0s autopkgtest [10:25:26]: starting date and time: 2024-11-11 10:25:26+0000 0s autopkgtest [10:25:26]: git checkout: 0acbae0a WIP show VirtSubproc stderr in real-time 0s autopkgtest [10:25:26]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.pajhs59n/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:fftw3 --apt-upgrade opentsne --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=fftw3/3.3.10-2fakesync1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor builder-cpu2-ram4-disk20 --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@bos03-27.secgroup --name adt-plucky-amd64-opentsne-20241111-102526-juju-7f2275-prod-proposed-migration-environment-2-9f7ff1f9-2f36-4779-85fa-47f0872a178a --image adt/ubuntu-plucky-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration-amd64 -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,keyserver.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 80s autopkgtest [10:26:46]: testbed dpkg architecture: amd64 80s autopkgtest [10:26:46]: testbed apt version: 2.9.8 80s autopkgtest [10:26:46]: @@@@@@@@@@@@@@@@@@@@ test bed setup 81s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB] 81s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB] 81s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B] 81s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [913 kB] 81s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [91.3 kB] 81s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main i386 Packages [78.4 kB] 81s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 Packages [132 kB] 81s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/restricted amd64 Packages [32.6 kB] 81s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/universe i386 Packages [293 kB] 81s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/universe amd64 Packages [696 kB] 82s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse i386 Packages [13.0 kB] 82s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse amd64 Packages [37.7 kB] 82s Fetched 2383 kB in 1s (2809 kB/s) 82s Reading package lists... 84s Reading package lists... 84s Building dependency tree... 84s Reading state information... 84s Calculating upgrade... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 85s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 85s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease 85s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease 85s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease 86s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease 86s Reading package lists... 86s Reading package lists... 86s Building dependency tree... 86s Reading state information... 87s Calculating upgrade... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 87s Reading package lists... 87s Building dependency tree... 87s Reading state information... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 90s autopkgtest [10:26:56]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP PREEMPT_DYNAMIC Mon Sep 16 13:41:20 UTC 2024 90s autopkgtest [10:26:56]: @@@@@@@@@@@@@@@@@@@@ apt-source opentsne 92s Get:1 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu1 (dsc) [2377 B] 92s Get:2 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu1 (tar) [22.1 MB] 92s Get:3 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu1 (diff) [5320 B] 92s gpgv: Signature made Mon Sep 30 12:06:08 2024 UTC 92s gpgv: using RSA key 568BF22A66337CBFC9A6B9B72C83DBC8E9BD0E37 92s gpgv: Can't check signature: No public key 92s dpkg-source: warning: cannot verify inline signature for ./opentsne_1.0.2-1ubuntu1.dsc: no acceptable signature found 93s autopkgtest [10:26:59]: testing package opentsne version 1.0.2-1ubuntu1 93s autopkgtest [10:26:59]: build not needed 95s autopkgtest [10:27:01]: test python: preparing testbed 96s Reading package lists... 96s Building dependency tree... 96s Reading state information... 97s Starting pkgProblemResolver with broken count: 0 97s Starting 2 pkgProblemResolver with broken count: 0 97s Done 97s The following additional packages will be installed: 97s libblas3 libfftw3-double3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 97s python3-all python3-decorator python3-iniconfig python3-joblib python3-numpy 97s python3-opentsne python3-packaging python3-pluggy python3-pytest 97s python3-pytest-runner python3-scipy python3-sklearn python3-sklearn-lib 97s python3-threadpoolctl 97s Suggested packages: 97s libfftw3-bin libfftw3-dev python-joblib-doc gcc gfortran python-numpy-doc 97s python3-dev python-scipy-doc python3-dap python-sklearn-doc ipython3 97s Recommended packages: 97s python3-simplejson python3-psutil g++ | c++-compiler python3-pil 97s python3-matplotlib 97s The following NEW packages will be installed: 97s autopkgtest-satdep libblas3 libfftw3-double3 libgfortran5 libgomp1 97s liblapack3 liblbfgsb0 python3-all python3-decorator python3-iniconfig 97s python3-joblib python3-numpy python3-opentsne python3-packaging 97s python3-pluggy python3-pytest python3-pytest-runner python3-scipy 97s python3-sklearn python3-sklearn-lib python3-threadpoolctl 97s 0 upgraded, 21 newly installed, 0 to remove and 0 not upgraded. 97s Need to get 34.6 MB/34.6 MB of archives. 97s After this operation, 152 MB of additional disk space will be used. 97s Get:1 /tmp/autopkgtest.K9s8rm/1-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [728 B] 97s Get:2 http://ftpmaster.internal/ubuntu plucky/main amd64 libblas3 amd64 3.12.0-3build2 [247 kB] 97s Get:3 http://ftpmaster.internal/ubuntu plucky/main amd64 libgomp1 amd64 14.2.0-7ubuntu1 [148 kB] 97s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main amd64 libfftw3-double3 amd64 3.3.10-2fakesync1 [839 kB] 98s Get:5 http://ftpmaster.internal/ubuntu plucky/main amd64 libgfortran5 amd64 14.2.0-7ubuntu1 [909 kB] 98s Get:6 http://ftpmaster.internal/ubuntu plucky/main amd64 liblapack3 amd64 3.12.0-3build2 [2668 kB] 98s Get:7 http://ftpmaster.internal/ubuntu plucky/universe amd64 liblbfgsb0 amd64 3.0+dfsg.4-1build1 [29.9 kB] 98s Get:8 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-all amd64 3.12.6-0ubuntu1 [886 B] 98s Get:9 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-decorator all 5.1.1-5 [10.1 kB] 98s Get:10 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-iniconfig all 1.1.1-2 [6024 B] 98s Get:11 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-joblib all 1.3.2-5 [206 kB] 98s Get:12 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-numpy amd64 1:1.26.4+ds-11build1 [4479 kB] 98s Get:13 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-scipy amd64 1.13.1-5 [18.2 MB] 98s Get:14 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-threadpoolctl all 3.1.0-1 [21.3 kB] 98s Get:15 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn-lib amd64 1.4.2+dfsg-6 [3920 kB] 98s Get:16 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-sklearn all 1.4.2+dfsg-6 [2257 kB] 99s Get:17 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-opentsne amd64 1.0.2-1ubuntu1 [388 kB] 99s Get:18 http://ftpmaster.internal/ubuntu plucky/main amd64 python3-packaging all 24.1-1 [41.4 kB] 99s Get:19 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pluggy all 1.5.0-1 [21.0 kB] 99s Get:20 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest all 8.3.3-1 [251 kB] 99s Get:21 http://ftpmaster.internal/ubuntu plucky/universe amd64 python3-pytest-runner all 2.11.1-4 [7450 B] 99s Fetched 34.6 MB in 2s (21.1 MB/s) 99s Selecting previously unselected package libblas3:amd64. 99s (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 ... 75552 files and directories currently installed.) 99s Preparing to unpack .../00-libblas3_3.12.0-3build2_amd64.deb ... 99s Unpacking libblas3:amd64 (3.12.0-3build2) ... 99s Selecting previously unselected package libgomp1:amd64. 99s Preparing to unpack .../01-libgomp1_14.2.0-7ubuntu1_amd64.deb ... 99s Unpacking libgomp1:amd64 (14.2.0-7ubuntu1) ... 99s Selecting previously unselected package libfftw3-double3:amd64. 99s Preparing to unpack .../02-libfftw3-double3_3.3.10-2fakesync1_amd64.deb ... 99s Unpacking libfftw3-double3:amd64 (3.3.10-2fakesync1) ... 99s Selecting previously unselected package libgfortran5:amd64. 99s Preparing to unpack .../03-libgfortran5_14.2.0-7ubuntu1_amd64.deb ... 99s Unpacking libgfortran5:amd64 (14.2.0-7ubuntu1) ... 99s Selecting previously unselected package liblapack3:amd64. 99s Preparing to unpack .../04-liblapack3_3.12.0-3build2_amd64.deb ... 99s Unpacking liblapack3:amd64 (3.12.0-3build2) ... 99s Selecting previously unselected package liblbfgsb0:amd64. 99s Preparing to unpack .../05-liblbfgsb0_3.0+dfsg.4-1build1_amd64.deb ... 99s Unpacking liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 99s Selecting previously unselected package python3-all. 99s Preparing to unpack .../06-python3-all_3.12.6-0ubuntu1_amd64.deb ... 99s Unpacking python3-all (3.12.6-0ubuntu1) ... 99s Selecting previously unselected package python3-decorator. 99s Preparing to unpack .../07-python3-decorator_5.1.1-5_all.deb ... 99s Unpacking python3-decorator (5.1.1-5) ... 99s Selecting previously unselected package python3-iniconfig. 99s Preparing to unpack .../08-python3-iniconfig_1.1.1-2_all.deb ... 99s Unpacking python3-iniconfig (1.1.1-2) ... 99s Selecting previously unselected package python3-joblib. 99s Preparing to unpack .../09-python3-joblib_1.3.2-5_all.deb ... 99s Unpacking python3-joblib (1.3.2-5) ... 99s Selecting previously unselected package python3-numpy. 99s Preparing to unpack .../10-python3-numpy_1%3a1.26.4+ds-11build1_amd64.deb ... 99s Unpacking python3-numpy (1:1.26.4+ds-11build1) ... 100s Selecting previously unselected package python3-scipy. 100s Preparing to unpack .../11-python3-scipy_1.13.1-5_amd64.deb ... 100s Unpacking python3-scipy (1.13.1-5) ... 100s Selecting previously unselected package python3-threadpoolctl. 100s Preparing to unpack .../12-python3-threadpoolctl_3.1.0-1_all.deb ... 100s Unpacking python3-threadpoolctl (3.1.0-1) ... 100s Selecting previously unselected package python3-sklearn-lib:amd64. 100s Preparing to unpack .../13-python3-sklearn-lib_1.4.2+dfsg-6_amd64.deb ... 100s Unpacking python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 100s Selecting previously unselected package python3-sklearn. 100s Preparing to unpack .../14-python3-sklearn_1.4.2+dfsg-6_all.deb ... 100s Unpacking python3-sklearn (1.4.2+dfsg-6) ... 100s Selecting previously unselected package python3-opentsne. 100s Preparing to unpack .../15-python3-opentsne_1.0.2-1ubuntu1_amd64.deb ... 100s Unpacking python3-opentsne (1.0.2-1ubuntu1) ... 100s Selecting previously unselected package python3-packaging. 100s Preparing to unpack .../16-python3-packaging_24.1-1_all.deb ... 100s Unpacking python3-packaging (24.1-1) ... 100s Selecting previously unselected package python3-pluggy. 100s Preparing to unpack .../17-python3-pluggy_1.5.0-1_all.deb ... 100s Unpacking python3-pluggy (1.5.0-1) ... 100s Selecting previously unselected package python3-pytest. 100s Preparing to unpack .../18-python3-pytest_8.3.3-1_all.deb ... 100s Unpacking python3-pytest (8.3.3-1) ... 100s Selecting previously unselected package python3-pytest-runner. 100s Preparing to unpack .../19-python3-pytest-runner_2.11.1-4_all.deb ... 100s Unpacking python3-pytest-runner (2.11.1-4) ... 100s Selecting previously unselected package autopkgtest-satdep. 100s Preparing to unpack .../20-1-autopkgtest-satdep.deb ... 100s Unpacking autopkgtest-satdep (0) ... 100s Setting up python3-iniconfig (1.1.1-2) ... 100s Setting up python3-joblib (1.3.2-5) ... 101s Setting up python3-threadpoolctl (3.1.0-1) ... 101s Setting up python3-all (3.12.6-0ubuntu1) ... 101s Setting up libgomp1:amd64 (14.2.0-7ubuntu1) ... 101s Setting up python3-decorator (5.1.1-5) ... 101s Setting up libblas3:amd64 (3.12.0-3build2) ... 101s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 101s Setting up python3-packaging (24.1-1) ... 101s Setting up libfftw3-double3:amd64 (3.3.10-2fakesync1) ... 101s Setting up libgfortran5:amd64 (14.2.0-7ubuntu1) ... 101s Setting up python3-pluggy (1.5.0-1) ... 101s Setting up python3-pytest-runner (2.11.1-4) ... 101s Setting up liblapack3:amd64 (3.12.0-3build2) ... 101s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 101s Setting up python3-pytest (8.3.3-1) ... 101s Setting up python3-numpy (1:1.26.4+ds-11build1) ... 103s Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1build1) ... 103s Setting up python3-scipy (1.13.1-5) ... 105s Setting up python3-sklearn-lib:amd64 (1.4.2+dfsg-6) ... 105s Setting up python3-sklearn (1.4.2+dfsg-6) ... 107s Setting up python3-opentsne (1.0.2-1ubuntu1) ... 107s Setting up autopkgtest-satdep (0) ... 107s Processing triggers for man-db (2.12.1-3) ... 107s Processing triggers for libc-bin (2.40-1ubuntu3) ... 110s (Reading database ... 79153 files and directories currently installed.) 110s Removing autopkgtest-satdep (0) ... 111s autopkgtest [10:27:17]: test python: [----------------------- 111s + cp -rf tests /tmp/autopkgtest.K9s8rm/autopkgtest_tmp 111s + py3versions --supported 111s + cd /tmp/autopkgtest.K9s8rm/autopkgtest_tmp 111s + echo Testing with python3.12: 111s Testing with python3.12: 111s + python3.12 -m pytest 112s ============================= test session starts ============================== 112s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0 112s rootdir: /tmp/autopkgtest.K9s8rm/autopkgtest_tmp 112s plugins: typeguard-4.4.1 112s collected 163 items 112s 113s tests/test_affinities.py ......................... [ 15%] 141s tests/test_correctness.py ......................X... [ 31%] 150s tests/test_different_usages.py ............ [ 38%] 151s tests/test_nearest_neighbors.py ..................ssssssssssssssssssssss [ 63%] 151s ss [ 64%] 152s tests/test_sklearn_wrapper.py ... [ 66%] 157s tests/test_tsne.py ...ss............................................... [ 98%] 157s tests/test_utils.py ... [100%] 157s 157s =============================== warnings summary =============================== 157s tests/test_correctness.py::TestDataMatricesWithDuplicatedRows::test_works_without_error 157s /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. 157s warnings.warn( 157s 157s tests/test_different_usages.py::TestUsageWithCustomAffinity::test_affinity 157s tests/test_different_usages.py::TestUsageWithCustomAffinity::test_precomputed_affinity 157s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_precomputed_distances 157s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_precomputed_neighbors 157s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_queryable_knn_index 157s tests/test_tsne.py::TestAffinityIntegration::test_transform_with_nonstandard_affinity 157s /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. 157s warnings.warn( 157s 157s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 157s =========== 136 passed, 26 skipped, 1 xpassed, 7 warnings in 45.63s ============ 158s autopkgtest [10:28:04]: test python: -----------------------] 158s python PASS 158s autopkgtest [10:28:04]: test python: - - - - - - - - - - results - - - - - - - - - - 158s autopkgtest [10:28:04]: @@@@@@@@@@@@@@@@@@@@ summary 158s python PASS 164s virt: nova [W] Skipping flock for amd64 164s virt: Creating nova instance adt-plucky-amd64-opentsne-20241111-102526-juju-7f2275-prod-proposed-migration-environment-2-9f7ff1f9-2f36-4779-85fa-47f0872a178a from image adt/ubuntu-plucky-amd64-server-20241111.img (UUID 26095e4c-07f6-404e-b69f-183f750334aa)...