0s autopkgtest [01:30:30]: starting date and time: 2025-03-16 01:30:30+0000 0s autopkgtest [01:30:30]: git checkout: 325255d2 Merge branch 'pin-any-arch' into 'ubuntu/production' 0s autopkgtest [01:30:30]: host juju-7f2275-prod-proposed-migration-environment-9; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.u3lnukpf/out --timeout-copy=6000 --setup-commands 'ln -s /dev/null /etc/systemd/system/bluetooth.service; printf "http_proxy=http://squid.internal:3128\nhttps_proxy=http://squid.internal:3128\nno_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,radosgw.ps5.canonical.com\n" >> /etc/environment' --apt-pocket=proposed=src:scikit-learn --apt-upgrade opentsne --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=scikit-learn/1.4.2+dfsg-8 -- lxd -r lxd-armhf-10.145.243.210 lxd-armhf-10.145.243.210:autopkgtest/ubuntu/plucky/armhf 20s autopkgtest [01:30:50]: testbed dpkg architecture: armhf 22s autopkgtest [01:30:52]: testbed apt version: 2.9.33 26s autopkgtest [01:30:56]: @@@@@@@@@@@@@@@@@@@@ test bed setup 28s autopkgtest [01:30:58]: testbed release detected to be: None 36s autopkgtest [01:31:06]: updating testbed package index (apt update) 38s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [126 kB] 38s Get:2 http://ftpmaster.internal/ubuntu plucky InRelease [257 kB] 38s Get:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease [126 kB] 38s Get:4 http://ftpmaster.internal/ubuntu plucky-security InRelease [126 kB] 39s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [41.4 kB] 39s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [17.7 kB] 39s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [365 kB] 39s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf Packages [74.9 kB] 39s Get:9 http://ftpmaster.internal/ubuntu plucky-proposed/main armhf c-n-f Metadata [1792 B] 39s Get:10 http://ftpmaster.internal/ubuntu plucky-proposed/restricted armhf c-n-f Metadata [116 B] 39s Get:11 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf Packages [290 kB] 39s Get:12 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf c-n-f Metadata [10.5 kB] 39s Get:13 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf Packages [4168 B] 39s Get:14 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse armhf c-n-f Metadata [240 B] 39s Get:15 http://ftpmaster.internal/ubuntu plucky/main Sources [1389 kB] 40s Get:16 http://ftpmaster.internal/ubuntu plucky/universe Sources [21.0 MB] 55s Get:17 http://ftpmaster.internal/ubuntu plucky/multiverse Sources [299 kB] 55s Get:18 http://ftpmaster.internal/ubuntu plucky/main armhf Packages [1378 kB] 56s Get:19 http://ftpmaster.internal/ubuntu plucky/main armhf c-n-f Metadata [29.5 kB] 56s Get:20 http://ftpmaster.internal/ubuntu plucky/restricted armhf c-n-f Metadata [108 B] 56s Get:21 http://ftpmaster.internal/ubuntu plucky/universe armhf Packages [15.3 MB] 66s Get:22 http://ftpmaster.internal/ubuntu plucky/multiverse armhf Packages [172 kB] 68s Fetched 41.1 MB in 30s (1366 kB/s) 69s Reading package lists... 75s autopkgtest [01:31:45]: upgrading testbed (apt dist-upgrade and autopurge) 77s Reading package lists... 77s Building dependency tree... 77s Reading state information... 77s Calculating upgrade...Starting pkgProblemResolver with broken count: 0 78s Starting 2 pkgProblemResolver with broken count: 0 78s Done 78s Entering ResolveByKeep 79s 79s Calculating upgrade... 79s The following packages will be upgraded: 79s pinentry-curses python3-jinja2 sos strace 80s 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 80s Need to get 960 kB of archives. 80s After this operation, 23.6 kB of additional disk space will be used. 80s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf strace armhf 6.13+ds-1ubuntu1 [445 kB] 80s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf pinentry-curses armhf 1.3.1-2ubuntu3 [40.6 kB] 80s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf python3-jinja2 all 3.1.5-2ubuntu1 [109 kB] 80s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf sos all 4.9.0-5 [365 kB] 81s Fetched 960 kB in 1s (1216 kB/s) 81s (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 ... 64655 files and directories currently installed.) 81s Preparing to unpack .../strace_6.13+ds-1ubuntu1_armhf.deb ... 81s Unpacking strace (6.13+ds-1ubuntu1) over (6.11-0ubuntu1) ... 81s Preparing to unpack .../pinentry-curses_1.3.1-2ubuntu3_armhf.deb ... 81s Unpacking pinentry-curses (1.3.1-2ubuntu3) over (1.3.1-2ubuntu2) ... 81s Preparing to unpack .../python3-jinja2_3.1.5-2ubuntu1_all.deb ... 81s Unpacking python3-jinja2 (3.1.5-2ubuntu1) over (3.1.5-2) ... 81s Preparing to unpack .../archives/sos_4.9.0-5_all.deb ... 81s Unpacking sos (4.9.0-5) over (4.9.0-4) ... 81s Setting up sos (4.9.0-5) ... 82s Setting up pinentry-curses (1.3.1-2ubuntu3) ... 82s Setting up python3-jinja2 (3.1.5-2ubuntu1) ... 82s Setting up strace (6.13+ds-1ubuntu1) ... 82s Processing triggers for man-db (2.13.0-1) ... 85s Reading package lists... 85s Building dependency tree... 85s Reading state information... 86s Starting pkgProblemResolver with broken count: 0 86s Starting 2 pkgProblemResolver with broken count: 0 86s Done 86s Solving dependencies... 87s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 89s autopkgtest [01:31:59]: rebooting testbed after setup commands that affected boot 129s autopkgtest [01:32:39]: testbed running kernel: Linux 6.8.0-52-generic #53~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Wed Jan 15 18:10:51 UTC 2 154s autopkgtest [01:33:04]: @@@@@@@@@@@@@@@@@@@@ apt-source opentsne 174s Get:1 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu4 (dsc) [2377 B] 174s Get:2 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu4 (tar) [22.1 MB] 174s Get:3 http://ftpmaster.internal/ubuntu plucky/universe opentsne 1.0.2-1ubuntu4 (diff) [5396 B] 174s gpgv: Signature made Tue Mar 4 17:45:11 2025 UTC 174s gpgv: using RSA key 25E3FF2D7F469DBE7D0D4E50AFCFEC8E669CE1C2 174s gpgv: Can't check signature: No public key 174s dpkg-source: warning: cannot verify inline signature for ./opentsne_1.0.2-1ubuntu4.dsc: no acceptable signature found 175s autopkgtest [01:33:25]: testing package opentsne version 1.0.2-1ubuntu4 177s autopkgtest [01:33:27]: build not needed 180s autopkgtest [01:33:30]: test python: preparing testbed 183s Reading package lists... 183s Building dependency tree... 183s Reading state information... 183s Starting pkgProblemResolver with broken count: 0 183s Starting 2 pkgProblemResolver with broken count: 0 183s Done 184s The following NEW packages will be installed: 184s libblas3 libfftw3-double3 libgfortran5 libgomp1 liblapack3 liblbfgsb0 184s python3-all python3-decorator python3-iniconfig python3-joblib python3-numpy 184s python3-numpy-dev python3-opentsne python3-pluggy python3-pytest 184s python3-pytest-runner python3-scipy python3-sklearn python3-sklearn-lib 184s python3-threadpoolctl 184s 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. 184s Need to get 30.8 MB of archives. 184s After this operation, 119 MB of additional disk space will be used. 184s Get:1 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy-dev armhf 1:2.2.3+ds-5 [141 kB] 185s Get:2 http://ftpmaster.internal/ubuntu plucky/main armhf libblas3 armhf 3.12.1-2 [132 kB] 185s Get:3 http://ftpmaster.internal/ubuntu plucky/main armhf libgfortran5 armhf 15-20250222-0ubuntu1 [330 kB] 185s Get:4 http://ftpmaster.internal/ubuntu plucky/main armhf liblapack3 armhf 3.12.1-2 [2091 kB] 186s Get:5 http://ftpmaster.internal/ubuntu plucky/main armhf python3-numpy armhf 1:2.2.3+ds-5 [3725 kB] 187s Get:6 http://ftpmaster.internal/ubuntu plucky/main armhf libgomp1 armhf 15-20250222-0ubuntu1 [128 kB] 187s Get:7 http://ftpmaster.internal/ubuntu plucky/main armhf libfftw3-double3 armhf 3.3.10-2fakesync1build1 [369 kB] 188s Get:8 http://ftpmaster.internal/ubuntu plucky/universe armhf liblbfgsb0 armhf 3.0+dfsg.4-1build1 [27.4 kB] 188s Get:9 http://ftpmaster.internal/ubuntu plucky/main armhf python3-all armhf 3.13.2-2 [886 B] 188s Get:10 http://ftpmaster.internal/ubuntu plucky/main armhf python3-decorator all 5.1.1-5 [10.1 kB] 188s Get:11 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-iniconfig all 1.1.1-2 [6024 B] 188s Get:12 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-joblib all 1.4.2-3 [205 kB] 188s Get:13 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-scipy armhf 1.14.1-4ubuntu2 [16.7 MB] 195s Get:14 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-threadpoolctl all 3.1.0-1 [21.3 kB] 195s Get:15 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-sklearn-lib armhf 1.4.2+dfsg-8 [4014 kB] 196s Get:16 http://ftpmaster.internal/ubuntu plucky-proposed/universe armhf python3-sklearn all 1.4.2+dfsg-8 [2258 kB] 197s Get:17 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-opentsne armhf 1.0.2-1ubuntu4 [355 kB] 197s Get:18 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pluggy all 1.5.0-1 [21.0 kB] 197s Get:19 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest all 8.3.5-1 [252 kB] 197s Get:20 http://ftpmaster.internal/ubuntu plucky/universe armhf python3-pytest-runner all 2.11.1-4 [7450 B] 198s Fetched 30.8 MB in 13s (2377 kB/s) 198s Selecting previously unselected package python3-numpy-dev:armhf. 198s (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 ... 64655 files and directories currently installed.) 198s Preparing to unpack .../00-python3-numpy-dev_1%3a2.2.3+ds-5_armhf.deb ... 198s Unpacking python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 198s Selecting previously unselected package libblas3:armhf. 198s Preparing to unpack .../01-libblas3_3.12.1-2_armhf.deb ... 198s Unpacking libblas3:armhf (3.12.1-2) ... 198s Selecting previously unselected package libgfortran5:armhf. 198s Preparing to unpack .../02-libgfortran5_15-20250222-0ubuntu1_armhf.deb ... 198s Unpacking libgfortran5:armhf (15-20250222-0ubuntu1) ... 198s Selecting previously unselected package liblapack3:armhf. 198s Preparing to unpack .../03-liblapack3_3.12.1-2_armhf.deb ... 198s Unpacking liblapack3:armhf (3.12.1-2) ... 198s Selecting previously unselected package python3-numpy. 198s Preparing to unpack .../04-python3-numpy_1%3a2.2.3+ds-5_armhf.deb ... 198s Unpacking python3-numpy (1:2.2.3+ds-5) ... 198s Selecting previously unselected package libgomp1:armhf. 198s Preparing to unpack .../05-libgomp1_15-20250222-0ubuntu1_armhf.deb ... 198s Unpacking libgomp1:armhf (15-20250222-0ubuntu1) ... 198s Selecting previously unselected package libfftw3-double3:armhf. 198s Preparing to unpack .../06-libfftw3-double3_3.3.10-2fakesync1build1_armhf.deb ... 198s Unpacking libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 198s Selecting previously unselected package liblbfgsb0:armhf. 198s Preparing to unpack .../07-liblbfgsb0_3.0+dfsg.4-1build1_armhf.deb ... 198s Unpacking liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 198s Selecting previously unselected package python3-all. 198s Preparing to unpack .../08-python3-all_3.13.2-2_armhf.deb ... 198s Unpacking python3-all (3.13.2-2) ... 198s Selecting previously unselected package python3-decorator. 198s Preparing to unpack .../09-python3-decorator_5.1.1-5_all.deb ... 198s Unpacking python3-decorator (5.1.1-5) ... 198s Selecting previously unselected package python3-iniconfig. 198s Preparing to unpack .../10-python3-iniconfig_1.1.1-2_all.deb ... 198s Unpacking python3-iniconfig (1.1.1-2) ... 198s Selecting previously unselected package python3-joblib. 198s Preparing to unpack .../11-python3-joblib_1.4.2-3_all.deb ... 198s Unpacking python3-joblib (1.4.2-3) ... 198s Selecting previously unselected package python3-scipy. 198s Preparing to unpack .../12-python3-scipy_1.14.1-4ubuntu2_armhf.deb ... 198s Unpacking python3-scipy (1.14.1-4ubuntu2) ... 199s Selecting previously unselected package python3-threadpoolctl. 199s Preparing to unpack .../13-python3-threadpoolctl_3.1.0-1_all.deb ... 199s Unpacking python3-threadpoolctl (3.1.0-1) ... 199s Selecting previously unselected package python3-sklearn-lib:armhf. 199s Preparing to unpack .../14-python3-sklearn-lib_1.4.2+dfsg-8_armhf.deb ... 199s Unpacking python3-sklearn-lib:armhf (1.4.2+dfsg-8) ... 199s Selecting previously unselected package python3-sklearn. 199s Preparing to unpack .../15-python3-sklearn_1.4.2+dfsg-8_all.deb ... 199s Unpacking python3-sklearn (1.4.2+dfsg-8) ... 199s Selecting previously unselected package python3-opentsne. 199s Preparing to unpack .../16-python3-opentsne_1.0.2-1ubuntu4_armhf.deb ... 199s Unpacking python3-opentsne (1.0.2-1ubuntu4) ... 199s Selecting previously unselected package python3-pluggy. 199s Preparing to unpack .../17-python3-pluggy_1.5.0-1_all.deb ... 199s Unpacking python3-pluggy (1.5.0-1) ... 199s Selecting previously unselected package python3-pytest. 199s Preparing to unpack .../18-python3-pytest_8.3.5-1_all.deb ... 199s Unpacking python3-pytest (8.3.5-1) ... 199s Selecting previously unselected package python3-pytest-runner. 199s Preparing to unpack .../19-python3-pytest-runner_2.11.1-4_all.deb ... 199s Unpacking python3-pytest-runner (2.11.1-4) ... 199s Setting up python3-iniconfig (1.1.1-2) ... 200s Setting up python3-joblib (1.4.2-3) ... 200s Setting up python3-threadpoolctl (3.1.0-1) ... 200s Setting up python3-all (3.13.2-2) ... 200s Setting up libgomp1:armhf (15-20250222-0ubuntu1) ... 200s Setting up python3-decorator (5.1.1-5) ... 200s Setting up libblas3:armhf (3.12.1-2) ... 200s update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode 200s Setting up python3-numpy-dev:armhf (1:2.2.3+ds-5) ... 200s Setting up libfftw3-double3:armhf (3.3.10-2fakesync1build1) ... 200s Setting up libgfortran5:armhf (15-20250222-0ubuntu1) ... 200s Setting up python3-pluggy (1.5.0-1) ... 200s Setting up python3-pytest-runner (2.11.1-4) ... 200s Setting up liblapack3:armhf (3.12.1-2) ... 200s update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode 200s Setting up python3-pytest (8.3.5-1) ... 201s Setting up python3-numpy (1:2.2.3+ds-5) ... 203s Setting up liblbfgsb0:armhf (3.0+dfsg.4-1build1) ... 203s Setting up python3-scipy (1.14.1-4ubuntu2) ... 206s Setting up python3-sklearn-lib:armhf (1.4.2+dfsg-8) ... 206s Setting up python3-sklearn (1.4.2+dfsg-8) ... 209s Setting up python3-opentsne (1.0.2-1ubuntu4) ... 209s Processing triggers for man-db (2.13.0-1) ... 209s Processing triggers for libc-bin (2.41-1ubuntu1) ... 218s autopkgtest [01:34:08]: test python: [----------------------- 220s + cp -rf tests /tmp/autopkgtest.W16lWh/autopkgtest_tmp 220s + py3versions --supported 220s + cd /tmp/autopkgtest.W16lWh/autopkgtest_tmp 220s + echo Testing with python3.13: 220s + python3.13 -m pytest 220s Testing with python3.13: 221s ============================= test session starts ============================== 221s platform linux -- Python 3.13.2, pytest-8.3.5, pluggy-1.5.0 221s rootdir: /tmp/autopkgtest.W16lWh/autopkgtest_tmp 221s plugins: typeguard-4.4.2 221s collected 163 items 221s 222s tests/test_affinities.py ......................... [ 15%] 277s tests/test_correctness.py ......................X... [ 31%] 293s tests/test_different_usages.py ............ [ 38%] 296s tests/test_nearest_neighbors.py ..................ssssssssssssssssssssss [ 63%] 296s ss [ 64%] 298s tests/test_sklearn_wrapper.py ... [ 66%] 306s tests/test_tsne.py ...ss............................................... [ 98%] 306s tests/test_utils.py ... [100%] 306s 306s =============================== warnings summary =============================== 306s tests/test_correctness.py::TestDataMatricesWithDuplicatedRows::test_works_without_error 306s /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. 306s warnings.warn( 306s 306s tests/test_different_usages.py::TestUsageWithCustomAffinity::test_affinity 306s tests/test_different_usages.py::TestUsageWithCustomAffinity::test_precomputed_affinity 306s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_precomputed_distances 306s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_precomputed_neighbors 306s tests/test_different_usages.py::TestUsageWithCustomAffinityAndCustomNeighbors::test_affinity_with_queryable_knn_index 306s tests/test_tsne.py::TestAffinityIntegration::test_transform_with_nonstandard_affinity 306s /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. 306s warnings.warn( 306s 306s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html 306s ====== 136 passed, 26 skipped, 1 xpassed, 7 warnings in 86.02s (0:01:26) ======= 307s autopkgtest [01:35:37]: test python: -----------------------] 311s python PASS 311s autopkgtest [01:35:41]: test python: - - - - - - - - - - results - - - - - - - - - - 315s autopkgtest [01:35:45]: @@@@@@@@@@@@@@@@@@@@ summary 315s python PASS