0s autopkgtest [11:50:05]: starting date and time: 2024-11-10 11:50:05+0000 0s autopkgtest [11:50:05]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [11:50:05]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.6iwzharr/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:fftw3,src:openmpi --apt-upgrade opentsne --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 '--env=ADT_TEST_TRIGGERS=fftw3/3.3.10-2fakesync1 openmpi/5.0.5-3' -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-arm64-34.secgroup --name adt-plucky-arm64-opentsne-20241110-115005-juju-7f2275-prod-proposed-migration-environment-2-f7c6e71e-1f3a-4487-a6d0-ff38f8bdf895 --image adt/ubuntu-plucky-arm64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --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/ 74s autopkgtest [11:51:19]: testbed dpkg architecture: arm64 74s autopkgtest [11:51:19]: testbed apt version: 2.9.8 74s autopkgtest [11:51:19]: @@@@@@@@@@@@@@@@@@@@ test bed setup 75s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 75s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 76s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 76s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [938 kB] 76s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [98.4 kB] 76s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 Packages [135 kB] 76s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/restricted arm64 Packages [50.3 kB] 76s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/universe arm64 Packages [670 kB] 76s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse arm64 Packages [17.1 kB] 76s Fetched 2004 kB in 1s (1910 kB/s) 76s Reading package lists... 79s Reading package lists... 80s Building dependency tree... 80s Reading state information... 81s Calculating upgrade... 83s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 83s Reading package lists... 83s Building dependency tree... 83s Reading state information... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 86s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 86s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 86s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 87s Reading package lists... 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 88s Calculating upgrade... 88s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 88s Reading package lists... 89s Building dependency tree... 89s Reading state information... 89s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 92s autopkgtest [11:51:37]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 14:19:41 UTC 2024 92s autopkgtest [11:51:37]: @@@@@@@@@@@@@@@@@@@@ apt-source opentsne 95s Get:1 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu1 (dsc) [2377 B] 95s Get:2 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu1 (tar) [22.1 MB] 95s Get:3 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu1 (diff) [5320 B] 95s gpgv: Signature made Mon Sep 30 12:06:08 2024 UTC 95s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 95s gpgv: Can't check signature: No public key 95s dpkg-source: warning: cannot verify inline signature for ./opentsne_1.0.2-1ubuntu1.dsc: no acceptable signature found 96s autopkgtest [11:51:41]: testing package opentsne version 1.0.2-1ubuntu1 96s autopkgtest [11:51:41]: build not needed 97s autopkgtest [11:51:42]: test python: preparing testbed 98s Reading package lists... 99s Building dependency tree... 99s Reading state information... 100s Starting pkgProblemResolver with broken count: 0 100s Starting 2 pkgProblemResolver with broken count: 0 100s Done 101s The following additional packages will be installed: 101s libblas3 libfftw3-double3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 101s python3-all python3-decorator python3-iniconfig python3-joblib python3-numpy 101s python3-opentsne python3-packaging python3-pluggy python3-pytest 101s python3-pytest-runner python3-scipy python3-sklearn python3-sklearn-lib 101s python3-threadpoolctl 101s Suggested packages: 101s libfftw3-bin libfftw3-dev python-joblib-doc gcc gfortran python-numpy-doc 101s python3-dev python-scipy-doc python3-dap python-sklearn-doc ipython3 101s Recommended packages: 101s python3-simplejson python3-psutil g++ | c++-compiler python3-pil 101s python3-matplotlib 101s The following NEW packages will be installed: 101s autopkgtest-satdep libblas3 libfftw3-double3 libgfortran5 libgomp1 101s liblapack3 liblbfgsb0 python3-all python3-decorator python3-iniconfig 101s python3-joblib python3-numpy python3-opentsne python3-packaging 101s python3-pluggy python3-pytest python3-pytest-runner python3-scipy 101s python3-sklearn python3-sklearn-lib python3-threadpoolctl 101s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 101s Need to get 30.4 MB/30.4 MB of archives. 101s After this operation, 134 MB of additional disk space will be used. 101s Get:1 /tmp/autopkgtest.UzoFGD/1-autopkgtest-satdep.deb autopkgtest-satdep arm64 0 [728 B] 101s Get:2 http://ftpmaster.internal/ubuntu plucky/main arm64 libblas3 arm64 3.12.0-3build2 [152 kB] 101s Get:3 http://ftpmaster.internal/ubuntu plucky/main arm64 libgomp1 arm64 14.2.0-7ubuntu1 [145 kB] 101s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main arm64 libfftw3-double3 arm64 3.3.10-2fakesync1 [392 kB] 101s Get:5 http://ftpmaster.internal/ubuntu plucky/main arm64 libgfortran5 arm64 14.2.0-7ubuntu1 [438 kB] 102s Get:6 http://ftpmaster.internal/ubuntu plucky/main arm64 liblapack3 arm64 3.12.0-3build2 [2293 kB] 102s Get:7 http://ftpmaster.internal/ubuntu plucky/universe arm64 liblbfgsb0 arm64 3.0+dfsg.4-1build1 [27.7 kB] 102s Get:8 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-all arm64 3.12.6-0ubuntu1 [886 B] 102s Get:9 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-decorator all 5.1.1-5 [10.1 kB] 102s Get:10 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-iniconfig all 1.1.1-2 [6024 B] 102s Get:11 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-joblib all 1.3.2-5 [206 kB] 102s Get:12 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-numpy arm64 1:1.26.4+ds-11build1 [3654 kB] 102s Get:13 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-scipy arm64 1.13.1-3 [16.3 MB] 102s Get:14 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 102s Get:15 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn-lib arm64 1.4.2+dfsg-6 [3806 kB] 102s Get:16 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 102s Get:17 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-opentsne arm64 1.0.2-1ubuntu1 [376 kB] 102s Get:18 http://ftpmaster.internal/ubuntu plucky/main arm64 python3-packaging all 24.1-1 [41.4 kB] 102s Get:19 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pluggy all 1.5.0-1 [21.0 kB] 102s Get:20 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest all 8.3.2-1 [251 kB] 102s Get:21 http://ftpmaster.internal/ubuntu plucky/universe arm64 python3-pytest-runner all 2.11.1-4 [7450 B] 103s Fetched 30.4 MB in 1s (20.8 MB/s) 103s Selecting previously unselected package libblas3:arm64. 103s (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 ... 79933 files and directories currently installed.) 103s Preparing to unpack .../00-libblas3_3.12.0-3build2_arm64.deb ... 103s Unpacking libblas3:arm64 (3.12.0-3build2) ... 103s Selecting previously unselected package libgomp1:arm64. 103s Preparing to unpack .../01-libgomp1_14.2.0-7ubuntu1_arm64.deb ... 103s Unpacking libgomp1:arm64 (14.2.0-7ubuntu1) ... 103s Selecting previously unselected package libfftw3-double3:arm64. 103s Preparing to unpack .../02-libfftw3-double3_3.3.10-2fakesync1_arm64.deb ... 103s Unpacking libfftw3-double3:arm64 (3.3.10-2fakesync1) ... 103s Selecting previously unselected package libgfortran5:arm64. 103s Preparing to unpack .../03-libgfortran5_14.2.0-7ubuntu1_arm64.deb ... 103s Unpacking libgfortran5:arm64 (14.2.0-7ubuntu1) ... 103s Selecting previously unselected package liblapack3:arm64. 103s Preparing to unpack .../04-liblapack3_3.12.0-3build2_arm64.deb ... 103s Unpacking liblapack3:arm64 (3.12.0-3build2) ... 103s Selecting previously unselected package liblbfgsb0:arm64. 103s Preparing to unpack .../05-liblbfgsb0_3.0+dfsg.4-1build1_arm64.deb ... 103s Unpacking liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 103s Selecting previously unselected package python3-all. 103s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_arm64.deb ... 103s Unpacking python3-all (3.12.6-0ubuntu1) ... 103s Selecting previously unselected package python3-decorator. 103s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 103s Unpacking python3-decorator (5.1.1-5) ... 103s Selecting previously unselected package python3-iniconfig. 103s Preparing to unpack .../08-python3-iniconfig_1.1.1-2_all.deb ... 103s Unpacking python3-iniconfig (1.1.1-2) ... 104s Selecting previously unselected package python3-joblib. 104s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 104s Unpacking python3-joblib (1.3.2-5) ... 104s Selecting previously unselected package python3-numpy. 104s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_arm64.deb ... 104s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 104s Selecting previously unselected package python3-scipy. 104s Preparing to unpack .../11-python3-scipy_1.13.1-3_arm64.deb ... 104s Unpacking python3-scipy (1.13.1-3) ... 104s Selecting previously unselected package python3-threadpoolctl. 104s Preparing to unpack .../12-python3-threadpoolctl_3.1.0-1_all.deb ... 104s Unpacking python3-threadpoolctl (3.1.0-1) ... 104s Selecting previously unselected package python3-sklearn-lib:arm64. 104s Preparing to unpack .../13-python3-sklearn-lib_1.4.2+dfsg-6_arm64.deb ... 104s Unpacking python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 104s Selecting previously unselected package python3-sklearn. 104s Preparing to unpack .../14-python3-sklearn_1.4.2+dfsg-6_all.deb ... 104s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 105s Selecting previously unselected package python3-opentsne. 105s Preparing to unpack .../15-python3-opentsne_1.0.2-1ubuntu1_arm64.deb ... 105s Unpacking python3-opentsne (1.0.2-1ubuntu1) ... 105s Selecting previously unselected package python3-packaging. 105s Preparing to unpack .../16-python3-packaging_24.1-1_all.deb ... 105s Unpacking python3-packaging (24.1-1) ... 105s Selecting previously unselected package python3-pluggy. 105s Preparing to unpack .../17-python3-pluggy_1.5.0-1_all.deb ... 105s Unpacking python3-pluggy (1.5.0-1) ... 105s Selecting previously unselected package python3-pytest. 105s Preparing to unpack .../18-python3-pytest_8.3.2-1_all.deb ... 105s Unpacking python3-pytest (8.3.2-1) ... 105s Selecting previously unselected package python3-pytest-runner. 105s Preparing to unpack .../19-python3-pytest-runner_2.11.1-4_all.deb ... 105s Unpacking python3-pytest-runner (2.11.1-4) ... 105s Selecting previously unselected package autopkgtest-satdep. 105s Preparing to unpack .../20-1-autopkgtest-satdep.deb ... 105s Unpacking autopkgtest-satdep (0) ... 105s Setting up python3-iniconfig (1.1.1-2) ... 105s Setting up python3-joblib (1.3.2-5) ... 105s Setting up python3-threadpoolctl (3.1.0-1) ... 105s Setting up python3-all (3.12.6-0ubuntu1) ... 105s Setting up libgomp1:arm64 (14.2.0-7ubuntu1) ... 105s Setting up python3-decorator (5.1.1-5) ... 106s Setting up libblas3:arm64 (3.12.0-3build2) ... 106s 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 106s Setting up python3-packaging (24.1-1) ... 106s Setting up libfftw3-double3:arm64 (3.3.10-2fakesync1) ... 106s Setting up libgfortran5:arm64 (14.2.0-7ubuntu1) ... 106s Setting up python3-pluggy (1.5.0-1) ... 106s Setting up python3-pytest-runner (2.11.1-4) ... 106s Setting up liblapack3:arm64 (3.12.0-3build2) ... 106s 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 106s Setting up python3-pytest (8.3.2-1) ... 106s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 108s Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1build1) ... 108s Setting up python3-scipy (1.13.1-3) ... 112s Setting up python3-sklearn-lib:arm64 (1.4.2+dfsg-6) ... 112s Setting up python3-sklearn (1.4.2+dfsg-6) ... 113s Setting up python3-opentsne (1.0.2-1ubuntu1) ... 114s Setting up autopkgtest-satdep (0) ... 114s Processing triggers for man-db (2.12.1-3) ... 114s Processing triggers for libc-bin (2.40-1ubuntu3) ... 117s (Reading database ... 83534 files and directories currently installed.) 117s Removing autopkgtest-satdep (0) ... 118s autopkgtest [11:52:03]: test python: [----------------------- 118s + cp -rf tests /tmp/autopkgtest.UzoFGD/autopkgtest_tmp 118s + py3versions --supported 118s Testing with python3.12: 118s + cd /tmp/autopkgtest.UzoFGD/autopkgtest_tmp 118s + echo Testing with python3.12: 118s + python3.12 -m pytest 119s ============================= test session starts ============================== 119s platform linux -- Python 3.12.7+, pytest-8.3.2, pluggy-1.5.0 119s rootdir: /tmp/autopkgtest.UzoFGD/autopkgtest_tmp 119s plugins: typeguard-4.4.1 119s collected 163 items 119s 120s tests/test_affinities.py ......................... [ 15%] 165s tests/test_correctness.py ......................X... [ 31%] 179s tests/test_different_usages.py ............ [ 38%] 182s tests/test_nearest_neighbors.py ..................ssssssssssssssssssssss [ 63%] 182s ss [ 64%] 183s tests/test_sklearn_wrapper.py ... [ 66%] 190s tests/test_tsne.py ...ss............................................... [ 98%] 190s tests/test_utils.py ... [100%] 190s 190s =============================== warnings summary =============================== 190s tests/test_correctness.py::TestDataMatricesWithDuplicatedRows::test_works_without_error 190s /usr/lib/python3/dist-packages/sklearn/preprocessing/_discretization.py:248: FutureWarning: In version 1.5 onwards, subsample=200_000 will be used by default. Set subsample explicitly to silence this warning in the mean time. Set subsample=None to disable subsampling explicitly. 190s warnings.warn( 190s 190s tests/test_different_usages.py::TestUsageWithCustomAffinity::test_affinity 190s tests/test_different_usages.py::TestUsageWithCustomAffinity::test_precomputed_affinity 190s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_precomputed_distances 190s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_precomputed_neighbors 190s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_queryable_knn_index 190s tests/test_tsne.py::TestAffinityIntegration::test_transform_with_nonstandard_affinity 190s /usr/lib/python3/dist-packages/openTSNE/affinity.py:1219: FutureWarning: Using `mean` symmetrization, but the default behaviour is going to change to `max` in future versions. 190s warnings.warn( 190s 190s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 190s ====== 136 passed, 26 skipped, 1 xpassed, 7 warnings in 71.72s (0:01:11) ======= 191s autopkgtest [11:53:16]: test python: -----------------------] 191s autopkgtest [11:53:16]: test python: - - - - - - - - - - results - - - - - - - - - - 191s python PASS 191s autopkgtest [11:53:16]: @@@@@@@@@@@@@@@@@@@@ summary 191s python PASS 204s virt: nova [W] Skipping flock in bos03-arm64 204s virt: Creating nova instance adt-plucky-arm64-opentsne-20241110-115005-juju-7f2275-prod-proposed-migration-environment-2-f7c6e71e-1f3a-4487-a6d0-ff38f8bdf895 from image adt/ubuntu-plucky-arm64-server-20241110.img (UUID e13e6f16-be78-4d1c-9ff1-d003ea84cfa0)...