0s autopkgtest [13:11:59]: starting date and time: 2024-06-08 13:11:59+0000 0s autopkgtest [13:11:59]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [13:11:59]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u63ucnx9/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@bos03-arm64-8.secgroup --name adt-oracular-arm64-python-pymbar-20240608-131159-juju-7f2275-prod-proposed-migration-environment-3-9ac138a6-33b7-4f66-a086-1f1e383cc6c9 --image adt/ubuntu-oracular-arm64-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://ftpmaster.internal/ubuntu/ 83s autopkgtest [13:13:22]: testbed dpkg architecture: arm64 83s autopkgtest [13:13:22]: testbed apt version: 2.9.3 83s autopkgtest [13:13:22]: @@@@@@@@@@@@@@@@@@@@ test bed setup 84s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 84s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.2 kB] 84s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2420 B] 84s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 84s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [338 kB] 84s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [67.9 kB] 84s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [31.8 kB] 84s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [306 kB] 84s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [9556 B] 84s Fetched 918 kB in 1s (1052 kB/s) 85s Reading package lists... 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s Calculating upgrade... 90s The following packages will be upgraded: 90s bash 90s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s Need to get 781 kB of archives. 90s After this operation, 0 B of additional disk space will be used. 90s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 bash arm64 5.2.21-2.1ubuntu1 [781 kB] 91s Fetched 781 kB in 0s (1581 kB/s) 91s (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 ... 78200 files and directories currently installed.) 91s Preparing to unpack .../bash_5.2.21-2.1ubuntu1_arm64.deb ... 91s Unpacking bash (5.2.21-2.1ubuntu1) over (5.2.21-2ubuntu5) ... 91s Setting up bash (5.2.21-2.1ubuntu1) ... 91s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 91s Processing triggers for debianutils (5.18) ... 92s Processing triggers for install-info (7.1-3build2) ... 92s Processing triggers for man-db (2.12.1-1) ... 93s Reading package lists... 94s Building dependency tree... 94s Reading state information... 95s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 96s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 96s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 96s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 96s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 97s Reading package lists... 98s Reading package lists... 98s Building dependency tree... 98s Reading state information... 99s Calculating upgrade... 99s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 100s Reading package lists... 100s Building dependency tree... 100s Reading state information... 101s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 104s autopkgtest [13:13:43]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP PREEMPT_DYNAMIC Sat Apr 20 02:32:42 UTC 2024 104s autopkgtest [13:13:43]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 106s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (dsc) [2363 B] 106s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (tar) [17.1 MB] 106s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (diff) [3916 B] 107s gpgv: Signature made Wed Feb 1 21:01:41 2023 UTC 107s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 107s gpgv: issuer "emollier@debian.org" 107s gpgv: Can't check signature: No public key 107s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found 107s autopkgtest [13:13:46]: testing package python-pymbar version 3.1.0-4 108s autopkgtest [13:13:47]: build not needed 109s autopkgtest [13:13:48]: test command1: preparing testbed 111s Reading package lists... 111s Building dependency tree... 111s Reading state information... 111s Starting pkgProblemResolver with broken count: 0 111s Starting 2 pkgProblemResolver with broken count: 0 111s Done 112s The following additional packages will be installed: 112s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 112s python3-iniconfig python3-numpy python3-packaging python3-pluggy 112s python3-pymbar python3-pytest python3-scipy 112s Suggested packages: 112s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 112s Recommended packages: 112s g++ | c++-compiler python3-pil 112s The following NEW packages will be installed: 112s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 112s python3-decorator python3-iniconfig python3-numpy python3-packaging 112s python3-pluggy python3-pymbar python3-pytest python3-scipy 112s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 112s Need to get 21.8 MB/21.8 MB of archives. 112s After this operation, 91.3 MB of additional disk space will be used. 112s Get:1 /tmp/autopkgtest.57j7Z4/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [712 B] 112s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 113s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 113s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 113s Get:5 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 113s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 113s Get:7 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 113s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-10 [3565 kB] 113s Get:9 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-packaging all 24.0-1 [41.1 kB] 113s Get:10 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 113s Get:11 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-scipy arm64 1.11.4-10 [15.0 MB] 113s Get:12 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pymbar all 3.1.0-4 [67.8 kB] 113s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 python3-pytest all 8.2.2-1ubuntu1 [250 kB] 114s Fetched 21.8 MB in 1s (18.1 MB/s) 114s Selecting previously unselected package libblas3:arm64. 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 ... 78200 files and directories currently installed.) 114s Preparing to unpack .../00-libblas3_3.12.0-3build1_arm64.deb ... 114s Unpacking libblas3:arm64 (3.12.0-3build1) ... 114s Selecting previously unselected package libgfortran5:arm64. 114s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 114s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 114s Selecting previously unselected package liblapack3:arm64. 114s Preparing to unpack .../02-liblapack3_3.12.0-3build1_arm64.deb ... 114s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 115s Selecting previously unselected package liblbfgsb0:arm64. 115s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 115s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 115s Selecting previously unselected package python3-decorator. 115s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 115s Unpacking python3-decorator (5.1.1-5) ... 115s Selecting previously unselected package python3-iniconfig. 115s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 115s Unpacking python3-iniconfig (1.1.1-2) ... 115s Selecting previously unselected package python3-numpy. 115s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-10_arm64.deb ... 115s Unpacking python3-numpy (1:1.26.4+ds-10) ... 115s Selecting previously unselected package python3-packaging. 115s Preparing to unpack .../07-python3-packaging_24.0-1_all.deb ... 115s Unpacking python3-packaging (24.0-1) ... 116s Selecting previously unselected package python3-pluggy. 116s Preparing to unpack .../08-python3-pluggy_1.5.0-1_all.deb ... 116s Unpacking python3-pluggy (1.5.0-1) ... 116s Selecting previously unselected package python3-scipy. 116s Preparing to unpack .../09-python3-scipy_1.11.4-10_arm64.deb ... 116s Unpacking python3-scipy (1.11.4-10) ... 116s Selecting previously unselected package python3-pymbar. 116s Preparing to unpack .../10-python3-pymbar_3.1.0-4_all.deb ... 116s Unpacking python3-pymbar (3.1.0-4) ... 116s Selecting previously unselected package python3-pytest. 117s Preparing to unpack .../11-python3-pytest_8.2.2-1ubuntu1_all.deb ... 117s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 117s Selecting previously unselected package autopkgtest-satdep. 117s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 117s Unpacking autopkgtest-satdep (0) ... 117s Setting up python3-iniconfig (1.1.1-2) ... 117s Setting up python3-decorator (5.1.1-5) ... 118s Setting up libblas3:arm64 (3.12.0-3build1) ... 118s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 118s Setting up python3-packaging (24.0-1) ... 118s Setting up libgfortran5:arm64 (14.1.0-1ubuntu1) ... 118s Setting up python3-pluggy (1.5.0-1) ... 118s Setting up liblapack3:arm64 (3.12.0-3build1) ... 118s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 118s Setting up python3-pytest (8.2.2-1ubuntu1) ... 119s Setting up python3-numpy (1:1.26.4+ds-10) ... 121s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 121s Setting up python3-scipy (1.11.4-10) ... 126s Setting up python3-pymbar (3.1.0-4) ... 126s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 126s """A function that when zeroed is equivalent to the solution of 126s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 126s """ 126s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 126s """ 126s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 126s """ 126s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 126s """ 126s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 126s """ 126s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 126s """Compute estimate of overlap matrix between the states. 126s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 126s """Compute the free energy of occupying a number of bins. 126s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 126s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 126s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 126s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 126s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 126s """ 126s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 126s """Generate samples from forward and reverse Gaussian work distributions. 126s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 126s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 126s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 126s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 126s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 126s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 126s Setting up autopkgtest-satdep (0) ... 126s Processing triggers for man-db (2.12.1-1) ... 126s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 131s (Reading database ... 80674 files and directories currently installed.) 131s Removing autopkgtest-satdep (0) ... 133s autopkgtest [13:14:12]: test command1: rm pymbar/*.py && pytest-3 133s autopkgtest [13:14:12]: test command1: [----------------------- 135s ============================= test session starts ============================== 135s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 135s rootdir: /tmp/autopkgtest.57j7Z4/build.V8j/src 135s collected 37 items 135s 135s pymbar/tests/test_bar.py .. [ 5%] 257s pymbar/tests/test_covariance.py ... [ 13%] 281s pymbar/tests/test_mbar.py ................ [ 56%] 307s pymbar/tests/test_mbar_solvers.py .... [ 67%] 312s pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] 313s pymbar/tests/test_utils.py ... [100%] 313s 313s =============================== warnings summary =============================== 313s ../../../../usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29 313s /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 313s from pkg_resources import resource_filename 313s 313s pymbar/tests/test_bar.py: 4 warnings 313s pymbar/tests/test_covariance.py: 9 warnings 313s pymbar/tests/test_mbar.py: 8 warnings 313s pymbar/tests/test_mbar_solvers.py: 11 warnings 313s /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. 313s f_i = np.matrix(self.f_k) 313s 313s pymbar/tests/test_bar.py: 4 warnings 313s pymbar/tests/test_covariance.py: 3 warnings 313s pymbar/tests/test_mbar.py: 29 warnings 313s pymbar/tests/test_mbar_solvers.py: 11 warnings 313s /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. 313s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 313s 313s pymbar/tests/test_bar.py: 4 warnings 313s pymbar/tests/test_covariance.py: 3 warnings 313s pymbar/tests/test_mbar.py: 29 warnings 313s pymbar/tests/test_mbar_solvers.py: 11 warnings 313s /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. 313s W = np.matrix(W, dtype=np.float64) 313s 313s pymbar/tests/test_bar.py: 40 warnings 313s pymbar/tests/test_covariance.py: 78 warnings 313s pymbar/tests/test_mbar.py: 287 warnings 313s pymbar/tests/test_mbar_solvers.py: 99 warnings 313s /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. 313s return matrix(data, dtype=dtype, copy=False) 313s 313s pymbar/tests/test_bar.py: 4 warnings 313s pymbar/tests/test_covariance.py: 3 warnings 313s pymbar/tests/test_mbar.py: 29 warnings 313s pymbar/tests/test_mbar_solvers.py: 11 warnings 313s /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. 313s Sigma = np.matrix(np.diag(np.sqrt(S2))) 313s 313s pymbar/tests/test_bar.py: 4 warnings 313s pymbar/tests/test_covariance.py: 3 warnings 313s pymbar/tests/test_mbar.py: 29 warnings 313s pymbar/tests/test_mbar_solvers.py: 11 warnings 313s /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. 313s V = np.matrix(V) 313s 313s pymbar/tests/test_bar.py: 4 warnings 313s pymbar/tests/test_covariance.py: 9 warnings 313s pymbar/tests/test_mbar.py: 23 warnings 313s pymbar/tests/test_mbar_solvers.py: 11 warnings 313s /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. 313s diag = np.matrix(cov.diagonal()) 313s 313s pymbar/tests/test_bar.py::test_bar_computeOverlap 313s pymbar/tests/test_bar.py::test_bar_computeOverlap 313s /usr/lib/python3/dist-packages/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases 313s warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) 313s 313s pymbar/tests/test_bar.py::test_bar_computeOverlap 313s pymbar/tests/test_bar.py::test_bar_computeOverlap 313s pymbar/tests/test_bar.py::test_bar_computeOverlap 313s pymbar/tests/test_bar.py::test_bar_computeOverlap 313s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 313s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 313s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 313s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 313s /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. 313s W = np.matrix(self.getWeights(), np.float64) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s W = np.matrix(W, dtype=np.float64) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s Sigma = np.matrix(np.diag(S)) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s V = np.matrix(Vt).T 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s f_i = np.matrix(self.f_k) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s W = np.matrix(W, dtype=np.float64) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s Sigma = np.matrix(np.diag(S)) 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s V = np.matrix(Vt).T 313s 313s pymbar/tests/test_covariance.py::test_100x100_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_oscillators 313s pymbar/tests/test_covariance.py::test_200x50_exponentials 313s /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. 313s Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) 313s 313s pymbar/tests/test_mbar.py: 560 warnings 313s /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. 313s diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 313s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 313s /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. 313s A_im = np.matrix(inner_results['observables']) 313s 313s pymbar/tests/test_mbar.py: 16 warnings 313s /tmp/autopkgtest.57j7Z4/build.V8j/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. 313s xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s /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. 313s Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s /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. 313s f_k = np.matrix(inner_results['f']) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s /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. 313s u_k = np.matrix(inner_results['observables']) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s /tmp/autopkgtest.57j7Z4/build.V8j/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. 313s fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s /tmp/autopkgtest.57j7Z4/build.V8j/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. 313s ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 313s /tmp/autopkgtest.57j7Z4/build.V8j/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. 313s sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 313s /tmp/autopkgtest.57j7Z4/build.V8j/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. 313s reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) 313s 313s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 313s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 313s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 313s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 313s /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. 313s f_k = np.matrix(inner_results['f']) 313s 313s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 313s =========== 33 passed, 4 skipped, 1431 warnings in 179.58s (0:02:59) =========== 313s autopkgtest [13:17:12]: test command1: -----------------------] 314s autopkgtest [13:17:13]: test command1: - - - - - - - - - - results - - - - - - - - - - 314s command1 PASS 314s autopkgtest [13:17:13]: test autodep8-python3: preparing testbed 394s autopkgtest [13:18:33]: testbed dpkg architecture: arm64 394s autopkgtest [13:18:33]: testbed apt version: 2.9.3 394s autopkgtest [13:18:33]: @@@@@@@@@@@@@@@@@@@@ test bed setup 394s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 395s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 395s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.2 kB] 395s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [338 kB] 395s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2420 B] 395s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main arm64 Packages [67.9 kB] 395s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted arm64 Packages [31.8 kB] 395s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe arm64 Packages [306 kB] 395s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse arm64 Packages [9556 B] 395s Fetched 918 kB in 1s (1102 kB/s) 395s Reading package lists... 398s Reading package lists... 398s Building dependency tree... 398s Reading state information... 399s Calculating upgrade... 399s The following packages will be upgraded: 399s bash 400s 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 400s Need to get 781 kB of archives. 400s After this operation, 0 B of additional disk space will be used. 400s Get:1 http://ftpmaster.internal/ubuntu oracular/main arm64 bash arm64 5.2.21-2.1ubuntu1 [781 kB] 400s Fetched 781 kB in 1s (1418 kB/s) 401s (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 ... 78200 files and directories currently installed.) 401s Preparing to unpack .../bash_5.2.21-2.1ubuntu1_arm64.deb ... 401s Unpacking bash (5.2.21-2.1ubuntu1) over (5.2.21-2ubuntu5) ... 401s Setting up bash (5.2.21-2.1ubuntu1) ... 401s update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode 401s Processing triggers for debianutils (5.18) ... 401s Processing triggers for install-info (7.1-3build2) ... 402s Processing triggers for man-db (2.12.1-1) ... 402s Reading package lists... 403s Building dependency tree... 403s Reading state information... 404s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 404s Hit:1 http://ftpmaster.internal/ubuntu oracular InRelease 404s Hit:2 http://ftpmaster.internal/ubuntu oracular-updates InRelease 404s Hit:3 http://ftpmaster.internal/ubuntu oracular-security InRelease 405s Hit:4 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 406s Reading package lists... 406s Reading package lists... 406s Building dependency tree... 406s Reading state information... 407s Calculating upgrade... 407s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 407s Reading package lists... 407s Building dependency tree... 407s Reading state information... 408s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 413s Reading package lists... 413s Building dependency tree... 413s Reading state information... 413s Starting pkgProblemResolver with broken count: 0 413s Starting 2 pkgProblemResolver with broken count: 0 413s Done 414s The following additional packages will be installed: 414s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all python3-decorator 414s python3-numpy python3-pymbar python3-scipy 414s Suggested packages: 414s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 414s Recommended packages: 414s g++ | c++-compiler python3-pil 414s The following NEW packages will be installed: 414s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all 414s python3-decorator python3-numpy python3-pymbar python3-scipy 414s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 414s Need to get 21.5 MB/21.5 MB of archives. 414s After this operation, 89.7 MB of additional disk space will be used. 414s Get:1 /tmp/autopkgtest.57j7Z4/2-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [716 B] 414s Get:2 http://ftpmaster.internal/ubuntu oracular/main arm64 libblas3 arm64 3.12.0-3build1 [143 kB] 414s Get:3 http://ftpmaster.internal/ubuntu oracular/main arm64 libgfortran5 arm64 14.1.0-1ubuntu1 [443 kB] 414s Get:4 http://ftpmaster.internal/ubuntu oracular/main arm64 liblapack3 arm64 3.12.0-3build1 [2241 kB] 415s Get:5 http://ftpmaster.internal/ubuntu oracular/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 415s Get:6 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-all arm64 3.12.3-0ubuntu1 [888 B] 415s Get:7 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 415s Get:8 http://ftpmaster.internal/ubuntu oracular/main arm64 python3-numpy arm64 1:1.26.4+ds-10 [3565 kB] 415s Get:9 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-scipy arm64 1.11.4-10 [15.0 MB] 415s Get:10 http://ftpmaster.internal/ubuntu oracular/universe arm64 python3-pymbar all 3.1.0-4 [67.8 kB] 416s Fetched 21.5 MB in 1s (16.9 MB/s) 416s Selecting previously unselected package libblas3:arm64. 416s (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 ... 78200 files and directories currently installed.) 416s Preparing to unpack .../0-libblas3_3.12.0-3build1_arm64.deb ... 416s Unpacking libblas3:arm64 (3.12.0-3build1) ... 416s Selecting previously unselected package libgfortran5:arm64. 416s Preparing to unpack .../1-libgfortran5_14.1.0-1ubuntu1_arm64.deb ... 416s Unpacking libgfortran5:arm64 (14.1.0-1ubuntu1) ... 416s Selecting previously unselected package liblapack3:arm64. 416s Preparing to unpack .../2-liblapack3_3.12.0-3build1_arm64.deb ... 416s Unpacking liblapack3:arm64 (3.12.0-3build1) ... 416s Selecting previously unselected package liblbfgsb0:arm64. 416s Preparing to unpack .../3-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 416s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 416s Selecting previously unselected package python3-all. 416s Preparing to unpack .../4-python3-all_3.12.3-0ubuntu1_arm64.deb ... 416s Unpacking python3-all (3.12.3-0ubuntu1) ... 416s Selecting previously unselected package python3-decorator. 416s Preparing to unpack .../5-python3-decorator_5.1.1-5_all.deb ... 416s Unpacking python3-decorator (5.1.1-5) ... 416s Selecting previously unselected package python3-numpy. 416s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-10_arm64.deb ... 416s Unpacking python3-numpy (1:1.26.4+ds-10) ... 416s Selecting previously unselected package python3-scipy. 416s Preparing to unpack .../7-python3-scipy_1.11.4-10_arm64.deb ... 416s Unpacking python3-scipy (1.11.4-10) ... 417s Selecting previously unselected package python3-pymbar. 417s Preparing to unpack .../8-python3-pymbar_3.1.0-4_all.deb ... 417s Unpacking python3-pymbar (3.1.0-4) ... 417s Selecting previously unselected package autopkgtest-satdep. 417s Preparing to unpack .../9-2-autopkgtest-satdep.deb ... 417s Unpacking autopkgtest-satdep (0) ... 417s Setting up python3-all (3.12.3-0ubuntu1) ... 417s Setting up python3-decorator (5.1.1-5) ... 417s Setting up libblas3:arm64 (3.12.0-3build1) ... 417s update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode 417s Setting up libgfortran5:arm64 (14.1.0-1ubuntu1) ... 417s Setting up liblapack3:arm64 (3.12.0-3build1) ... 417s update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode 417s Setting up python3-numpy (1:1.26.4+ds-10) ... 419s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 419s Setting up python3-scipy (1.11.4-10) ... 422s Setting up python3-pymbar (3.1.0-4) ... 422s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 422s """A function that when zeroed is equivalent to the solution of 422s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 422s """ 422s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 422s """ 422s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 422s """ 422s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 422s """ 422s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 422s """ 422s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 422s """Compute estimate of overlap matrix between the states. 422s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 422s """Compute the free energy of occupying a number of bins. 422s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 422s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 422s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 422s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 422s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 422s """ 422s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 422s """Generate samples from forward and reverse Gaussian work distributions. 422s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 422s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 422s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 422s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 422s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 422s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 422s Setting up autopkgtest-satdep (0) ... 422s Processing triggers for man-db (2.12.1-1) ... 423s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 427s (Reading database ... 80511 files and directories currently installed.) 427s Removing autopkgtest-satdep (0) ... 430s autopkgtest [13:19:09]: 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 430s autopkgtest [13:19:09]: test autodep8-python3: [----------------------- 430s Testing with python3.12: 431s 432s autopkgtest [13:19:11]: test autodep8-python3: -----------------------] 432s autopkgtest [13:19:11]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 432s autodep8-python3 PASS (superficial) 433s autopkgtest [13:19:12]: @@@@@@@@@@@@@@@@@@@@ summary 433s command1 PASS 433s autodep8-python3 PASS (superficial) 444s nova [W] Skipping flock in bos03-arm64 444s Creating nova instance adt-oracular-arm64-python-pymbar-20240608-131159-juju-7f2275-prod-proposed-migration-environment-3-9ac138a6-33b7-4f66-a086-1f1e383cc6c9 from image adt/ubuntu-oracular-arm64-server-20240608.img (UUID 22fa5d69-8269-442f-bb5d-fd1454f7b08f)... 444s nova [W] Skipping flock in bos03-arm64 444s Creating nova instance adt-oracular-arm64-python-pymbar-20240608-131159-juju-7f2275-prod-proposed-migration-environment-3-9ac138a6-33b7-4f66-a086-1f1e383cc6c9 from image adt/ubuntu-oracular-arm64-server-20240608.img (UUID 22fa5d69-8269-442f-bb5d-fd1454f7b08f)...