0s autopkgtest [01:41:43]: starting date and time: 2024-06-08 01:41:43+0000 0s autopkgtest [01:41:43]: git checkout: 433ed4cb Merge branch 'skia/nova_flock' into 'ubuntu/5.34+prod' 0s autopkgtest [01:41:43]: host juju-7f2275-prod-proposed-migration-environment-3; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.w814p4qp/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-ppc64el-21.secgroup --name adt-oracular-ppc64el-python-pymbar-20240608-014143-juju-7f2275-prod-proposed-migration-environment-3-326b2c1a-8813-4918-a816-1fd69e4b4672 --image adt/ubuntu-oracular-ppc64el-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/ 186s autopkgtest [01:44:49]: testbed dpkg architecture: ppc64el 186s autopkgtest [01:44:49]: testbed apt version: 2.9.3 186s autopkgtest [01:44:49]: @@@@@@@@@@@@@@@@@@@@ test bed setup 187s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 187s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 187s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 187s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [336 kB] 187s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 187s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [54.3 kB] 187s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1860 B] 187s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [300 kB] 187s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1768 B] 188s Fetched 858 kB in 1s (1119 kB/s) 188s Reading package lists... 191s Reading package lists... 191s Building dependency tree... 191s Reading state information... 191s Calculating upgrade... 191s The following packages will be upgraded: 191s debianutils libheif-plugin-aomdec libheif-plugin-aomenc 191s libheif-plugin-libde265 libheif1 libnetplan1 liburcu8t64 netplan-generator 191s netplan.io python3-netplan 191s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 191s Need to get 804 kB of archives. 191s After this operation, 5120 B of additional disk space will be used. 191s Get:1 http://ftpmaster.internal/ubuntu oracular/main ppc64el debianutils ppc64el 5.18 [90.5 kB] 192s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el netplan-generator ppc64el 1.0-3ubuntu1 [59.3 kB] 192s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-netplan ppc64el 1.0-3ubuntu1 [21.8 kB] 192s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el netplan.io ppc64el 1.0-3ubuntu1 [66.6 kB] 192s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnetplan1 ppc64el 1.0-3ubuntu1 [138 kB] 192s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-aomdec ppc64el 1.17.6-3 [10.2 kB] 192s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-aomenc ppc64el 1.17.6-3 [16.6 kB] 192s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif1 ppc64el 1.17.6-3 [320 kB] 192s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-libde265 ppc64el 1.17.6-3 [8484 B] 192s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el liburcu8t64 ppc64el 0.14.0-4 [72.9 kB] 193s Fetched 804 kB in 1s (763 kB/s) 193s (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 ... 72612 files and directories currently installed.) 193s Preparing to unpack .../debianutils_5.18_ppc64el.deb ... 193s Unpacking debianutils (5.18) over (5.17build1) ... 193s Setting up debianutils (5.18) ... 193s (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 ... 72612 files and directories currently installed.) 193s Preparing to unpack .../0-netplan-generator_1.0-3ubuntu1_ppc64el.deb ... 193s Adding 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 193s Unpacking netplan-generator (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 193s Preparing to unpack .../1-python3-netplan_1.0-3ubuntu1_ppc64el.deb ... 193s Unpacking python3-netplan (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 193s Preparing to unpack .../2-netplan.io_1.0-3ubuntu1_ppc64el.deb ... 193s Unpacking netplan.io (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 193s Preparing to unpack .../3-libnetplan1_1.0-3ubuntu1_ppc64el.deb ... 193s Unpacking libnetplan1:ppc64el (1.0-3ubuntu1) over (1.0-2ubuntu1) ... 193s Preparing to unpack .../4-libheif-plugin-aomdec_1.17.6-3_ppc64el.deb ... 193s Unpacking libheif-plugin-aomdec:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 193s Preparing to unpack .../5-libheif-plugin-aomenc_1.17.6-3_ppc64el.deb ... 193s Unpacking libheif-plugin-aomenc:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 193s Preparing to unpack .../6-libheif1_1.17.6-3_ppc64el.deb ... 193s Unpacking libheif1:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 193s Preparing to unpack .../7-libheif-plugin-libde265_1.17.6-3_ppc64el.deb ... 193s Unpacking libheif-plugin-libde265:ppc64el (1.17.6-3) over (1.17.6-1ubuntu4) ... 193s Preparing to unpack .../8-liburcu8t64_0.14.0-4_ppc64el.deb ... 193s Unpacking liburcu8t64:ppc64el (0.14.0-4) over (0.14.0-3.1build1) ... 193s Setting up liburcu8t64:ppc64el (0.14.0-4) ... 193s Setting up libnetplan1:ppc64el (1.0-3ubuntu1) ... 193s Setting up python3-netplan (1.0-3ubuntu1) ... 193s Setting up netplan-generator (1.0-3ubuntu1) ... 193s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 193s Setting up netplan.io (1.0-3ubuntu1) ... 193s Setting up libheif-plugin-aomdec:ppc64el (1.17.6-3) ... 193s Setting up libheif-plugin-libde265:ppc64el (1.17.6-3) ... 193s Setting up libheif1:ppc64el (1.17.6-3) ... 193s Setting up libheif-plugin-aomenc:ppc64el (1.17.6-3) ... 193s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 193s Processing triggers for man-db (2.12.1-1) ... 195s Processing triggers for dbus (1.14.10-4ubuntu4) ... 195s Reading package lists... 195s Building dependency tree... 195s Reading state information... 195s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 196s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 196s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 196s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 196s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 197s Reading package lists... 197s Reading package lists... 197s Building dependency tree... 197s Reading state information... 197s Calculating upgrade... 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 198s Reading package lists... 198s Building dependency tree... 198s Reading state information... 198s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 202s autopkgtest [01:45:05]: testbed running kernel: Linux 6.8.0-31-generic #31-Ubuntu SMP Sat Apr 20 00:05:55 UTC 2024 202s autopkgtest [01:45:05]: @@@@@@@@@@@@@@@@@@@@ apt-source python-pymbar 207s Get:1 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (dsc) [2363 B] 207s Get:2 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (tar) [17.1 MB] 207s Get:3 http://ftpmaster.internal/ubuntu oracular/universe python-pymbar 3.1.0-4 (diff) [3916 B] 208s gpgv: Signature made Wed Feb 1 21:01:41 2023 UTC 208s gpgv: using RSA key 8F91B227C7D6F2B1948C8236793CF67E8F0D11DA 208s gpgv: issuer "emollier@debian.org" 208s gpgv: Can't check signature: No public key 208s dpkg-source: warning: cannot verify inline signature for ./python-pymbar_3.1.0-4.dsc: no acceptable signature found 208s autopkgtest [01:45:11]: testing package python-pymbar version 3.1.0-4 208s autopkgtest [01:45:11]: build not needed 277s autopkgtest [01:46:20]: test command1: preparing testbed 278s Reading package lists... 278s Building dependency tree... 278s Reading state information... 278s Starting pkgProblemResolver with broken count: 0 278s Starting 2 pkgProblemResolver with broken count: 0 278s Done 278s The following additional packages will be installed: 278s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-decorator 278s python3-iniconfig python3-numpy python3-packaging python3-pluggy 278s python3-pymbar python3-pytest python3-scipy 278s Suggested packages: 278s gcc gfortran python-numpy-doc python3-dev python-scipy-doc 278s Recommended packages: 278s g++ | c++-compiler python3-pil 278s The following NEW packages will be installed: 278s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 278s python3-decorator python3-iniconfig python3-numpy python3-packaging 278s python3-pluggy python3-pymbar python3-pytest python3-scipy 278s 0 upgraded, 13 newly installed, 0 to remove and 0 not upgraded. 278s Need to get 25.4 MB/25.4 MB of archives. 278s After this operation, 110 MB of additional disk space will be used. 278s Get:1 /tmp/autopkgtest.t1mh1L/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [716 B] 279s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 279s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-1ubuntu1 [573 kB] 279s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 279s Get:5 http://ftpmaster.internal/ubuntu oracular/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 279s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 279s Get:7 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B] 279s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 280s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-packaging all 24.0-1 [41.1 kB] 280s Get:10 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB] 280s Get:11 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-scipy ppc64el 1.11.4-10 [16.9 MB] 281s Get:12 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pymbar all 3.1.0-4 [67.8 kB] 281s Get:13 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el python3-pytest all 8.2.2-1ubuntu1 [250 kB] 281s Fetched 25.4 MB in 2s (10.6 MB/s) 281s Selecting previously unselected package libblas3:ppc64el. 281s (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 ... 72612 files and directories currently installed.) 281s Preparing to unpack .../00-libblas3_3.12.0-3build1_ppc64el.deb ... 281s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 281s Selecting previously unselected package libgfortran5:ppc64el. 281s Preparing to unpack .../01-libgfortran5_14.1.0-1ubuntu1_ppc64el.deb ... 281s Unpacking libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 281s Selecting previously unselected package liblapack3:ppc64el. 281s Preparing to unpack .../02-liblapack3_3.12.0-3build1_ppc64el.deb ... 281s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 281s Selecting previously unselected package liblbfgsb0:ppc64el. 281s Preparing to unpack .../03-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 281s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 281s Selecting previously unselected package python3-decorator. 281s Preparing to unpack .../04-python3-decorator_5.1.1-5_all.deb ... 281s Unpacking python3-decorator (5.1.1-5) ... 281s Selecting previously unselected package python3-iniconfig. 281s Preparing to unpack .../05-python3-iniconfig_1.1.1-2_all.deb ... 281s Unpacking python3-iniconfig (1.1.1-2) ... 281s Selecting previously unselected package python3-numpy. 281s Preparing to unpack .../06-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 281s Unpacking python3-numpy (1:1.26.4+ds-10) ... 282s Selecting previously unselected package python3-packaging. 282s Preparing to unpack .../07-python3-packaging_24.0-1_all.deb ... 282s Unpacking python3-packaging (24.0-1) ... 282s Selecting previously unselected package python3-pluggy. 282s Preparing to unpack .../08-python3-pluggy_1.5.0-1_all.deb ... 282s Unpacking python3-pluggy (1.5.0-1) ... 282s Selecting previously unselected package python3-scipy. 282s Preparing to unpack .../09-python3-scipy_1.11.4-10_ppc64el.deb ... 282s Unpacking python3-scipy (1.11.4-10) ... 282s Selecting previously unselected package python3-pymbar. 282s Preparing to unpack .../10-python3-pymbar_3.1.0-4_all.deb ... 282s Unpacking python3-pymbar (3.1.0-4) ... 282s Selecting previously unselected package python3-pytest. 282s Preparing to unpack .../11-python3-pytest_8.2.2-1ubuntu1_all.deb ... 282s Unpacking python3-pytest (8.2.2-1ubuntu1) ... 282s Selecting previously unselected package autopkgtest-satdep. 282s Preparing to unpack .../12-1-autopkgtest-satdep.deb ... 282s Unpacking autopkgtest-satdep (0) ... 282s Setting up python3-iniconfig (1.1.1-2) ... 282s Setting up python3-decorator (5.1.1-5) ... 282s Setting up libblas3:ppc64el (3.12.0-3build1) ... 282s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 282s Setting up python3-packaging (24.0-1) ... 283s Setting up libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 283s Setting up python3-pluggy (1.5.0-1) ... 283s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 283s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 283s Setting up python3-pytest (8.2.2-1ubuntu1) ... 283s Setting up python3-numpy (1:1.26.4+ds-10) ... 285s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 285s Setting up python3-scipy (1.11.4-10) ... 289s Setting up python3-pymbar (3.1.0-4) ... 289s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 289s """A function that when zeroed is equivalent to the solution of 289s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 289s """ 289s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 289s """ 289s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 289s """ 289s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 289s """ 289s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 289s """ 289s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 289s """Compute estimate of overlap matrix between the states. 289s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 289s """Compute the free energy of occupying a number of bins. 289s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 289s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 289s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 289s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 289s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 289s """ 289s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 289s """Generate samples from forward and reverse Gaussian work distributions. 289s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 289s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 289s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 289s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 289s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 289s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 289s Setting up autopkgtest-satdep (0) ... 289s Processing triggers for man-db (2.12.1-1) ... 290s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 293s (Reading database ... 75086 files and directories currently installed.) 293s Removing autopkgtest-satdep (0) ... 293s autopkgtest [01:46:36]: test command1: rm pymbar/*.py && pytest-3 293s autopkgtest [01:46:36]: test command1: [----------------------- 295s ============================= test session starts ============================== 295s platform linux -- Python 3.12.3, pytest-8.2.2, pluggy-1.5.0 295s rootdir: /tmp/autopkgtest.t1mh1L/build.kop/src 295s collected 37 items 295s 295s pymbar/tests/test_bar.py .. [ 5%] 464s pymbar/tests/test_covariance.py ... [ 13%] 489s pymbar/tests/test_mbar.py ................ [ 56%] 525s pymbar/tests/test_mbar_solvers.py .... [ 67%] 532s pymbar/tests/test_timeseries.py ..ss.ss.. [ 91%] 532s pymbar/tests/test_utils.py ... [100%] 532s 532s =============================== warnings summary =============================== 532s ../../../../usr/lib/python3/dist-packages/pymbar/utils_for_testing.py:29 532s /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 532s from pkg_resources import resource_filename 532s 532s pymbar/tests/test_bar.py: 4 warnings 532s pymbar/tests/test_covariance.py: 9 warnings 532s pymbar/tests/test_mbar.py: 8 warnings 532s pymbar/tests/test_mbar_solvers.py: 11 warnings 532s /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. 532s f_i = np.matrix(self.f_k) 532s 532s pymbar/tests/test_bar.py: 4 warnings 532s pymbar/tests/test_covariance.py: 3 warnings 532s pymbar/tests/test_mbar.py: 29 warnings 532s pymbar/tests/test_mbar_solvers.py: 11 warnings 532s /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. 532s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 532s 532s pymbar/tests/test_bar.py: 4 warnings 532s pymbar/tests/test_covariance.py: 3 warnings 532s pymbar/tests/test_mbar.py: 29 warnings 532s pymbar/tests/test_mbar_solvers.py: 11 warnings 532s /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. 532s W = np.matrix(W, dtype=np.float64) 532s 532s pymbar/tests/test_bar.py: 40 warnings 532s pymbar/tests/test_covariance.py: 78 warnings 532s pymbar/tests/test_mbar.py: 287 warnings 532s pymbar/tests/test_mbar_solvers.py: 99 warnings 532s /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. 532s return matrix(data, dtype=dtype, copy=False) 532s 532s pymbar/tests/test_bar.py: 4 warnings 532s pymbar/tests/test_covariance.py: 3 warnings 532s pymbar/tests/test_mbar.py: 29 warnings 532s pymbar/tests/test_mbar_solvers.py: 11 warnings 532s /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. 532s Sigma = np.matrix(np.diag(np.sqrt(S2))) 532s 532s pymbar/tests/test_bar.py: 4 warnings 532s pymbar/tests/test_covariance.py: 3 warnings 532s pymbar/tests/test_mbar.py: 29 warnings 532s pymbar/tests/test_mbar_solvers.py: 11 warnings 532s /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. 532s V = np.matrix(V) 532s 532s pymbar/tests/test_bar.py: 4 warnings 532s pymbar/tests/test_covariance.py: 9 warnings 532s pymbar/tests/test_mbar.py: 23 warnings 532s pymbar/tests/test_mbar_solvers.py: 11 warnings 532s /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. 532s diag = np.matrix(cov.diagonal()) 532s 532s pymbar/tests/test_bar.py::test_bar_computeOverlap 532s pymbar/tests/test_bar.py::test_bar_computeOverlap 532s /usr/lib/python3/dist-packages/pymbar/bar.py:527: FutureWarning: Warning: This API is experimental and subject to change in future releases 532s warnings.warn("Warning: This API is experimental and subject to change in future releases", FutureWarning) 532s 532s pymbar/tests/test_bar.py::test_bar_computeOverlap 532s pymbar/tests/test_bar.py::test_bar_computeOverlap 532s pymbar/tests/test_bar.py::test_bar_computeOverlap 532s pymbar/tests/test_bar.py::test_bar_computeOverlap 532s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 532s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 532s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 532s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 532s /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. 532s W = np.matrix(self.getWeights(), np.float64) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s W = np.matrix(W, dtype=np.float64) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s Sigma = np.matrix(np.diag(S)) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s V = np.matrix(Vt).T 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s f_i = np.matrix(self.f_k) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s Ndiag = np.matrix(np.diag(N_k), dtype=np.float64) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s W = np.matrix(W, dtype=np.float64) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s Sigma = np.matrix(np.diag(S)) 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s V = np.matrix(Vt).T 532s 532s pymbar/tests/test_covariance.py::test_100x100_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_oscillators 532s pymbar/tests/test_covariance.py::test_200x50_exponentials 532s /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. 532s Ainv = np.matrix(np.zeros([M, M], dtype=np.float64)) 532s 532s pymbar/tests/test_mbar.py: 560 warnings 532s /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. 532s diffm[:,:,b] = np.matrix(self.f_k_boots[b,:]) - np.matrix(self.f_k_boots[b,:]).transpose() 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 532s pymbar/tests/test_mbar.py::test_mbar_computeExpectations_position_differences 532s /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. 532s A_im = np.matrix(inner_results['observables']) 532s 532s pymbar/tests/test_mbar.py: 16 warnings 532s /tmp/autopkgtest.t1mh1L/build.kop/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. 532s xa_ij = np.array(np.matrix(xa) - np.matrix(xa).transpose()) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s /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. 532s Adiag = np.matrix(np.zeros([3*K,3*K],dtype=np.float64)) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s /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. 532s f_k = np.matrix(inner_results['f']) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s /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. 532s u_k = np.matrix(inner_results['observables']) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s /tmp/autopkgtest.t1mh1L/build.kop/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. 532s fa_ij = np.array(np.matrix(fa) - np.matrix(fa).transpose()) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s /tmp/autopkgtest.t1mh1L/build.kop/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. 532s ua_ij = np.array(np.matrix(ua) - np.matrix(ua).transpose()) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s pymbar/tests/test_mbar.py::test_mbar_computeEntropyAndEnthalpy 532s /tmp/autopkgtest.t1mh1L/build.kop/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. 532s sa_ij = np.array(np.matrix(sa) - np.matrix(sa).transpose()) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computeOverlap 532s /tmp/autopkgtest.t1mh1L/build.kop/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. 532s reference_matrix = np.matrix((1.0/d)*np.ones([d,d])) 532s 532s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 532s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 532s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 532s pymbar/tests/test_mbar.py::test_mbar_computePerturbedFreeEnergeies 532s /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. 532s f_k = np.matrix(inner_results['f']) 532s 532s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 532s =========== 33 passed, 4 skipped, 1431 warnings in 238.35s (0:03:58) =========== 533s autopkgtest [01:50:36]: test command1: -----------------------] 533s command1 PASS 533s autopkgtest [01:50:36]: test command1: - - - - - - - - - - results - - - - - - - - - - 534s autopkgtest [01:50:37]: test autodep8-python3: preparing testbed 651s autopkgtest [01:52:34]: testbed dpkg architecture: ppc64el 651s autopkgtest [01:52:34]: testbed apt version: 2.9.3 651s autopkgtest [01:52:34]: @@@@@@@@@@@@@@@@@@@@ test bed setup 652s Get:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease [110 kB] 653s Get:2 http://ftpmaster.internal/ubuntu oracular-proposed/restricted Sources [7972 B] 653s Get:3 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse Sources [2864 B] 653s Get:4 http://ftpmaster.internal/ubuntu oracular-proposed/main Sources [44.3 kB] 653s Get:5 http://ftpmaster.internal/ubuntu oracular-proposed/universe Sources [336 kB] 653s Get:6 http://ftpmaster.internal/ubuntu oracular-proposed/main ppc64el Packages [54.3 kB] 653s Get:7 http://ftpmaster.internal/ubuntu oracular-proposed/restricted ppc64el Packages [1860 B] 653s Get:8 http://ftpmaster.internal/ubuntu oracular-proposed/universe ppc64el Packages [300 kB] 653s Get:9 http://ftpmaster.internal/ubuntu oracular-proposed/multiverse ppc64el Packages [1768 B] 653s Fetched 858 kB in 1s (933 kB/s) 653s Reading package lists... 656s Reading package lists... 656s Building dependency tree... 656s Reading state information... 656s Calculating upgrade... 656s The following packages will be upgraded: 656s debianutils libheif-plugin-aomdec libheif-plugin-aomenc 656s libheif-plugin-libde265 libheif1 libnetplan1 liburcu8t64 netplan-generator 656s netplan.io python3-netplan 657s 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 657s Need to get 804 kB of archives. 657s After this operation, 5120 B of additional disk space will be used. 657s Get:1 http://ftpmaster.internal/ubuntu oracular/main ppc64el debianutils ppc64el 5.18 [90.5 kB] 657s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el netplan-generator ppc64el 1.0-3ubuntu1 [59.3 kB] 657s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-netplan ppc64el 1.0-3ubuntu1 [21.8 kB] 657s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el netplan.io ppc64el 1.0-3ubuntu1 [66.6 kB] 657s Get:5 http://ftpmaster.internal/ubuntu oracular/main ppc64el libnetplan1 ppc64el 1.0-3ubuntu1 [138 kB] 657s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-aomdec ppc64el 1.17.6-3 [10.2 kB] 657s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-aomenc ppc64el 1.17.6-3 [16.6 kB] 657s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif1 ppc64el 1.17.6-3 [320 kB] 657s Get:9 http://ftpmaster.internal/ubuntu oracular/main ppc64el libheif-plugin-libde265 ppc64el 1.17.6-3 [8484 B] 657s Get:10 http://ftpmaster.internal/ubuntu oracular/main ppc64el liburcu8t64 ppc64el 0.14.0-4 [72.9 kB] 657s Fetched 804 kB in 0s (1616 kB/s) 658s (Reading database ... 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.../8-liburcu8t64_0.14.0-4_ppc64el.deb ... 658s Unpacking liburcu8t64:ppc64el (0.14.0-4) over (0.14.0-3.1build1) ... 658s Setting up liburcu8t64:ppc64el (0.14.0-4) ... 658s Setting up libnetplan1:ppc64el (1.0-3ubuntu1) ... 658s Setting up python3-netplan (1.0-3ubuntu1) ... 658s Setting up netplan-generator (1.0-3ubuntu1) ... 658s Removing 'diversion of /lib/systemd/system-generators/netplan to /lib/systemd/system-generators/netplan.usr-is-merged by netplan-generator' 658s Setting up netplan.io (1.0-3ubuntu1) ... 658s Setting up libheif-plugin-aomdec:ppc64el (1.17.6-3) ... 658s Setting up libheif-plugin-libde265:ppc64el (1.17.6-3) ... 658s Setting up libheif1:ppc64el (1.17.6-3) ... 658s Setting up libheif-plugin-aomenc:ppc64el (1.17.6-3) ... 658s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 658s Processing triggers for man-db (2.12.1-1) ... 660s Processing triggers for dbus (1.14.10-4ubuntu4) ... 660s Reading package lists... 660s Building dependency tree... 660s Reading state information... 660s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 661s Hit:1 http://ftpmaster.internal/ubuntu oracular-proposed InRelease 661s Hit:2 http://ftpmaster.internal/ubuntu oracular InRelease 661s Hit:3 http://ftpmaster.internal/ubuntu oracular-updates InRelease 661s Hit:4 http://ftpmaster.internal/ubuntu oracular-security InRelease 662s Reading package lists... 662s Reading package lists... 662s Building dependency tree... 662s Reading state information... 663s Calculating upgrade... 663s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 663s Reading package lists... 663s Building dependency tree... 663s Reading state information... 664s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 668s Reading package lists... 668s Building dependency tree... 668s Reading state information... 668s Starting pkgProblemResolver with broken count: 0 668s Starting 2 pkgProblemResolver with broken count: 0 668s Done 669s The following additional packages will be installed: 669s libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all python3-decorator 669s python3-numpy python3-pymbar python3-scipy 669s Suggested packages: 669s gcc gfortran python-numpy-doc python3-dev python3-pytest python-scipy-doc 669s Recommended packages: 669s g++ | c++-compiler python3-pil 669s The following NEW packages will be installed: 669s autopkgtest-satdep libblas3 libgfortran5 liblapack3 liblbfgsb0 python3-all 669s python3-decorator python3-numpy python3-pymbar python3-scipy 669s 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. 669s Need to get 25.0 MB/25.0 MB of archives. 669s After this operation, 108 MB of additional disk space will be used. 669s Get:1 /tmp/autopkgtest.t1mh1L/2-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [720 B] 669s Get:2 http://ftpmaster.internal/ubuntu oracular/main ppc64el libblas3 ppc64el 3.12.0-3build1 [227 kB] 669s Get:3 http://ftpmaster.internal/ubuntu oracular/main ppc64el libgfortran5 ppc64el 14.1.0-1ubuntu1 [573 kB] 669s Get:4 http://ftpmaster.internal/ubuntu oracular/main ppc64el liblapack3 ppc64el 3.12.0-3build1 [2804 kB] 669s Get:5 http://ftpmaster.internal/ubuntu oracular/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB] 669s Get:6 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-all ppc64el 3.12.3-0ubuntu1 [888 B] 669s Get:7 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB] 669s Get:8 http://ftpmaster.internal/ubuntu oracular/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-10 [4408 kB] 670s Get:9 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-scipy ppc64el 1.11.4-10 [16.9 MB] 670s Get:10 http://ftpmaster.internal/ubuntu oracular/universe ppc64el python3-pymbar all 3.1.0-4 [67.8 kB] 671s Fetched 25.0 MB in 1s (17.1 MB/s) 671s Selecting previously unselected package libblas3:ppc64el. 671s (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 ... 72612 files and directories currently installed.) 671s Preparing to unpack .../0-libblas3_3.12.0-3build1_ppc64el.deb ... 671s Unpacking libblas3:ppc64el (3.12.0-3build1) ... 671s Selecting previously unselected package libgfortran5:ppc64el. 671s Preparing to unpack .../1-libgfortran5_14.1.0-1ubuntu1_ppc64el.deb ... 671s Unpacking libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 671s Selecting previously unselected package liblapack3:ppc64el. 671s Preparing to unpack .../2-liblapack3_3.12.0-3build1_ppc64el.deb ... 671s Unpacking liblapack3:ppc64el (3.12.0-3build1) ... 671s Selecting previously unselected package liblbfgsb0:ppc64el. 671s Preparing to unpack .../3-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ... 671s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 671s Selecting previously unselected package python3-all. 671s Preparing to unpack .../4-python3-all_3.12.3-0ubuntu1_ppc64el.deb ... 671s Unpacking python3-all (3.12.3-0ubuntu1) ... 671s Selecting previously unselected package python3-decorator. 671s Preparing to unpack .../5-python3-decorator_5.1.1-5_all.deb ... 671s Unpacking python3-decorator (5.1.1-5) ... 671s Selecting previously unselected package python3-numpy. 671s Preparing to unpack .../6-python3-numpy_1%3a1.26.4+ds-10_ppc64el.deb ... 671s Unpacking python3-numpy (1:1.26.4+ds-10) ... 671s Selecting previously unselected package python3-scipy. 671s Preparing to unpack .../7-python3-scipy_1.11.4-10_ppc64el.deb ... 671s Unpacking python3-scipy (1.11.4-10) ... 672s Selecting previously unselected package python3-pymbar. 672s Preparing to unpack .../8-python3-pymbar_3.1.0-4_all.deb ... 672s Unpacking python3-pymbar (3.1.0-4) ... 672s Selecting previously unselected package autopkgtest-satdep. 672s Preparing to unpack .../9-2-autopkgtest-satdep.deb ... 672s Unpacking autopkgtest-satdep (0) ... 672s Setting up python3-all (3.12.3-0ubuntu1) ... 672s Setting up python3-decorator (5.1.1-5) ... 672s Setting up libblas3:ppc64el (3.12.0-3build1) ... 672s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/blas/libblas.so.3 to provide /usr/lib/powerpc64le-linux-gnu/libblas.so.3 (libblas.so.3-powerpc64le-linux-gnu) in auto mode 672s Setting up libgfortran5:ppc64el (14.1.0-1ubuntu1) ... 672s Setting up liblapack3:ppc64el (3.12.0-3build1) ... 672s update-alternatives: using /usr/lib/powerpc64le-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/powerpc64le-linux-gnu/liblapack.so.3 (liblapack.so.3-powerpc64le-linux-gnu) in auto mode 672s Setting up python3-numpy (1:1.26.4+ds-10) ... 675s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ... 675s Setting up python3-scipy (1.11.4-10) ... 679s Setting up python3-pymbar (3.1.0-4) ... 679s /usr/lib/python3/dist-packages/pymbar/bar.py:56: SyntaxWarning: invalid escape sequence '\s' 679s """A function that when zeroed is equivalent to the solution of 679s /usr/lib/python3/dist-packages/pymbar/mbar.py:381: SyntaxWarning: invalid escape sequence '\s' 679s """ 679s /usr/lib/python3/dist-packages/pymbar/mbar.py:442: SyntaxWarning: invalid escape sequence '\i' 679s """ 679s /usr/lib/python3/dist-packages/pymbar/mbar.py:865: SyntaxWarning: invalid escape sequence '\s' 679s """ 679s /usr/lib/python3/dist-packages/pymbar/mbar.py:1436: SyntaxWarning: invalid escape sequence '\s' 679s """ 679s /usr/lib/python3/dist-packages/pymbar/mbar.py:1866: SyntaxWarning: invalid escape sequence '\l' 679s """ 679s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:957: SyntaxWarning: invalid escape sequence '\i' 679s """Compute estimate of overlap matrix between the states. 679s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1376: SyntaxWarning: invalid escape sequence '\s' 679s """Compute the free energy of occupying a number of bins. 679s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1864: SyntaxWarning: invalid escape sequence '\s' 679s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 679s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:1873: SyntaxWarning: invalid escape sequence '\s' 679s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 679s /usr/lib/python3/dist-packages/pymbar/old_mbar.py:2078: SyntaxWarning: invalid escape sequence '\l' 679s """ 679s /usr/lib/python3/dist-packages/pymbar/testsystems/gaussian_work.py:5: SyntaxWarning: invalid escape sequence '\e' 679s """Generate samples from forward and reverse Gaussian work distributions. 679s /usr/lib/python3/dist-packages/pymbar/utils.py:230: SyntaxWarning: invalid escape sequence '\l' 679s """Compute the log of a sum of exponentiated terms exp(a_n) in a numerically-stable manner. 679s /usr/lib/python3/dist-packages/pymbar/utils.py:359: SyntaxWarning: invalid escape sequence '\s' 679s 'Warning: Should have \sum_n W_nk = 1. Actual column sum for state %d was %f. %d other columns have similar problems' % 679s /usr/lib/python3/dist-packages/pymbar/utils.py:368: SyntaxWarning: invalid escape sequence '\s' 679s 'Warning: Should have \sum_k N_k W_nk = 1. Actual row sum for sample %d was %f. %d other rows have similar problems' % 679s Setting up autopkgtest-satdep (0) ... 679s Processing triggers for man-db (2.12.1-1) ... 680s Processing triggers for libc-bin (2.39-0ubuntu8.1) ... 682s (Reading database ... 74923 files and directories currently installed.) 682s Removing autopkgtest-satdep (0) ... 689s autopkgtest [01:53:12]: 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 689s autopkgtest [01:53:12]: test autodep8-python3: [----------------------- 690s Testing with python3.12: 690s 691s autopkgtest [01:53:14]: test autodep8-python3: -----------------------] 691s autodep8-python3 PASS (superficial) 691s autopkgtest [01:53:14]: test autodep8-python3: - - - - - - - - - - results - - - - - - - - - - 692s autopkgtest [01:53:15]: @@@@@@@@@@@@@@@@@@@@ summary 692s command1 PASS 692s autodep8-python3 PASS (superficial) 704s nova [W] Using flock in scalingstack-bos01-ppc64el 704s flock: timeout while waiting to get lock 704s Creating nova instance adt-oracular-ppc64el-python-pymbar-20240608-014143-juju-7f2275-prod-proposed-migration-environment-3-326b2c1a-8813-4918-a816-1fd69e4b4672 from image adt/ubuntu-oracular-ppc64el-server-20240607.img (UUID 3fb9a257-7646-4253-9bcd-b14e4853c723)... 704s nova [W] Using flock in scalingstack-bos01-ppc64el 704s Creating nova instance adt-oracular-ppc64el-python-pymbar-20240608-014143-juju-7f2275-prod-proposed-migration-environment-3-326b2c1a-8813-4918-a816-1fd69e4b4672 from image adt/ubuntu-oracular-ppc64el-server-20240607.img (UUID 3fb9a257-7646-4253-9bcd-b14e4853c723)...