../4-python3-all_3.12.3-0ubuntu1_s390x.deb ... 1062s Unpacking python3-all (3.12.3-0ubuntu1) ... 1062s Selecting previously unselected package python3-decorator. 1062s Preparing to unpack .../5-python3-decorator_5.1.1-5_all.deb ... 1062s Unpacking python3-decorator (5.1.1-5) ... 1062s Selecting previously unselected package python3-numpy. 1062s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-10_s390x.deb ... 1062s Unpacking python3-numpy (1:1.26.4+ds-10) ... 1063s Selecting previously unselected package python3-scipy. 1063s Preparing to unpack .../7-python3-scipy_1.11.4-10_s390x.deb ... 1063s Unpacking python3-scipy (1.11.4-10) ... 1064s Selecting previously unselected package python3-pymbar. 1064s Preparing to unpack .../8-python3-pymbar_3.1.0-4_all.deb ... 1064s Unpacking python3-pymbar (3.1.0-4) ... 1064s Selecting previously unselected package autopkgtest-satdep. 1064s Preparing to unpack .../9-2-autopkgtest-satdep.deb ... 1064s Unpacking autopkgtest-satdep (0) ... 1064s Setting up python3-all (3.12.3-0ubuntu1) ... 1064s Setting up python3-decorator (5.1.1-5) ... 1064s Setting up libblas3:s390x (3.12.0-3build1) ... 1064s 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 1064s Setting up libgfortran5:s390x (14.1.0-1ubuntu1) ... 1064s Setting up liblapack3:s390x (3.12.0-3build1) ... 1064s 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 1064s Setting up python3-numpy (1:1.26.4+ds-10) ... 1067s Setting up liblbfgsb0:s390x (3.0+dfsg.4-1build1) ... 1067s Setting up python3-scipy (1.11.4-10) ... 1073s Setting up python3-pymbar (3.1.0-4) ... 1073s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 1073s """A function that when zeroed is equivalent to the solution of 1073s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 1073s """ 1073s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 1073s """ 1073s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 1073s """ 1073s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 1073s """ 1073s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 1073s """ 1073s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 1073s """Compute estimate of overlap matrix between the states. 1073s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 1073s """Compute the free energy of occupying a number of bins. 1073s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 1073s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 1073s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 1073s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 1073s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 1073s """ 1073s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 1073s """Generate samples from forward and reverse Gaussian work distributions. 1073s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 1073s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 1073s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 1073s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 1073s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 1073s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 1073s Setting up autopkgtest-satdep (0) ... 1073s Processing triggers for man-db (2.12.1-1) ... 1074s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 1076s (Reading database ... 56918 files and directories currently installed.) 1076s Removing autopkgtest-satdep (0) ... 1080s autopkgtest [02:53:11]: 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 1080s autopkgtest [02:53:11]: test autodep8-python3: [----------------------- 1080s Testing with python3.12: 1081s 1081s autopkgtest [02:53:12]: test autodep8-python3: -----------------------] 1081s autodep8-python3 PASS (superficial) 1081s autopkgtest [02:53:12]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 1082s autopkgtest [02:53:13]: @@@@@@@@@@@@@@@@@@@@ summary 1082s command1 PASS 1082s autodep8-python3 PASS (superficial) 1096s nova [W] Using flock in scalingstack-bos01-s390x 1096s Creating nova instance adt-oracular-s390x-python-pymbar-20240608-023511-juju-7f2275-prod-proposed-migration-environment-3-bf1275f7-70ef-411d-a376-33a78f98eb0b from image adt/ubuntu-oracular-s390x-server-20240607.img (UUID 7eeb2415-a1eb-49f2-b205-8690074843ed)... 1096s nova [W] Using flock in scalingstack-bos01-s390x 1096s flock: timeout while waiting to get lock 1096s Creating nova instance adt-oracular-s390x-python-pymbar-20240608-023511-juju-7f2275-prod-proposed-migration-environment-3-bf1275f7-70ef-411d-a376-33a78f98eb0b from image adt/ubuntu-oracular-s390x-server-20240607.img (UUID 7eeb2415-a1eb-49f2-b205-8690074843ed)...