0s autopkgtest [19:06:46]: starting date and time: 2024-11-14 19:06:46+0000
  0s autopkgtest [19:06:46]: git checkout: 6f3be7a8 Fix armhf LXD image generation for plucky
  0s autopkgtest [19:06:46]: host juju-7f2275-prod-proposed-migration-environment-15; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.yjym3wdc/out --timeout-copy=6000 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --apt-pocket=proposed=src:numpy --apt-upgrade mdanalysis --timeout-short=300 --timeout-copy=20000 --timeout-test=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=numpy/1:1.26.4+ds-11ubuntu1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest-big-ppc64el --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-4.secgroup --name adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c --image adt/ubuntu-plucky-ppc64el-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-15 --net-id=net_prod-proposed-migration-ppc64el -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/
1643s nova [W] Using flock in prodstack6-ppc64el
1643s flock: timeout while waiting to get lock
1643s Creating nova instance adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c from image adt/ubuntu-plucky-ppc64el-server-20241113.img (UUID 0c5715b6-5cca-4485-b8bf-b85dfd917a5f)...
1643s nova [W] nova quota exceeded (attempt #0)
1643s nova [W] nova quota exceeded (attempt #1)
1643s nova [W] nova quota exceeded (attempt #2)
1643s nova [W] nova quota exceeded (attempt #3)
1643s nova [E] nova boot failed (attempt #0):
1643s nova [E] DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader')
1643s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader')
1643s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken')
1643s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth')
1643s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP')
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://keystone.ps6.canonical.com:5000/v3 -H "Accept: application/json" -H "User-Agent: nova keystoneauth1/4.0.0 python-requests/2.22.0 CPython/3.8.10"
1643s DEBUG (connectionpool:962) Starting new HTTPS connection (1): keystone.ps6.canonical.com:5000
1643s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "GET /v3 HTTP/1.1" 200 267
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 267 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:05 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) Vary: X-Auth-Token x-openstack-request-id: req-29d7dde5-f2be-458a-92fa-1e52b415a324
1643s DEBUG (session:580) RESP BODY: {"version": {"id": "v3.14", "status": "stable", "updated": "2020-04-07T00:00:00Z", "links": [{"rel": "self", "href": "https://keystone.ps6.canonical.com:5000/v3/"}], "media-types": [{"base": "application/json", "type": "application/vnd.openstack.identity-v3+json"}]}}
1643s DEBUG (session:946) GET call to https://keystone.ps6.canonical.com:5000/v3 used request id req-29d7dde5-f2be-458a-92fa-1e52b415a324
1643s DEBUG (base:182) Making authentication request to https://keystone.ps6.canonical.com:5000/v3/auth/tokens
1643s DEBUG (connectionpool:429) https://keystone.ps6.canonical.com:5000 "POST /v3/auth/tokens HTTP/1.1" 201 12525
1643s DEBUG (base:187) {"token": {"methods": ["password"], "user": {"domain": {"id": "default", "name": "Default"}, "id": "c871debdeffd4cb8b69ce618fc4aa361", "name": "prod-proposed-migration-ppc64el", "password_expires_at": null}, "audit_ids": ["68aUxRofSSCTtnITBuEDgA"], "expires_at": "2024-11-15T19:28:06.000000Z", "issued_at": "2024-11-14T19:28:06.000000Z", "project": {"domain": {"id": "default", "name": "Default"}, "id": "623df63b80274c21bc79a0c35e68d615", "name": "prod-proposed-migration-ppc64el_project"}, "is_domain": false, "roles": [{"id": "80674fb26dab46e9a6bd57e7f8193360", "name": "load-balancer_member"}, {"id": "15cf997650e345b7b21c02b5cdb7d84a", "name": "member"}, {"id": "86bf3043974746c2bf52c2a9f362f986", "name": "reader"}], "is_admin_project": false, "catalog": [{"endpoints": [{"id": "213cdf38198c4581bd5b7d6d0836923b", "interface": "internal", "region_id": "prodstack6", "url": "https://radosgw-internal.ps6.canonical.com:443/", "region": "prodstack6"}, {"id": "67061eee26944a1a8009f9d07be19738", "interface": "public", "region_id": "prodstack6", "url": "https://radosgw.ps6.canonical.com:443/", "region": "prodstack6"}, {"id": "fc88c52c749a47d08a24a2c7efbde01b", "interface": "admin", "region_id": "prodstack6", "url": "https://radosgw-admin.ps6.canonical.com:443/", "region": "prodstack6"}], "id": "06e4714942634054bf9aa11715312b4e", "type": "s3", "name": "s3"}, {"endpoints": [{"id": "8aa44c94b63746bd9b37f1008ad55fa8", "interface": "admin", "region_id": "prodstack6", "url": "https://aodh-admin.ps6.canonical.com:8042", "region": "prodstack6"}, {"id": "92cf08a80a0242ebbca8ec893cf332b1", "interface": "public", "region_id": "prodstack6", "url": "https://aodh.ps6.canonical.com:8042", "region": "prodstack6"}, {"id": "d8139c6e11ae4edcb78981c12bd53212", "interface": "internal", "region_id": "prodstack6", "url": "https://aodh-internal.ps6.canonical.com:8042", "region": "prodstack6"}], "id": "2fb939b0b969435c8f0c5fa4edb4de94", "type": "alarming", "name": "aodh"}, {"endpoints": [{"id": "a49fcc80e658411885f88cdd8432a571", "interface": "internal", "region_id": "prodstack6", "url": "https://heat-internal.ps6.canonical.com:8000/v1", "region": "prodstack6"}, {"id": "b23866fddba8415885b06c064c34b94b", "interface": "public", "region_id": "prodstack6", "url": "https://heat.ps6.canonical.com:8000/v1", "region": "prodstack6"}, {"id": "f84ae55197f94b8392a678f35c82ca26", "interface": "admin", "region_id": "prodstack6", "url": "https://heat-admin.ps6.canonical.com:8000/v1", "region": "prodstack6"}], "id": "3d4b59f7dab644b2b527e8e96b697545", "type": "cloudformation", "name": "heat-cfn"}, {"endpoints": [{"id": "2e0143334c6241169f45f1c11970c6bc", "interface": "public", "region_id": "prodstack6", "url": "https://heat.ps6.canonical.com:8004/v1/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "5e19c32243c04a3faf1e5f9ab900c260", "interface": "internal", "region_id": "prodstack6", "url": "https://heat-internal.ps6.canonical.com:8004/v1/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "b3fc5c88ec8543a691fec75726b86967", "interface": "admin", "region_id": "prodstack6", "url": "https://heat-admin.ps6.canonical.com:8004/v1/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}], "id": "43b926205044476b8093b18d8ce0a9e4", "type": "orchestration", "name": "heat"}, {"endpoints": [{"id": "a47569b96e5b4146a312e4673504557c", "interface": "public", "region_id": "prodstack6", "url": "https://glance.ps6.canonical.com:9292", "region": "prodstack6"}, {"id": "bba35c4ab04f4114a2a34e65568537bd", "interface": "internal", "region_id": "prodstack6", "url": "https://glance-internal.ps6.canonical.com:9292", "region": "prodstack6"}, {"id": "ef769f1117c74a62a279131486c89628", "interface": "admin", "region_id": "prodstack6", "url": "https://glance-admin.ps6.canonical.com:9292", "region": "prodstack6"}], "id": "49de724549524bd78e9cd46a4477226f", "type": "image", "name": "glance"}, {"endpoints": [{"id": "a1a41e9a1e2d42e5b6cd5380cd1e21bf", "interface": "admin", "region_id": "prodstack6", "url": "https://cinder-admin.ps6.canonical.com:8776/v3/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "d2309a99724b4111827482c68a832c0c", "interface": "public", "region_id": "prodstack6", "url": "https://cinder.ps6.canonical.com:8776/v3/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "f8a02e3949ff42afa772eb5e74dbef9f", "interface": "internal", "region_id": "prodstack6", "url": "https://cinder-internal.ps6.canonical.com:8776/v3/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}], "id": "5bf6578a631349e3af4bf36d7adb18e1", "type": "volumev3", "name": "cinderv3"}, {"endpoints": [{"id": "01d84128f36444e9b01549b86bd69116", "interface": "admin", "region_id": "prodstack6", "url": "https://barbican-admin.ps6.canonical.com:9312", "region": "prodstack6"}, {"id": "0ce4a8777e0b40a88f7fc0f77e34a605", "interface": "public", "region_id": "prodstack6", "url": "https://barbican.ps6.canonical.com:9311", "region": "prodstack6"}, {"id": "f507ba49e4a7435cb330234217c92449", "interface": "internal", "region_id": "prodstack6", "url": "https://barbican-internal.ps6.canonical.com:9311", "region": "prodstack6"}], "id": "62cb1c3d9f6c45979c13516a6b3ff114", "type": "key-manager", "name": "barbican"}, {"endpoints": [{"id": "3cb6121bd8f14da8aa2fba7be823a2b4", "interface": "internal", "region_id": "prodstack6", "url": "https://neutron-internal.ps6.canonical.com:9696", "region": "prodstack6"}, {"id": "46ba11d133fe4e8f9e8f9097ba737682", "interface": "admin", "region_id": "prodstack6", "url": "https://neutron-admin.ps6.canonical.com:9696", "region": "prodstack6"}, {"id": "d872eb6aa23d40009165aa3dcdce3948", "interface": "public", "region_id": "prodstack6", "url": "https://neutron.ps6.canonical.com:9696", "region": "prodstack6"}], "id": "759cb6fdfbc146dd8b9d1ba444c4b9db", "type": "network", "name": "neutron"}, {"endpoints": [{"id": "4349d565f72446da9699269f85df5e8b", "interface": "internal", "region_id": "prodstack6", "url": "https://manila-internal.ps6.canonical.com:8786/v2/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "a483dcc58f5e415e9ec739c94474e609", "interface": "public", "region_id": "prodstack6", "url": "https://manila.ps6.canonical.com:8786/v2/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "c1f14236723e42878562d8dd63d5a6a0", "interface": "admin", "region_id": "prodstack6", "url": "https://manila-admin.ps6.canonical.com:8786/v2/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}], "id": "93fc4008035946deb1f433c2dd905a5d", "type": "sharev2", "name": "manilav2"}, {"endpoints": [{"id": "0fa148793c7249c8b187b6b4ff425731", "interface": "internal", "region_id": "prodstack6", "url": "https://radosgw-internal.ps6.canonical.com:443/swift/v1/AUTH_e4b04ca58d734ed0aa29e306adad4f79/simplestreams/data", "region": "prodstack6"}, {"id": "555ade266a6b4bcc81b6e5abf607aec5", "interface": "public", "region_id": "prodstack6", "url": "https://radosgw.ps6.canonical.com:443/swift/v1/AUTH_e4b04ca58d734ed0aa29e306adad4f79/simplestreams/data", "region": "prodstack6"}, {"id": "7dad1a7b1552465686424fc014463173", "interface": "admin", "region_id": "prodstack6", "url": "https://radosgw-admin.ps6.canonical.com:443/swift/simplestreams/data", "region": "prodstack6"}], "id": "977dd359af1a4fcc91a9daf4dc33b0f3", "type": "product-streams", "name": "image-stream"}, {"endpoints": [{"id": "12d30eabcdec4831bd15273d55b1cbab", "interface": "internal", "region_id": "prodstack6", "url": "https://manila-internal.ps6.canonical.com:8786/v1/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "29d35b2b483346479f1ff1a13604d50e", "interface": "admin", "region_id": "prodstack6", "url": "https://manila-admin.ps6.canonical.com:8786/v1/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "4aa1422b8f5945d8aed9ba6a8d670e5c", "interface": "public", "region_id": "prodstack6", "url": "https://manila.ps6.canonical.com:8786/v1/623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}], "id": "ac5e4f28fa794cde99f1d7ffc1b664e5", "type": "share", "name": "manila"}, {"endpoints": [{"id": "c7db93d54a684d8caeae1d9e18a59118", "interface": "admin", "region_id": "prodstack6", "url": "https://nova-admin.ps6.canonical.com:8774/v2.1", "region": "prodstack6"}, {"id": "dd7a796f401b477f9f1b5bbc05747d8d", "interface": "public", "region_id": "prodstack6", "url": "https://nova.ps6.canonical.com:8774/v2.1", "region": "prodstack6"}, {"id": "e7ecb038d830462ea67b0b463af5e013", "interface": "internal", "region_id": "prodstack6", "url": "https://nova-internal.ps6.canonical.com:8774/v2.1", "region": "prodstack6"}], "id": "b4519af08e174d4a8333a2d14ac3ba3b", "type": "compute", "name": "nova"}, {"endpoints": [{"id": "02ef5b6154934ffd97d8b5b8e4d70d2a", "interface": "internal", "region_id": "prodstack6", "url": "https://radosgw-internal.ps6.canonical.com:443/swift/v1/AUTH_623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "2741abe526e94842a4fa801423ba1ef0", "interface": "public", "region_id": "prodstack6", "url": "https://radosgw.ps6.canonical.com:443/swift/v1/AUTH_623df63b80274c21bc79a0c35e68d615", "region": "prodstack6"}, {"id": "3742f9406c604516933d6fd8c29e0880", "interface": "admin", "region_id": "prodstack6", "url": "https://radosgw-admin.ps6.canonical.com:443/swift", "region": "prodstack6"}], "id": "c7f07a7b3b3c408c96200dfd1d1a0f6f", "type": "object-store", "name": "swift"}, {"endpoints": [{"id": "06d4ed6c160a43f2b7fa7f80ad1dc709", "interface": "internal", "region_id": "prodstack6", "url": "https://designate-internal.ps6.canonical.com:9001", "region": "prodstack6"}, {"id": "1e240624a50c4ca0aaa6ef63cbc94f1b", "interface": "admin", "region_id": "prodstack6", "url": "https://designate-admin.ps6.canonical.com:9001", "region": "prodstack6"}, {"id": "f94d7d17997a43fd9c63b34c43301c6e", "interface": "public", "region_id": "prodstack6", "url": "https://designate.ps6.canonical.com:9001", "region": "prodstack6"}], "id": "cf82013d63844fedbe96bcacb6bd1fef", "type": "dns", "name": "designate"}, {"endpoints": [{"id": "4a688340be464710bfa60bf3f88f41c4", "interface": "admin", "region_id": "prodstack6", "url": "https://gnocchi-admin.ps6.canonical.com:8041", "region": "prodstack6"}, {"id": "a5a95506c96d4716adb4efc3ac9051be", "interface": "public", "region_id": "prodstack6", "url": "https://gnocchi.ps6.canonical.com:8041", "region": "prodstack6"}, {"id": "eebc17a086834f8fa8bb6b35c8061a8c", "interface": "internal", "region_id": "prodstack6", "url": "https://gnocchi-internal.ps6.canonical.com:8041", "region": "prodstack6"}], "id": "d10589e854a446a5b852593f33f170a7", "type": "metric", "name": "gnocchi"}, {"endpoints": [{"id": "08f66df28d0f47f3bec12f29e06d85ac", "interface": "admin", "region_id": "prodstack6", "url": "https://keystone-admin.ps6.canonical.com:35357/v3", "region": "prodstack6"}, {"id": "46d270b45ceb42db902f4d241afa6a70", "interface": "public", "region_id": "prodstack6", "url": "https://keystone.ps6.canonical.com:5000/v3", "region": "prodstack6"}, {"id": "a4addee11d9349cfa46ec6660dbad947", "interface": "internal", "region_id": "prodstack6", "url": "https://keystone-internal.ps6.canonical.com:5000/v3", "region": "prodstack6"}], "id": "deb38a775a9b4e87a8de9e3eed779882", "type": "identity", "name": "keystone"}, {"endpoints": [{"id": "18b4af5f40664babb94e884c6a53ccf3", "interface": "admin", "region_id": "prodstack6", "url": "https://octavia-admin.ps6.canonical.com:9876", "region": "prodstack6"}, {"id": "2b6f7ba7f9944ee1aebd6dccc5223b2d", "interface": "internal", "region_id": "prodstack6", "url": "https://octavia-internal.ps6.canonical.com:9876", "region": "prodstack6"}, {"id": "5e3012e9c79e4890be4d964b6208f5c6", "interface": "public", "region_id": "prodstack6", "url": "https://octavia.ps6.canonical.com:9876", "region": "prodstack6"}], "id": "e00337be20d54948b66a1c3109b885c6", "type": "load-balancer", "name": "octavia"}, {"endpoints": [{"id": "2d2942b35f3041389ad810f679d02f22", "interface": "public", "region_id": "prodstack6", "url": "https://placement.ps6.canonical.com:8778", "region": "prodstack6"}, {"id": "2e3beaac7ac14284b72e2592820ad725", "interface": "admin", "region_id": "prodstack6", "url": "https://placement-admin.ps6.canonical.com:8778", "region": "prodstack6"}, {"id": "91060f6df9ae444f81808adf40540d94", "interface": "internal", "region_id": "prodstack6", "url": "https://placement-internal.ps6.canonical.com:8778", "region": "prodstack6"}], "id": "edc6e37f154f4c0ab3dd4d52b82bf873", "type": "placement", "name": "placement"}]}}
1643s REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1 -H "Accept: application/json" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443"
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1 -H "Accept: application/json" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443"
1643s DEBUG (connectionpool:962) Starting new HTTPS connection (1): nova.ps6.canonical.com:8774
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1 HTTP/1.1" 302 0
1643s RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Thu, 14 Nov 2024 19:28:06 GMT Keep-Alive: timeout=75, max=1000 Location: https://nova.ps6.canonical.com:8774/v2.1/ Server: Apache/2.4.52 (Ubuntu) x-compute-request-id: req-374ae1b5-ee7e-46be-94ed-0b1e875ef12c x-openstack-request-id: req-374ae1b5-ee7e-46be-94ed-0b1e875ef12c
1643s DEBUG (session:548) RESP: [302] Connection: Keep-Alive Content-Length: 0 Content-Type: text/plain; charset=utf8 Date: Thu, 14 Nov 2024 19:28:06 GMT Keep-Alive: timeout=75, max=1000 Location: https://nova.ps6.canonical.com:8774/v2.1/ Server: Apache/2.4.52 (Ubuntu) x-compute-request-id: req-374ae1b5-ee7e-46be-94ed-0b1e875ef12c x-openstack-request-id: req-374ae1b5-ee7e-46be-94ed-0b1e875ef12c
1643s RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged.
1643s DEBUG (session:580) RESP BODY: Omitted, Content-Type is set to text/plain; charset=utf8. Only application/json responses have their bodies logged.
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/ HTTP/1.1" 200 397
1643s RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:06 GMT Keep-Alive: timeout=75, max=999 OpenStack-API-Version: compute 2.1 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.1 x-compute-request-id: req-fee0e332-3bf7-4e2b-af7a-9bf99f2fce3b x-openstack-request-id: req-fee0e332-3bf7-4e2b-af7a-9bf99f2fce3b
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 397 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:06 GMT Keep-Alive: timeout=75, max=999 OpenStack-API-Version: compute 2.1 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.1 x-compute-request-id: req-fee0e332-3bf7-4e2b-af7a-9bf99f2fce3b x-openstack-request-id: req-fee0e332-3bf7-4e2b-af7a-9bf99f2fce3b
1643s RESP BODY: {"version": {"id": "v2.1", "status": "CURRENT", "version": "2.90", "min_version": "2.1", "updated": "2013-07-23T11:33:21Z", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/"}, {"rel": "describedby", "type": "text/html", "href": "http://docs.openstack.org/"}], "media-types": [{"base": "application/json", "type": "application/vnd.openstack.compute+json;version=2.1"}]}}
1643s DEBUG (session:580) RESP BODY: {"version": {"id": "v2.1", "status": "CURRENT", "version": "2.90", "min_version": "2.1", "updated": "2013-07-23T11:33:21Z", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/"}, {"rel": "describedby", "type": "text/html", "href": "http://docs.openstack.org/"}], "media-types": [{"base": "application/json", "type": "application/vnd.openstack.compute+json;version=2.1"}]}}
1643s GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-fee0e332-3bf7-4e2b-af7a-9bf99f2fce3b
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/ used request id req-fee0e332-3bf7-4e2b-af7a-9bf99f2fce3b
1643s DEBUG (extension:189) found extension EntryPoint.parse('v1password = swiftclient.authv1:PasswordLoader')
1643s DEBUG (extension:189) found extension EntryPoint.parse('noauth = cinderclient.contrib.noauth:CinderNoAuthLoader')
1643s DEBUG (extension:189) found extension EntryPoint.parse('admin_token = keystoneauth1.loading._plugins.admin_token:AdminToken')
1643s DEBUG (extension:189) found extension EntryPoint.parse('none = keystoneauth1.loading._plugins.noauth:NoAuth')
1643s DEBUG (extension:189) found extension EntryPoint.parse('password = keystoneauth1.loading._plugins.identity.generic:Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('token = keystoneauth1.loading._plugins.identity.generic:Token')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v2password = keystoneauth1.loading._plugins.identity.v2:Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v2token = keystoneauth1.loading._plugins.identity.v2:Token')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3adfspassword = keystoneauth1.extras._saml2._loading:ADFSPassword')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3applicationcredential = keystoneauth1.loading._plugins.identity.v3:ApplicationCredential')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3fedkerb = keystoneauth1.extras.kerberos._loading:MappedKerberos')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3kerberos = keystoneauth1.extras.kerberos._loading:Kerberos')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3multifactor = keystoneauth1.loading._plugins.identity.v3:MultiFactor')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oauth1 = keystoneauth1.extras.oauth1._loading:V3OAuth1')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcaccesstoken = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAccessToken')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcauthcode = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectAuthorizationCode')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcclientcredentials = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectClientCredentials')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3oidcpassword = keystoneauth1.loading._plugins.identity.v3:OpenIDConnectPassword')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3password = keystoneauth1.loading._plugins.identity.v3:Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3samlpassword = keystoneauth1.extras._saml2._loading:Saml2Password')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3token = keystoneauth1.loading._plugins.identity.v3:Token')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3tokenlessauth = keystoneauth1.loading._plugins.identity.v3:TokenlessAuth')
1643s DEBUG (extension:189) found extension EntryPoint.parse('v3totp = keystoneauth1.loading._plugins.identity.v3:TOTP')
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://glance.ps6.canonical.com:9292/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:962) Starting new HTTPS connection (1): glance.ps6.canonical.com:9292
1643s DEBUG (connectionpool:429) https://glance.ps6.canonical.com:9292 "GET /v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f HTTP/1.1" 200 2292
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 2292 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:06 GMT Keep-Alive: timeout=75, max=1000 Server: Apache/2.4.52 (Ubuntu) X-Openstack-Request-Id: req-36f489a6-2157-44a2-9244-54d4f19ea470
1643s DEBUG (session:580) RESP BODY: {"architecture": "ppc64le", "base_image_ref": "302dbebd-8fb5-46eb-aa5c-84ec11ab5c95", "boot_roles": "member,load-balancer_member,reader", "content_id": "auto.sync", "hw_cdrom_bus": "scsi", "hw_disk_bus": "virtio", "hw_machine_type": "pseries", "hw_video_model": "vga", "hw_vif_model": "virtio", "image_location": "snapshot", "image_state": "available", "image_type": "snapshot", "instance_uuid": "7e7a00e2-6c3a-40a2-8c07-f4d0c8706cf5", "item_name": "disk1.img", "os_distro": "ubuntu", "os_version": "24.10", "owner_id": "623df63b80274c21bc79a0c35e68d615", "owner_project_name": "prod-proposed-migration-ppc64el_project", "owner_user_name": "prod-proposed-migration-ppc64el", "product_name": "com.ubuntu.cloud.daily:server:24.10:ppc64el", "simplestreams_metadata": "{\"aliases\": \"24.10,o,oracular,devel\", \"arch\": \"ppc64el\", \"ftype\": \"disk1.img\", \"label\": \"daily\", \"md5\": \"fd88d9a689ac4d7ab4bea632de90d355\", \"os\": \"ubuntu\", \"pubname\": \"ubuntu-oracular-daily-ppc64el-server-20241009\", \"release\": \"oracular\", \"release_codenam", "source_content_id": "com.ubuntu.cloud:daily:download", "user_id": "c871debdeffd4cb8b69ce618fc4aa361", "version_name": "20241009", "name": "adt/ubuntu-plucky-ppc64el-server-20241113.img", "disk_format": "qcow2", "container_format": "bare", "visibility": "private", "size": 2751922176, "virtual_size": 21474836480, "status": "active", "checksum": "bcac3e03f6534f9b5e31609d24f6bd76", "protected": false, "min_ram": 0, "min_disk": 20, "owner": "623df63b80274c21bc79a0c35e68d615", "os_hidden": false, "os_hash_algo": "sha512", "os_hash_value": "76d837bfc30f1a0e4248983886948fe32ab2b5f05c4e0da0415911ea492f5a1ed3b2d0148f37fb0c16f1695e70f2423024b8d7edfb4e3e23e1edb91c8fd65daf", "id": "0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "created_at": "2024-11-13T04:34:00Z", "updated_at": "2024-11-13T04:35:23Z", "locations": [{"url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/0c5715b6-5cca-4485-b8bf-b85dfd917a5f/snap", "metadata": {"store": "ceph"}}], "direct_url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/0c5715b6-5cca-4485-b8bf-b85dfd917a5f/snap", "tags": [], "self": "/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "file": "/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f/file", "schema": "/v2/schemas/image", "stores": "ceph"}
1643s DEBUG (session:936) GET call to image for https://glance.ps6.canonical.com:9292/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f used request id req-36f489a6-2157-44a2-9244-54d4f19ea470
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big-ppc64el -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/autopkgtest-big-ppc64el HTTP/1.1" 404 96
1643s DEBUG (session:548) RESP: [404] Connection: Keep-Alive Content-Length: 96 Content-Type: application/json; charset=UTF-8 Date: Thu, 14 Nov 2024 19:28:06 GMT Keep-Alive: timeout=75, max=998 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-f5832b41-f865-45db-8648-51d31f4535ae x-openstack-request-id: req-f5832b41-f865-45db-8648-51d31f4535ae
1643s DEBUG (session:580) RESP BODY: {"itemNotFound": {"code": 404, "message": "Flavor autopkgtest-big-ppc64el could not be found."}}
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/autopkgtest-big-ppc64el used request id req-f5832b41-f865-45db-8648-51d31f4535ae
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors?is_public=None HTTP/1.1" 200 40172
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 40172 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:07 GMT Keep-Alive: timeout=75, max=997 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-0234b877-6531-4937-92ed-c4759982d0a5 x-openstack-request-id: req-0234b877-6531-4937-92ed-c4759982d0a5
1643s DEBUG (session:580) RESP BODY: {"flavors": [{"id": "05338e57-e2ba-4813-9a8a-2f2af73f8ab2", "name": "builder-ppc64el-cpu2-ram4-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/05338e57-e2ba-4813-9a8a-2f2af73f8ab2"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/05338e57-e2ba-4813-9a8a-2f2af73f8ab2"}], "description": null}, {"id": "08090b4b-98a9-4c15-8ad4-cc6711700879", "name": "builder-ppc64el-cpu8-ram64-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/08090b4b-98a9-4c15-8ad4-cc6711700879"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/08090b4b-98a9-4c15-8ad4-cc6711700879"}], "description": null}, {"id": "0825b8b1-2b9c-42bf-b3e6-e827c22d8df5", "name": "builder-ppc64el-cpu8-ram4-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/0825b8b1-2b9c-42bf-b3e6-e827c22d8df5"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/0825b8b1-2b9c-42bf-b3e6-e827c22d8df5"}], "description": null}, {"id": "0b06db45-151e-44b2-b0f5-f069ad7fa1cb", "name": "builder-ppc64el-cpu2-ram12-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/0b06db45-151e-44b2-b0f5-f069ad7fa1cb"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/0b06db45-151e-44b2-b0f5-f069ad7fa1cb"}], "description": null}, {"id": "0dbf127e-3101-4f05-9d37-15ad6d2a45c1", "name": "builder-ppc64el-cpu2-ram16-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/0dbf127e-3101-4f05-9d37-15ad6d2a45c1"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/0dbf127e-3101-4f05-9d37-15ad6d2a45c1"}], "description": null}, {"id": "102d0b57-e8d2-46c6-9be4-f452119a0280", "name": "autopkgtest-ppc64el", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/102d0b57-e8d2-46c6-9be4-f452119a0280"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/102d0b57-e8d2-46c6-9be4-f452119a0280"}], "description": null}, {"id": "1219f5f0-83f3-4d33-a3bb-1a85c6303159", "name": "builder-ppc64el-cpu128-ram64-disk50", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/1219f5f0-83f3-4d33-a3bb-1a85c6303159"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/1219f5f0-83f3-4d33-a3bb-1a85c6303159"}], "description": null}, {"id": "1359c5a4-ee60-4855-9bcc-defd3bff7121", "name": "builder-ppc64el-cpu8-ram8-disk50", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/1359c5a4-ee60-4855-9bcc-defd3bff7121"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/1359c5a4-ee60-4855-9bcc-defd3bff7121"}], "description": null}, {"id": "161f21bc-11f7-4ec9-a322-04fc3e0d2a68", "name": "builder-ppc64el-cpu2-ram55-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/161f21bc-11f7-4ec9-a322-04fc3e0d2a68"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/161f21bc-11f7-4ec9-a322-04fc3e0d2a68"}], "description": null}, {"id": "166070cd-7110-473e-a6a2-5e25aa9eeefd", "name": "builder-ppc64el-cpu4-ram64-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/166070cd-7110-473e-a6a2-5e25aa9eeefd"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/166070cd-7110-473e-a6a2-5e25aa9eeefd"}], "description": null}, {"id": "16a0a259-4627-4fbd-bb9d-a3e69346467c", "name": "builder-ppc64el-cpu8-ram64-disk50", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/16a0a259-4627-4fbd-bb9d-a3e69346467c"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/16a0a259-4627-4fbd-bb9d-a3e69346467c"}], "description": null}, {"id": "1c59e50a-1a67-4691-8f2c-6954cb0f83ba", "name": "builder-ppc64el-cpu4-ram128-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/1c59e50a-1a67-4691-8f2c-6954cb0f83ba"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/1c59e50a-1a67-4691-8f2c-6954cb0f83ba"}], "description": null}, {"id": "1c94efa8-905a-4bff-8485-0aaf9ac47fe7", "name": "builder-ppc64el-cpu4-ram16-disk50", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/1c94efa8-905a-4bff-8485-0aaf9ac47fe7"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/1c94efa8-905a-4bff-8485-0aaf9ac47fe7"}], "description": null}, {"id": "213c954d-26ed-4c86-9592-66384bc22c82", "name": "builder-ppc64el-cpu4-ram16-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/213c954d-26ed-4c86-9592-66384bc22c82"}, {"rel": "bookmark", "href": 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"https://nova.ps6.canonical.com:8774/flavors/e4437d6f-4673-4fcb-89e8-1ce861789538"}], "description": null}, {"id": "e628d527-f077-426d-9380-5eea778aabc2", "name": "builder-ppc64el-cpu8-ram16-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/e628d527-f077-426d-9380-5eea778aabc2"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/e628d527-f077-426d-9380-5eea778aabc2"}], "description": null}, {"id": "e752e039-cbe4-4a16-8197-de87ba42b83e", "name": "builder-ppc64el-cpu64-ram256-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/e752e039-cbe4-4a16-8197-de87ba42b83e"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/e752e039-cbe4-4a16-8197-de87ba42b83e"}], "description": null}, {"id": "e7f811c8-a60c-45c6-86c8-8e4b025751df", "name": "builder-ppc64el-cpu4-ram16-disk40", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/e7f811c8-a60c-45c6-86c8-8e4b025751df"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/e7f811c8-a60c-45c6-86c8-8e4b025751df"}], "description": null}, {"id": "eb80d7e2-b6e1-42a5-b80d-3dad861f6989", "name": "builder-ppc64el-cpu16-ram4-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/eb80d7e2-b6e1-42a5-b80d-3dad861f6989"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/eb80d7e2-b6e1-42a5-b80d-3dad861f6989"}], "description": null}, {"id": "ed127e2b-02b8-4e61-bf10-0c89b90928e6", "name": "builder-ppc64el-cpu64-ram128-disk50", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/ed127e2b-02b8-4e61-bf10-0c89b90928e6"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/ed127e2b-02b8-4e61-bf10-0c89b90928e6"}], "description": null}, {"id": "ef7301a7-71f4-48ac-b387-23251f4060e1", "name": "builder-ppc64el-cpu16-ram8-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/ef7301a7-71f4-48ac-b387-23251f4060e1"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/ef7301a7-71f4-48ac-b387-23251f4060e1"}], "description": null}, {"id": "f0f1af4d-f230-40c1-b789-c94e02a68daa", "name": "builder-ppc64el-cpu16-ram8-disk20", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/f0f1af4d-f230-40c1-b789-c94e02a68daa"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/f0f1af4d-f230-40c1-b789-c94e02a68daa"}], "description": null}, {"id": "f40b2dbc-5d69-40b0-a9fc-71c32de93ca3", "name": "autopkgtest-big-ppc64el", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3"}], "description": null}, {"id": "f6aae414-e26b-4692-95d4-d851b6993c2a", "name": "builder-ppc64el-cpu2-ram8-disk50", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/f6aae414-e26b-4692-95d4-d851b6993c2a"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/f6aae414-e26b-4692-95d4-d851b6993c2a"}], "description": null}, {"id": "f91b245b-ad92-47f6-8861-d1e070fcc19c", "name": "builder-ppc64el-cpu2-ram64-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/f91b245b-ad92-47f6-8861-d1e070fcc19c"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/f91b245b-ad92-47f6-8861-d1e070fcc19c"}], "description": null}, {"id": "fa3bbba4-5e72-4ca3-9661-ccf45947bbf5", "name": "builder-ppc64el-cpu16-ram4-disk100", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/fa3bbba4-5e72-4ca3-9661-ccf45947bbf5"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/fa3bbba4-5e72-4ca3-9661-ccf45947bbf5"}], "description": null}, {"id": "ff4cf1ee-6e00-49b7-9d11-fafa69b910df", "name": "builder-ppc64el-cpu8-ram32-disk40", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/ff4cf1ee-6e00-49b7-9d11-fafa69b910df"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/ff4cf1ee-6e00-49b7-9d11-fafa69b910df"}], "description": null}]}
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors?is_public=None used request id req-0234b877-6531-4937-92ed-c4759982d0a5
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3 -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3 HTTP/1.1" 200 628
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 628 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:07 GMT Keep-Alive: timeout=75, max=996 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-7ef52589-77c2-4b01-be6b-5a7df02a903f x-openstack-request-id: req-7ef52589-77c2-4b01-be6b-5a7df02a903f
1643s DEBUG (session:580) RESP BODY: {"flavor": {"id": "f40b2dbc-5d69-40b0-a9fc-71c32de93ca3", "name": "autopkgtest-big-ppc64el", "ram": 8192, "disk": 100, "swap": 0, "OS-FLV-EXT-DATA:ephemeral": 0, "OS-FLV-DISABLED:disabled": false, "vcpus": 4, "os-flavor-access:is_public": false, "rxtx_factor": 1.0, "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3"}], "description": null, "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-ppc64el", "hw_rng:allowed": "True"}}}
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/flavors/f40b2dbc-5d69-40b0-a9fc-71c32de93ca3 used request id req-7ef52589-77c2-4b01-be6b-5a7df02a903f
1643s DEBUG (session:517) REQ: curl -g -i -X POST https://nova.ps6.canonical.com:8774/v2.1/servers -H "Accept: application/json" -H "Content-Type: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87" -d '{"server": {"name": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c", "imageRef": "0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "flavorRef": "f40b2dbc-5d69-40b0-a9fc-71c32de93ca3", "user_data": "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", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-15", "min_count": 1, "max_count": 1, "security_groups": [{"name": "autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-4.secgroup"}], "networks": [{"uuid": "3083d638-5564-4f5c-97ef-09f045123d20"}]}}'
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "POST /v2.1/servers HTTP/1.1" 202 478
1643s DEBUG (session:548) RESP: [202] Connection: Keep-Alive Content-Length: 478 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:07 GMT Keep-Alive: timeout=75, max=995 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 location: https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f x-compute-request-id: req-714c79b1-e40e-4811-82de-7d54e41930cd x-openstack-request-id: req-714c79b1-e40e-4811-82de-7d54e41930cd
1643s DEBUG (session:580) RESP BODY: {"server": {"id": "003a8574-e3cb-49d0-abed-3b188ad0f88f", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}], "OS-DCF:diskConfig": "MANUAL", "security_groups": [{"name": "autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-4.secgroup"}], "adminPass": "99Q2Ua4wgqQY"}}
1643s DEBUG (session:936) POST call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers used request id req-714c79b1-e40e-4811-82de-7d54e41930cd
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f HTTP/1.1" 200 3206
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 3206 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:07 GMT Keep-Alive: timeout=75, max=994 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-c20777ef-5d6b-45b3-be7a-d3610c8ffd1a x-openstack-request-id: req-c20777ef-5d6b-45b3-be7a-d3610c8ffd1a
1643s DEBUG (session:580) RESP BODY: {"server": {"id": "003a8574-e3cb-49d0-abed-3b188ad0f88f", "name": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c", "status": "BUILD", "tenant_id": "623df63b80274c21bc79a0c35e68d615", "user_id": "c871debdeffd4cb8b69ce618fc4aa361", "metadata": {}, "hostId": "", "image": {"id": "0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "links": [{"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f"}]}, "flavor": {"vcpus": 4, "ram": 8192, "disk": 100, "ephemeral": 0, "swap": 0, "original_name": "autopkgtest-big-ppc64el", "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-ppc64el", "hw_rng:allowed": "True"}}, "created": "2024-11-14T19:28:08Z", "updated": "2024-11-14T19:28:07Z", "addresses": {}, "accessIPv4": "", "accessIPv6": "", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}], "OS-DCF:diskConfig": "MANUAL", "progress": 0, "OS-EXT-AZ:availability_zone": "", "config_drive": "", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-15", "OS-SRV-USG:launched_at": null, "OS-SRV-USG:terminated_at": null, "OS-EXT-SRV-ATTR:host": null, "OS-EXT-SRV-ATTR:instance_name": "", "OS-EXT-SRV-ATTR:hypervisor_hostname": null, "OS-EXT-SRV-ATTR:reservation_id": "r-q287j6n0", "OS-EXT-SRV-ATTR:launch_index": 0, "OS-EXT-SRV-ATTR:hostname": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod", "OS-EXT-SRV-ATTR:kernel_id": "", "OS-EXT-SRV-ATTR:ramdisk_id": "", "OS-EXT-SRV-ATTR:root_device_name": null, "OS-EXT-SRV-ATTR:user_data": "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", "OS-EXT-STS:task_state": "scheduling", "OS-EXT-STS:vm_state": "building", "OS-EXT-STS:power_state": 0, "os-extended-volumes:volumes_attached": [], "locked": false, "locked_reason": null, "description": null, "tags": [], "trusted_image_certificates": null, "server_groups": []}}
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f used request id req-c20777ef-5d6b-45b3-be7a-d3610c8ffd1a
1643s DEBUG (session:517) REQ: curl -g -i -X GET https://glance.ps6.canonical.com:9292/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://glance.ps6.canonical.com:9292 "GET /v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f HTTP/1.1" 200 2292
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 2292 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:08 GMT Keep-Alive: timeout=75, max=999 Server: Apache/2.4.52 (Ubuntu) X-Openstack-Request-Id: req-d68d3992-029c-483d-b798-0e245bb209de
1643s DEBUG (session:580) RESP BODY: {"architecture": "ppc64le", "base_image_ref": "302dbebd-8fb5-46eb-aa5c-84ec11ab5c95", "boot_roles": "member,load-balancer_member,reader", "content_id": "auto.sync", "hw_cdrom_bus": "scsi", "hw_disk_bus": "virtio", "hw_machine_type": "pseries", "hw_video_model": "vga", "hw_vif_model": "virtio", "image_location": "snapshot", "image_state": "available", "image_type": "snapshot", "instance_uuid": "7e7a00e2-6c3a-40a2-8c07-f4d0c8706cf5", "item_name": "disk1.img", "os_distro": "ubuntu", "os_version": "24.10", "owner_id": "623df63b80274c21bc79a0c35e68d615", "owner_project_name": "prod-proposed-migration-ppc64el_project", "owner_user_name": "prod-proposed-migration-ppc64el", "product_name": "com.ubuntu.cloud.daily:server:24.10:ppc64el", "simplestreams_metadata": "{\"aliases\": \"24.10,o,oracular,devel\", \"arch\": \"ppc64el\", \"ftype\": \"disk1.img\", \"label\": \"daily\", \"md5\": \"fd88d9a689ac4d7ab4bea632de90d355\", \"os\": \"ubuntu\", \"pubname\": \"ubuntu-oracular-daily-ppc64el-server-20241009\", \"release\": \"oracular\", \"release_codenam", "source_content_id": "com.ubuntu.cloud:daily:download", "user_id": "c871debdeffd4cb8b69ce618fc4aa361", "version_name": "20241009", "name": "adt/ubuntu-plucky-ppc64el-server-20241113.img", "disk_format": "qcow2", "container_format": "bare", "visibility": "private", "size": 2751922176, "virtual_size": 21474836480, "status": "active", "checksum": "bcac3e03f6534f9b5e31609d24f6bd76", "protected": false, "min_ram": 0, "min_disk": 20, "owner": "623df63b80274c21bc79a0c35e68d615", "os_hidden": false, "os_hash_algo": "sha512", "os_hash_value": "76d837bfc30f1a0e4248983886948fe32ab2b5f05c4e0da0415911ea492f5a1ed3b2d0148f37fb0c16f1695e70f2423024b8d7edfb4e3e23e1edb91c8fd65daf", "id": "0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "created_at": "2024-11-13T04:34:00Z", "updated_at": "2024-11-13T04:35:23Z", "locations": [{"url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/0c5715b6-5cca-4485-b8bf-b85dfd917a5f/snap", "metadata": {"store": "ceph"}}], "direct_url": "rbd://eea9d068-c18c-11ed-8dc0-013aacb71b80/glance/0c5715b6-5cca-4485-b8bf-b85dfd917a5f/snap", "tags": [], "self": "/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "file": "/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f/file", "schema": "/v2/schemas/image", "stores": "ceph"}
1643s DEBUG (session:936) GET call to image for https://glance.ps6.canonical.com:9292/v2/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f used request id req-d68d3992-029c-483d-b798-0e245bb209de
1643s +--------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
1643s | Property                             | Value                                                                                                                                 |
1643s +--------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------+
1643s | OS-DCF:diskConfig                    | MANUAL                                                                                                                                |
1643s | OS-EXT-AZ:availability_zone          |                                                                                                                                       |
1643s | OS-EXT-SRV-ATTR:host                 | -                                                                                                                                     |
1643s | OS-EXT-SRV-ATTR:hostname             | adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod                                                                        |
1643s | OS-EXT-SRV-ATTR:hypervisor_hostname  | -                                                                                                                                     |
1643s | OS-EXT-SRV-ATTR:instance_name        |                                                                                                                                       |
1643s | OS-EXT-SRV-ATTR:kernel_id            |                                                                                                                                       |
1643s | OS-EXT-SRV-ATTR:launch_index         | 0                                                                                                                                     |
1643s | OS-EXT-SRV-ATTR:ramdisk_id           |                                                                                                                                       |
1643s | OS-EXT-SRV-ATTR:reservation_id       | r-q287j6n0                                                                                                                            |
1643s | OS-EXT-SRV-ATTR:root_device_name     | -                                                                                                                                     |
1643s | OS-EXT-STS:power_state               | 0                                                                                                                                     |
1643s | OS-EXT-STS:task_state                | scheduling                                                                                                                            |
1643s | OS-EXT-STS:vm_state                  | building                                                                                                                              |
1643s | OS-SRV-USG:launched_at               | -                                                                                                                                     |
1643s | OS-SRV-USG:terminated_at             | -                                                                                                                                     |
1643s | accessIPv4                           |                                                                                                                                       |
1643s | accessIPv6                           |                                                                                                                                       |
1643s | adminPass                            | 99Q2Ua4wgqQY                                                                                                                          |
1643s | config_drive                         |                                                                                                                                       |
1643s | created                              | 2024-11-14T19:28:08Z                                                                                                                  |
1643s | description                          | -                                                                                                                                     |
1643s | flavor:disk                          | 100                                                                                                                                   |
1643s | flavor:ephemeral                     | 0                                                                                                                                     |
1643s | flavor:extra_specs                   | {"aggregate_instance_extra_specs:commit": "builder-ppc64el", "hw_rng:allowed": "True"}                                                |
1643s | flavor:original_name                 | autopkgtest-big-ppc64el                                                                                                               |
1643s | flavor:ram                           | 8192                                                                                                                                  |
1643s | flavor:swap                          | 0                                                                                                                                     |
1643s | flavor:vcpus                         | 4                                                                                                                                     |
1643s | hostId                               |                                                                                                                                       |
1643s | id                                   | 003a8574-e3cb-49d0-abed-3b188ad0f88f                                                                                                  |
1643s | image                                | adt/ubuntu-plucky-ppc64el-server-20241113.img (0c5715b6-5cca-4485-b8bf-b85dfd917a5f)                                                  |
1643s | key_name                             | testbed-juju-7f2275-prod-proposed-migration-environment-15                                                                            |
1643s | locked                               | False                                                                                                                                 |
1643s | locked_reason                        | -                                                                                                                                     |
1643s | metadata                             | {}                                                                                                                                    |
1643s | name                                 | adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c |
1643s | os-extended-volumes:volumes_attached | []                                                                                                                                    |
1643s | progress                             | 0                                                                                                                                     |
1643s | security_groups                      | autopkgtest-juju-7f2275-prod-proposed-migration-environment-15@bos03-ppc64el-4.secgroup                                               |
1643s | server_groups                        | []                                                                                                                                    |
1643s | status                               | BUILD                                                                                                                                 |
1643s | tags                                 | []                                                                                                                                    |
1643s | tenant_id                            | 623df63b80274c21bc79a0c35e68d615                                                                                                      |
1643s | trusted_image_certificates           | -                                                                                                                                     |
1643s | updated                              | 2024-11-14T19:28:07Z                                                                                                                  |
1643s | user_id                              | c871debdeffd4cb8b69ce618fc4aa361                                                                                                      |
1643s +--------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------+DEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f HTTP/1.1" 200 3206
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 3206 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:08 GMT Keep-Alive: timeout=75, max=993 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-a5dd3d00-73cf-4923-85e5-a75cb547e671 x-openstack-request-id: req-a5dd3d00-73cf-4923-85e5-a75cb547e671
1643s DEBUG (session:580) RESP BODY: {"server": {"id": "003a8574-e3cb-49d0-abed-3b188ad0f88f", "name": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c", "status": "BUILD", "tenant_id": "623df63b80274c21bc79a0c35e68d615", "user_id": "c871debdeffd4cb8b69ce618fc4aa361", "metadata": {}, "hostId": "", "image": {"id": "0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "links": [{"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f"}]}, "flavor": {"vcpus": 4, "ram": 8192, "disk": 100, "ephemeral": 0, "swap": 0, "original_name": "autopkgtest-big-ppc64el", "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-ppc64el", "hw_rng:allowed": "True"}}, "created": "2024-11-14T19:28:08Z", "updated": "2024-11-14T19:28:08Z", "addresses": {}, "accessIPv4": "", "accessIPv6": "", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}], "OS-DCF:diskConfig": "MANUAL", "progress": 0, "OS-EXT-AZ:availability_zone": "", "config_drive": "", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-15", "OS-SRV-USG:launched_at": null, "OS-SRV-USG:terminated_at": null, "OS-EXT-SRV-ATTR:host": null, "OS-EXT-SRV-ATTR:instance_name": "", "OS-EXT-SRV-ATTR:hypervisor_hostname": null, "OS-EXT-SRV-ATTR:reservation_id": "r-q287j6n0", "OS-EXT-SRV-ATTR:launch_index": 0, "OS-EXT-SRV-ATTR:hostname": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod", "OS-EXT-SRV-ATTR:kernel_id": "", "OS-EXT-SRV-ATTR:ramdisk_id": "", "OS-EXT-SRV-ATTR:root_device_name": null, "OS-EXT-SRV-ATTR:user_data": "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", "OS-EXT-STS:task_state": "scheduling", "OS-EXT-STS:vm_state": "building", "OS-EXT-STS:power_state": 0, "os-extended-volumes:volumes_attached": [], "locked": false, "locked_reason": null, "description": null, "tags": [], "trusted_image_certificates": null, "server_groups": []}}
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f used request id req-a5dd3d00-73cf-4923-85e5-a75cb547e671
1643s 
1643s 
1643s 
Server building... 0% completeDEBUG (session:517) REQ: curl -g -i -X GET https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f -H "Accept: application/json" -H "OpenStack-API-Version: compute 2.87" -H "User-Agent: python-novaclient" -H "X-Auth-Token: {SHA256}1ade97737e8758744486b02664b45f960cc442bdab8c2997d42bbc5e22227443" -H "X-OpenStack-Nova-API-Version: 2.87"
1643s DEBUG (connectionpool:429) https://nova.ps6.canonical.com:8774 "GET /v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f HTTP/1.1" 200 3333
1643s DEBUG (session:548) RESP: [200] Connection: Keep-Alive Content-Length: 3333 Content-Type: application/json Date: Thu, 14 Nov 2024 19:28:13 GMT Keep-Alive: timeout=75, max=992 OpenStack-API-Version: compute 2.87 Server: Apache/2.4.52 (Ubuntu) Vary: OpenStack-API-Version,X-OpenStack-Nova-API-Version X-OpenStack-Nova-API-Version: 2.87 x-compute-request-id: req-9a1a26e2-e816-491d-ae60-ba921dc6bdf2 x-openstack-request-id: req-9a1a26e2-e816-491d-ae60-ba921dc6bdf2
1643s DEBUG (session:580) RESP BODY: {"server": {"id": "003a8574-e3cb-49d0-abed-3b188ad0f88f", "name": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c", "status": "ERROR", "tenant_id": "623df63b80274c21bc79a0c35e68d615", "user_id": "c871debdeffd4cb8b69ce618fc4aa361", "metadata": {}, "hostId": "", "image": {"id": "0c5715b6-5cca-4485-b8bf-b85dfd917a5f", "links": [{"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/images/0c5715b6-5cca-4485-b8bf-b85dfd917a5f"}]}, "flavor": {"vcpus": 4, "ram": 8192, "disk": 100, "ephemeral": 0, "swap": 0, "original_name": "autopkgtest-big-ppc64el", "extra_specs": {"aggregate_instance_extra_specs:commit": "builder-ppc64el", "hw_rng:allowed": "True"}}, "created": "2024-11-14T19:28:07Z", "updated": "2024-11-14T19:28:09Z", "addresses": {}, "accessIPv4": "", "accessIPv6": "", "links": [{"rel": "self", "href": "https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}, {"rel": "bookmark", "href": "https://nova.ps6.canonical.com:8774/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f"}], "OS-DCF:diskConfig": "MANUAL", "fault": {"code": 500, "created": "2024-11-14T19:28:09Z", "message": "No valid host was found. There are not enough hosts available."}, "OS-EXT-AZ:availability_zone": "", "config_drive": "", "key_name": "testbed-juju-7f2275-prod-proposed-migration-environment-15", "OS-SRV-USG:launched_at": null, "OS-SRV-USG:terminated_at": null, "OS-EXT-SRV-ATTR:host": null, "OS-EXT-SRV-ATTR:instance_name": "instance-0005a0f9", "OS-EXT-SRV-ATTR:hypervisor_hostname": null, "OS-EXT-SRV-ATTR:reservation_id": "r-q287j6n0", "OS-EXT-SRV-ATTR:launch_index": 0, "OS-EXT-SRV-ATTR:hostname": "adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod", "OS-EXT-SRV-ATTR:kernel_id": "", "OS-EXT-SRV-ATTR:ramdisk_id": "", "OS-EXT-SRV-ATTR:root_device_name": null, "OS-EXT-SRV-ATTR:user_data": "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", "OS-EXT-STS:task_state": null, "OS-EXT-STS:vm_state": "error", "OS-EXT-STS:power_state": 0, "os-extended-volumes:volumes_attached": [], "locked": false, "locked_reason": null, "description": null, "tags": [], "trusted_image_certificates": null, "server_groups": []}}
1643s DEBUG (session:936) GET call to compute for https://nova.ps6.canonical.com:8774/v2.1/servers/003a8574-e3cb-49d0-abed-3b188ad0f88f used request id req-9a1a26e2-e816-491d-ae60-ba921dc6bdf2
1643s DEBUG (shell:822) <Server: adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c>
1643s Traceback (most recent call last):
1643s   File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 820, in main
1643s     OpenStackComputeShell().main(argv)
1643s   File "/usr/lib/python3/dist-packages/novaclient/shell.py", line 742, in main
1643s     args.func(self.cs, args)
1643s   File "/usr/lib/python3/dist-packages/novaclient/v2/shell.py", line 980, in do_boot
1643s     _poll_for_status(cs.servers.get, server.id, 'building', ['active'])
1643s   File "/usr/lib/python3/dist-packages/novaclient/v2/shell.py", line 1019, in _poll_for_status
1643s     raise exceptions.ResourceInErrorState(obj)
1643s novaclient.exceptions.ResourceInErrorState: <Server: adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c>
1643s ERROR (ResourceInErrorState): <Server: adt-plucky-ppc64el-mdanalysis-20241114-190646-juju-7f2275-prod-proposed-migration-environment-15-43e3e30e-26ce-45f5-9e50-70cbd1e15e5c>
1643s 
1643s Error building server
1645s autopkgtest [19:34:11]: testbed dpkg architecture: ppc64el
1646s autopkgtest [19:34:12]: testbed apt version: 2.9.8
1646s autopkgtest [19:34:12]: @@@@@@@@@@@@@@@@@@@@ test bed setup
1647s Get:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease [73.9 kB]
1647s Get:2 http://ftpmaster.internal/ubuntu plucky-proposed/restricted Sources [7016 B]
1647s Get:3 http://ftpmaster.internal/ubuntu plucky-proposed/universe Sources [937 kB]
1647s Get:4 http://ftpmaster.internal/ubuntu plucky-proposed/main Sources [104 kB]
1647s Get:5 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse Sources [15.3 kB]
1647s Get:6 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el Packages [114 kB]
1647s Get:7 http://ftpmaster.internal/ubuntu plucky-proposed/universe ppc64el Packages [697 kB]
1647s Get:8 http://ftpmaster.internal/ubuntu plucky-proposed/multiverse ppc64el Packages [8632 B]
1648s Fetched 1957 kB in 1s (1709 kB/s)
1648s Reading package lists...
1651s Reading package lists...
1651s Building dependency tree...
1651s Reading state information...
1652s Calculating upgrade...
1652s The following packages will be upgraded:
1652s   bpfcc-tools bpftrace libbpfcc libcap-ng0 libgnutls30t64 libjson-glib-1.0-0
1652s   libjson-glib-1.0-common libnewt0.52 libutempter0 pastebinit python3-bpfcc
1652s   python3-newt python3-systemd whiptail
1652s 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1652s Need to get 4678 kB of archives.
1652s After this operation, 423 kB of additional disk space will be used.
1652s Get:1 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcap-ng0 ppc64el 0.8.5-3build1 [16.3 kB]
1652s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgnutls30t64 ppc64el 3.8.8-2ubuntu1 [1072 kB]
1653s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-newt ppc64el 0.52.24-2ubuntu4 [21.8 kB]
1653s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el libnewt0.52 ppc64el 0.52.24-2ubuntu4 [62.1 kB]
1653s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el whiptail ppc64el 0.52.24-2ubuntu4 [19.5 kB]
1653s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el libbpfcc ppc64el 0.30.0+ds-1ubuntu5 [696 kB]
1653s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-bpfcc all 0.30.0+ds-1ubuntu5 [40.4 kB]
1653s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpfcc-tools all 0.30.0+ds-1ubuntu5 [697 kB]
1653s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el bpftrace ppc64el 0.21.2-2ubuntu2 [1898 kB]
1653s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-common all 1.10.0+ds-3 [5586 B]
1653s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-glib-1.0-0 ppc64el 1.10.0+ds-3 [76.0 kB]
1653s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libutempter0 ppc64el 1.2.1-4 [9850 B]
1653s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el pastebinit all 1.7.1-1 [14.9 kB]
1653s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-systemd ppc64el 235-1build5 [48.7 kB]
1653s Fetched 4678 kB in 1s (5731 kB/s)
1654s (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 ... 73767 files and directories currently installed.)
1654s Preparing to unpack .../libcap-ng0_0.8.5-3build1_ppc64el.deb ...
1654s Unpacking libcap-ng0:ppc64el (0.8.5-3build1) over (0.8.5-1) ...
1654s Setting up libcap-ng0:ppc64el (0.8.5-3build1) ...
1654s (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 ... 73767 files and directories currently installed.)
1654s Preparing to unpack .../libgnutls30t64_3.8.8-2ubuntu1_ppc64el.deb ...
1654s Unpacking libgnutls30t64:ppc64el (3.8.8-2ubuntu1) over (3.8.6-2ubuntu1) ...
1654s Setting up libgnutls30t64:ppc64el (3.8.8-2ubuntu1) ...
1654s (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 ... 73767 files and directories currently installed.)
1654s Preparing to unpack .../00-python3-newt_0.52.24-2ubuntu4_ppc64el.deb ...
1654s Unpacking python3-newt:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
1655s Preparing to unpack .../01-libnewt0.52_0.52.24-2ubuntu4_ppc64el.deb ...
1655s Unpacking libnewt0.52:ppc64el (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
1655s Preparing to unpack .../02-whiptail_0.52.24-2ubuntu4_ppc64el.deb ...
1655s Unpacking whiptail (0.52.24-2ubuntu4) over (0.52.24-2ubuntu3) ...
1655s Preparing to unpack .../03-libbpfcc_0.30.0+ds-1ubuntu5_ppc64el.deb ...
1655s Unpacking libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
1655s Preparing to unpack .../04-python3-bpfcc_0.30.0+ds-1ubuntu5_all.deb ...
1655s Unpacking python3-bpfcc (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
1655s Preparing to unpack .../05-bpfcc-tools_0.30.0+ds-1ubuntu5_all.deb ...
1655s Unpacking bpfcc-tools (0.30.0+ds-1ubuntu5) over (0.30.0+ds-1ubuntu4) ...
1655s Preparing to unpack .../06-bpftrace_0.21.2-2ubuntu2_ppc64el.deb ...
1655s Unpacking bpftrace (0.21.2-2ubuntu2) over (0.21.2-2) ...
1655s Preparing to unpack .../07-libjson-glib-1.0-common_1.10.0+ds-3_all.deb ...
1655s Unpacking libjson-glib-1.0-common (1.10.0+ds-3) over (1.10.0+ds-2) ...
1655s Preparing to unpack .../08-libjson-glib-1.0-0_1.10.0+ds-3_ppc64el.deb ...
1655s Unpacking libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) over (1.10.0+ds-2) ...
1655s Preparing to unpack .../09-libutempter0_1.2.1-4_ppc64el.deb ...
1655s Unpacking libutempter0:ppc64el (1.2.1-4) over (1.2.1-3build1) ...
1655s Preparing to unpack .../10-pastebinit_1.7.1-1_all.deb ...
1655s Unpacking pastebinit (1.7.1-1) over (1.7.0-1) ...
1656s Preparing to unpack .../11-python3-systemd_235-1build5_ppc64el.deb ...
1656s Unpacking python3-systemd (235-1build5) over (235-1build4) ...
1656s Setting up libnewt0.52:ppc64el (0.52.24-2ubuntu4) ...
1656s Setting up pastebinit (1.7.1-1) ...
1656s Setting up python3-newt:ppc64el (0.52.24-2ubuntu4) ...
1656s Setting up libutempter0:ppc64el (1.2.1-4) ...
1656s Setting up whiptail (0.52.24-2ubuntu4) ...
1656s Setting up libjson-glib-1.0-common (1.10.0+ds-3) ...
1656s Setting up libbpfcc:ppc64el (0.30.0+ds-1ubuntu5) ...
1656s Setting up python3-bpfcc (0.30.0+ds-1ubuntu5) ...
1656s Setting up python3-systemd (235-1build5) ...
1657s Setting up bpftrace (0.21.2-2ubuntu2) ...
1657s Setting up libjson-glib-1.0-0:ppc64el (1.10.0+ds-3) ...
1657s Setting up bpfcc-tools (0.30.0+ds-1ubuntu5) ...
1657s Processing triggers for man-db (2.12.1-3) ...
1659s Processing triggers for libc-bin (2.40-1ubuntu3) ...
1660s Reading package lists...
1660s Building dependency tree...
1660s Reading state information...
1660s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1661s Hit:1 http://ftpmaster.internal/ubuntu plucky-proposed InRelease
1661s Hit:2 http://ftpmaster.internal/ubuntu plucky InRelease
1661s Hit:3 http://ftpmaster.internal/ubuntu plucky-updates InRelease
1661s Hit:4 http://ftpmaster.internal/ubuntu plucky-security InRelease
1662s Reading package lists...
1662s Reading package lists...
1663s Building dependency tree...
1663s Reading state information...
1663s Calculating upgrade...
1664s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1664s Reading package lists...
1664s Building dependency tree...
1664s Reading state information...
1665s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
1668s autopkgtest [19:34:34]: testbed running kernel: Linux 6.11.0-8-generic #8-Ubuntu SMP Mon Sep 16 13:49:23 UTC 2024
1668s autopkgtest [19:34:34]: @@@@@@@@@@@@@@@@@@@@ apt-source mdanalysis
1675s Get:1 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (dsc) [2889 B]
1675s Get:2 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (tar) [47.0 MB]
1675s Get:3 http://ftpmaster.internal/ubuntu plucky/universe mdanalysis 2.7.0-5 (diff) [10.9 kB]
1676s gpgv: Signature made Sat Aug 10 17:37:57 2024 UTC
1676s gpgv:                using RSA key 23C9A93E585819E9126D0A36573EF1E4BD5A01FA
1676s gpgv:                issuer "dparsons@debian.org"
1676s gpgv: Can't check signature: No public key
1676s dpkg-source: warning: cannot verify inline signature for ./mdanalysis_2.7.0-5.dsc: no acceptable signature found
1678s autopkgtest [19:34:44]: testing package mdanalysis version 2.7.0-5
1678s autopkgtest [19:34:44]: build not needed
1683s autopkgtest [19:34:49]: test test-mdanalysis: preparing testbed
1687s Reading package lists...
1688s Building dependency tree...
1688s Reading state information...
1688s Starting pkgProblemResolver with broken count: 0
1688s Starting 2 pkgProblemResolver with broken count: 0
1688s Done
1688s The following additional packages will be installed:
1688s   autoconf automake autopoint autotools-dev blt build-essential cpp cpp-14
1688s   cpp-14-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cython3 debhelper
1688s   debugedit dh-autoreconf dh-python dh-strip-nondeterminism docutils-common
1688s   dwz fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome
1688s   fonts-lato fonts-lyx fonts-mathjax fonts-urw-base35 g++ g++-14
1688s   g++-14-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc gcc-14
1688s   gcc-14-powerpc64le-linux-gnu gcc-powerpc64le-linux-gnu gettext
1688s   intltool-debian libaec0 libarchive-zip-perl libasan8 libblas3 libcairo2
1688s   libcc1-0 libdebhelper-perl libdeflate0 libexpat1-dev
1688s   libfile-stripnondeterminism-perl libfontconfig1 libfontenc1 libgcc-14-dev
1688s   libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b libhdf5-103-1t64
1688s   libhdf5-hl-100t64 libimagequant0 libisl23 libitm1 libjbig0 libjpeg-turbo8
1688s   libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax libjs-sphinxdoc
1688s   libjs-underscore libjson-perl liblapack3 liblbfgsb0 liblcms2-2 liblerc4
1688s   liblsan0 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7 libpixman-1-0
1688s   libpython3-all-dev libpython3-dev libpython3.12-dev libqhull-r8.0
1688s   libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2 libtcl8.6
1688s   libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7 libwebpdemux2
1688s   libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1 libxslt1.1
1688s   libxss1 m4 po-debconf pybuild-plugin-pyproject python-matplotlib-data
1688s   python-mdanalysis-doc python3-alabaster python3-all python3-all-dev
1688s   python3-appdirs python3-biopython python3-brotli python3-build python3-cairo
1688s   python3-cftime python3-citeproc python3-contourpy python3-cycler
1688s   python3-dateutil python3-decorator python3-defusedxml python3-dev
1688s   python3-docutils python3-duecredit python3-fasteners python3-fonttools
1688s   python3-freetype python3-fs python3-griddataformats python3-gsd python3-h5py
1688s   python3-h5py-serial python3-hypothesis python3-imagesize python3-iniconfig
1688s   python3-installer python3-joblib python3-kiwisolver python3-latexcodec
1688s   python3-looseversion python3-lxml python3-lz4 python3-matplotlib
1688s   python3-mda-xdrlib python3-mdanalysis python3-mmtf python3-monotonic
1688s   python3-mpmath python3-mrcfile python3-msgpack python3-msmb-theme
1688s   python3-netcdf4 python3-networkx python3-numpy python3-packaging
1688s   python3-pandas python3-pandas-lib python3-pil python3-pil.imagetk
1688s   python3-pluggy python3-pybtex python3-pybtex-docutils
1688s   python3-pyproject-hooks python3-pytest python3-reportlab python3-rlpycairo
1688s   python3-roman python3-scipy python3-seaborn python3-six python3-sklearn
1688s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
1688s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
1688s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
1688s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
1688s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
1688s   python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5
1688s   unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
1688s   zlib1g-dev
1688s Suggested packages:
1688s   autoconf-archive gnu-standards autoconf-doc blt-demo cpp-doc gcc-14-locales
1688s   cpp-14-doc cython-doc dh-make flit fonts-freefont-otf | fonts-freefont-ttf
1688s   fonts-texgyre gcc-14-doc gcc-multilib manpages-dev flex bison gdb gcc-doc
1688s   gdb-powerpc64le-linux-gnu gettext-doc libasprintf-dev libgettextpo-dev
1688s   libjs-jquery-ui-docs fonts-mathjax-extras fonts-stix libjs-mathjax-doc
1688s   liblcms2-utils libstdc++-14-doc tcl8.6 tk8.6 libtool-doc gfortran
1688s   | fortran95-compiler gcj-jdk m4-doc libmail-box-perl bwa clustalo clustalw
1688s   dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons
1688s   python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools t-coffee wise
1688s   python3-pip python3-venv python-build-doc python-cycler-doc docutils-doc
1688s   fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french
1688s   texlive-latex-base texlive-latex-recommended python-gsd-doc python-h5py-doc
1688s   python-hypothesis-doc python-installer-doc python-joblib-doc
1688s   python-latexcodec-doc python-lxml-doc cm-super-minimal dvipng ffmpeg
1688s   fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common
1688s   python-matplotlib-doc python3-cairocffi python3-gi-cairo python3-gobject
1688s   python3-pyqt5 python3-sip python3-tornado texlive-extra-utils
1688s   texlive-latex-extra python-mpmath-doc python3-gmpy2 jupyter python3-gdal
1688s   python3-pydot python3-pygraphviz gfortran python-numpy-doc python-pandas-doc
1688s   python3-statsmodels python-pil-doc python-pybtex-doc
1688s   python-pybtex-docutils-doc pdf-viewer python3-egenix-mxtexttools
1688s   python-reportlab-doc rl-accel rl-renderpm python-scipy-doc python3-dap
1688s   python-sklearn-doc python3-stemmer python-sortedcontainers-doc dvisvgm
1688s   fonts-freefont-otf imagemagick-6.q16 latexmk sphinx-doc tex-gyre
1688s   texlive-fonts-extra texlive-fonts-recommended texlive-plain-generic
1688s   python-sphinxcontrib.bibtex-doc python-sympy-doc tix python3-tk-dbg
1688s   python3.13-tk sgml-base-doc
1688s Recommended packages:
1688s   libarchive-cpio-perl javascript-common libjson-xs-perl libltdl-dev
1688s   libmail-sendmail-perl python-biopython-doc ncbi-blast+ libpaper-utils
1688s   python3-click python3-simplejson python3-psutil python3-bs4
1688s   python3-cssselect python3-html5lib python3-bottleneck python3-numexpr
1688s   python3-odf python3-openpyxl python3-tables python3-olefile
1688s   fonts-dejavu-extra isympy-common
1689s The following NEW packages will be installed:
1689s   autoconf automake autopkgtest-satdep autopoint autotools-dev blt
1689s   build-essential cpp cpp-14 cpp-14-powerpc64le-linux-gnu
1689s   cpp-powerpc64le-linux-gnu cython3 debhelper debugedit dh-autoreconf
1689s   dh-python dh-strip-nondeterminism docutils-common dwz fontconfig-config
1689s   fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx
1689s   fonts-mathjax fonts-urw-base35 g++ g++-14 g++-14-powerpc64le-linux-gnu
1689s   g++-powerpc64le-linux-gnu gcc gcc-14 gcc-14-powerpc64le-linux-gnu
1689s   gcc-powerpc64le-linux-gnu gettext intltool-debian libaec0
1689s   libarchive-zip-perl libasan8 libblas3 libcairo2 libcc1-0 libdebhelper-perl
1689s   libdeflate0 libexpat1-dev libfile-stripnondeterminism-perl libfontconfig1
1689s   libfontenc1 libgcc-14-dev libgfortran5 libgomp1 libgraphite2-3 libharfbuzz0b
1689s   libhdf5-103-1t64 libhdf5-hl-100t64 libimagequant0 libisl23 libitm1 libjbig0
1689s   libjpeg-turbo8 libjpeg8 libjs-jquery libjs-jquery-ui libjs-mathjax
1689s   libjs-sphinxdoc libjs-underscore libjson-perl liblapack3 liblbfgsb0
1689s   liblcms2-2 liblerc4 liblsan0 liblzf1 libmpc3 libnetcdf19t64 libopenjp2-7
1689s   libpixman-1-0 libpython3-all-dev libpython3-dev libpython3.12-dev
1689s   libqhull-r8.0 libquadmath0 libraqm0 libsharpyuv0 libstdc++-14-dev libsz2
1689s   libtcl8.6 libtiff6 libtk8.6 libtool libtsan2 libubsan1 libwebp7
1689s   libwebpdemux2 libwebpmux3 libxcb-render0 libxcb-shm0 libxft2 libxrender1
1689s   libxslt1.1 libxss1 m4 po-debconf pybuild-plugin-pyproject
1689s   python-matplotlib-data python-mdanalysis-doc python3-alabaster python3-all
1689s   python3-all-dev python3-appdirs python3-biopython python3-brotli
1689s   python3-build python3-cairo python3-cftime python3-citeproc
1689s   python3-contourpy python3-cycler python3-dateutil python3-decorator
1689s   python3-defusedxml python3-dev python3-docutils python3-duecredit
1689s   python3-fasteners python3-fonttools python3-freetype python3-fs
1689s   python3-griddataformats python3-gsd python3-h5py python3-h5py-serial
1689s   python3-hypothesis python3-imagesize python3-iniconfig python3-installer
1689s   python3-joblib python3-kiwisolver python3-latexcodec python3-looseversion
1689s   python3-lxml python3-lz4 python3-matplotlib python3-mda-xdrlib
1689s   python3-mdanalysis python3-mmtf python3-monotonic python3-mpmath
1689s   python3-mrcfile python3-msgpack python3-msmb-theme python3-netcdf4
1689s   python3-networkx python3-numpy python3-packaging python3-pandas
1689s   python3-pandas-lib python3-pil python3-pil.imagetk python3-pluggy
1689s   python3-pybtex python3-pybtex-docutils python3-pyproject-hooks
1689s   python3-pytest python3-reportlab python3-rlpycairo python3-roman
1689s   python3-scipy python3-seaborn python3-six python3-sklearn
1689s   python3-sklearn-lib python3-snowballstemmer python3-sortedcontainers
1689s   python3-sphinx python3-sphinx-rtd-theme python3-sphinx-sitemap
1689s   python3-sphinxcontrib.bibtex python3-sphinxcontrib.jquery python3-sympy
1689s   python3-threadpoolctl python3-tk python3-toml python3-tqdm python3-tz
1689s   python3-ufolib2 python3-unicodedata2 python3-wheel python3.12-dev
1689s   python3.12-tk sgml-base sphinx-common sphinx-rtd-theme-common tk8.6-blt2.5
1689s   unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core
1689s   zlib1g-dev
1689s 0 upgraded, 202 newly installed, 0 to remove and 0 not upgraded.
1689s Need to get 203 MB/203 MB of archives.
1689s After this operation, 901 MB of additional disk space will be used.
1689s Get:1 /tmp/autopkgtest.elFkPf/1-autopkgtest-satdep.deb autopkgtest-satdep ppc64el 0 [1020 B]
1689s Get:2 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-lato all 2.015-1 [2781 kB]
1690s Get:3 http://ftpmaster.internal/ubuntu plucky/main ppc64el sgml-base all 1.31 [11.4 kB]
1690s Get:4 http://ftpmaster.internal/ubuntu plucky/main ppc64el m4 ppc64el 1.4.19-4build1 [278 kB]
1690s Get:5 http://ftpmaster.internal/ubuntu plucky/main ppc64el autoconf all 2.72-3 [382 kB]
1690s Get:6 http://ftpmaster.internal/ubuntu plucky/main ppc64el autotools-dev all 20220109.1 [44.9 kB]
1690s Get:7 http://ftpmaster.internal/ubuntu plucky/main ppc64el automake all 1:1.16.5-1.3ubuntu1 [558 kB]
1690s Get:8 http://ftpmaster.internal/ubuntu plucky/main ppc64el autopoint all 0.22.5-2 [616 kB]
1690s Get:9 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtcl8.6 ppc64el 8.6.15+dfsg-2 [1201 kB]
1690s Get:10 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-mono all 2.37-8 [502 kB]
1690s Get:11 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-dejavu-core all 2.37-8 [835 kB]
1690s Get:12 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontenc1 ppc64el 1:1.1.8-1build1 [15.8 kB]
1690s Get:13 http://ftpmaster.internal/ubuntu plucky/main ppc64el x11-common all 1:7.7+23ubuntu3 [21.7 kB]
1690s Get:14 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-encodings all 1:1.0.5-0ubuntu2 [578 kB]
1690s Get:15 http://ftpmaster.internal/ubuntu plucky/main ppc64el xfonts-utils ppc64el 1:7.7+7 [114 kB]
1690s Get:16 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-urw-base35 all 20200910-8 [11.0 MB]
1691s Get:17 http://ftpmaster.internal/ubuntu plucky/main ppc64el fontconfig-config ppc64el 2.15.0-1.1ubuntu2 [37.4 kB]
1691s Get:18 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfontconfig1 ppc64el 2.15.0-1.1ubuntu2 [190 kB]
1691s Get:19 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxrender1 ppc64el 1:0.9.10-1.1build1 [23.1 kB]
1691s Get:20 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxft2 ppc64el 2.3.6-1build1 [61.5 kB]
1691s Get:21 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxss1 ppc64el 1:1.2.3-1build3 [7980 B]
1691s Get:22 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtk8.6 ppc64el 8.6.15-1 [942 kB]
1691s Get:23 http://ftpmaster.internal/ubuntu plucky/main ppc64el tk8.6-blt2.5 ppc64el 2.5.3+dfsg-7build1 [784 kB]
1691s Get:24 http://ftpmaster.internal/ubuntu plucky/main ppc64el blt ppc64el 2.5.3+dfsg-7build1 [4840 B]
1691s Get:25 http://ftpmaster.internal/ubuntu plucky/main ppc64el libisl23 ppc64el 0.27-1 [882 kB]
1691s Get:26 http://ftpmaster.internal/ubuntu plucky/main ppc64el libmpc3 ppc64el 1.3.1-1build2 [62.1 kB]
1691s Get:27 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [10.5 MB]
1691s Get:28 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-14 ppc64el 14.2.0-8ubuntu1 [1034 B]
1691s Get:29 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [5456 B]
1691s Get:30 http://ftpmaster.internal/ubuntu plucky/main ppc64el cpp ppc64el 4:14.1.0-2ubuntu1 [22.5 kB]
1691s Get:31 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcc1-0 ppc64el 14.2.0-8ubuntu1 [48.1 kB]
1691s Get:32 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgomp1 ppc64el 14.2.0-8ubuntu1 [161 kB]
1691s Get:33 http://ftpmaster.internal/ubuntu plucky/main ppc64el libitm1 ppc64el 14.2.0-8ubuntu1 [31.9 kB]
1691s Get:34 http://ftpmaster.internal/ubuntu plucky/main ppc64el libasan8 ppc64el 14.2.0-8ubuntu1 [2945 kB]
1691s Get:35 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblsan0 ppc64el 14.2.0-8ubuntu1 [1322 kB]
1691s Get:36 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtsan2 ppc64el 14.2.0-8ubuntu1 [2695 kB]
1692s Get:37 http://ftpmaster.internal/ubuntu plucky/main ppc64el libubsan1 ppc64el 14.2.0-8ubuntu1 [1191 kB]
1692s Get:38 http://ftpmaster.internal/ubuntu plucky/main ppc64el libquadmath0 ppc64el 14.2.0-8ubuntu1 [158 kB]
1692s Get:39 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgcc-14-dev ppc64el 14.2.0-8ubuntu1 [1619 kB]
1692s Get:40 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [20.6 MB]
1692s Get:41 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-14 ppc64el 14.2.0-8ubuntu1 [528 kB]
1692s Get:42 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [1222 B]
1692s Get:43 http://ftpmaster.internal/ubuntu plucky/main ppc64el gcc ppc64el 4:14.1.0-2ubuntu1 [5006 B]
1692s Get:44 http://ftpmaster.internal/ubuntu plucky/main ppc64el libstdc++-14-dev ppc64el 14.2.0-8ubuntu1 [2673 kB]
1692s Get:45 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14-powerpc64le-linux-gnu ppc64el 14.2.0-8ubuntu1 [12.0 MB]
1693s Get:46 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-14 ppc64el 14.2.0-8ubuntu1 [19.9 kB]
1693s Get:47 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++-powerpc64le-linux-gnu ppc64el 4:14.1.0-2ubuntu1 [968 B]
1693s Get:48 http://ftpmaster.internal/ubuntu plucky/main ppc64el g++ ppc64el 4:14.1.0-2ubuntu1 [1090 B]
1693s Get:49 http://ftpmaster.internal/ubuntu plucky/main ppc64el build-essential ppc64el 12.10ubuntu1 [4936 B]
1693s Get:50 http://ftpmaster.internal/ubuntu plucky/universe ppc64el cython3 ppc64el 3.0.11+dfsg-1ubuntu1 [2579 kB]
1693s Get:51 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdebhelper-perl all 13.20ubuntu1 [94.2 kB]
1693s Get:52 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtool all 2.4.7-7build1 [166 kB]
1693s Get:53 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-autoreconf all 20 [16.1 kB]
1693s Get:54 http://ftpmaster.internal/ubuntu plucky/main ppc64el libarchive-zip-perl all 1.68-1 [90.2 kB]
1693s Get:55 http://ftpmaster.internal/ubuntu plucky/main ppc64el libfile-stripnondeterminism-perl all 1.14.0-1 [20.1 kB]
1693s Get:56 http://ftpmaster.internal/ubuntu plucky/main ppc64el dh-strip-nondeterminism all 1.14.0-1 [5058 B]
1693s Get:57 http://ftpmaster.internal/ubuntu plucky/main ppc64el debugedit ppc64el 1:5.1-1 [52.1 kB]
1693s Get:58 http://ftpmaster.internal/ubuntu plucky/main ppc64el dwz ppc64el 0.15-1build6 [142 kB]
1693s Get:59 http://ftpmaster.internal/ubuntu plucky/main ppc64el gettext ppc64el 0.22.5-2 [1082 kB]
1693s Get:60 http://ftpmaster.internal/ubuntu plucky/main ppc64el intltool-debian all 0.35.0+20060710.6 [23.2 kB]
1693s Get:61 http://ftpmaster.internal/ubuntu plucky/main ppc64el po-debconf all 1.0.21+nmu1 [233 kB]
1693s Get:62 http://ftpmaster.internal/ubuntu plucky/main ppc64el debhelper all 13.20ubuntu1 [893 kB]
1693s Get:63 http://ftpmaster.internal/ubuntu plucky/universe ppc64el dh-python all 6.20241024 [112 kB]
1693s Get:64 http://ftpmaster.internal/ubuntu plucky/main ppc64el xml-core all 0.19 [20.3 kB]
1693s Get:65 http://ftpmaster.internal/ubuntu plucky/main ppc64el docutils-common all 0.21.2+dfsg-2 [131 kB]
1693s Get:66 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [516 kB]
1693s Get:67 http://ftpmaster.internal/ubuntu plucky/universe ppc64el fonts-lyx all 2.4.2.1-1 [171 kB]
1693s Get:68 http://ftpmaster.internal/ubuntu plucky/main ppc64el fonts-mathjax all 2.7.9+dfsg-1 [2208 kB]
1693s Get:69 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libaec0 ppc64el 1.1.3-1 [30.1 kB]
1693s Get:70 http://ftpmaster.internal/ubuntu plucky/main ppc64el libblas3 ppc64el 3.12.0-3build2 [222 kB]
1693s Get:71 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpixman-1-0 ppc64el 0.44.0-3 [334 kB]
1693s Get:72 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-render0 ppc64el 1.17.0-2 [17.2 kB]
1693s Get:73 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxcb-shm0 ppc64el 1.17.0-2 [5980 B]
1693s Get:74 http://ftpmaster.internal/ubuntu plucky/main ppc64el libcairo2 ppc64el 1.18.2-2 [747 kB]
1693s Get:75 http://ftpmaster.internal/ubuntu plucky/main ppc64el libdeflate0 ppc64el 1.22-1 [63.3 kB]
1693s Get:76 http://ftpmaster.internal/ubuntu plucky/main ppc64el libexpat1-dev ppc64el 2.6.2-2 [149 kB]
1693s Get:77 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgfortran5 ppc64el 14.2.0-8ubuntu1 [571 kB]
1693s Get:78 http://ftpmaster.internal/ubuntu plucky/main ppc64el libgraphite2-3 ppc64el 1.3.14-2ubuntu1 [84.6 kB]
1693s Get:79 http://ftpmaster.internal/ubuntu plucky/main ppc64el libharfbuzz0b ppc64el 10.0.1-1 [596 kB]
1693s Get:80 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libsz2 ppc64el 1.1.3-1 [5566 B]
1693s Get:81 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-103-1t64 ppc64el 1.10.10+repack-4ubuntu3 [1387 kB]
1693s Get:82 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libhdf5-hl-100t64 ppc64el 1.10.10+repack-4ubuntu3 [71.2 kB]
1693s Get:83 http://ftpmaster.internal/ubuntu plucky/main ppc64el libimagequant0 ppc64el 2.18.0-1build1 [43.2 kB]
1693s Get:84 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg-turbo8 ppc64el 2.1.5-2ubuntu2 [219 kB]
1693s Get:85 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjpeg8 ppc64el 8c-2ubuntu11 [2148 B]
1693s Get:86 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [328 kB]
1693s Get:87 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libjs-jquery-ui all 1.13.2+dfsg-1 [252 kB]
1693s Get:88 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [118 kB]
1693s Get:89 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-sphinxdoc all 7.4.7-4 [158 kB]
1693s Get:90 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjson-perl all 4.10000-1 [81.9 kB]
1693s Get:91 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblapack3 ppc64el 3.12.0-3build2 [2806 kB]
1693s Get:92 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblbfgsb0 ppc64el 3.0+dfsg.4-1build1 [33.0 kB]
1693s Get:93 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblcms2-2 ppc64el 2.16-2 [243 kB]
1693s Get:94 http://ftpmaster.internal/ubuntu plucky/main ppc64el liblerc4 ppc64el 4.0.0+ds-4ubuntu2 [270 kB]
1693s Get:95 http://ftpmaster.internal/ubuntu plucky/universe ppc64el liblzf1 ppc64el 3.6-4 [7920 B]
1693s Get:96 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libnetcdf19t64 ppc64el 1:4.9.2-6ubuntu1 [596 kB]
1693s Get:97 http://ftpmaster.internal/ubuntu plucky/main ppc64el zlib1g-dev ppc64el 1:1.3.dfsg+really1.3.1-1ubuntu1 [902 kB]
1693s Get:98 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3.12-dev ppc64el 3.12.7-3 [6136 kB]
1693s Get:99 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-dev ppc64el 3.12.6-0ubuntu1 [10.2 kB]
1693s Get:100 http://ftpmaster.internal/ubuntu plucky/main ppc64el libpython3-all-dev ppc64el 3.12.6-0ubuntu1 [916 B]
1693s Get:101 http://ftpmaster.internal/ubuntu plucky/universe ppc64el libqhull-r8.0 ppc64el 2020.2-6build1 [225 kB]
1693s Get:102 http://ftpmaster.internal/ubuntu plucky/main ppc64el libraqm0 ppc64el 0.10.1-1build1 [19.4 kB]
1694s Get:103 http://ftpmaster.internal/ubuntu plucky/main ppc64el libsharpyuv0 ppc64el 1.4.0-0.1 [22.0 kB]
1694s Get:104 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjbig0 ppc64el 2.1-6.1ubuntu2 [35.9 kB]
1694s Get:105 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebp7 ppc64el 1.4.0-0.1 [309 kB]
1694s Get:106 http://ftpmaster.internal/ubuntu plucky/main ppc64el libtiff6 ppc64el 4.5.1+git230720-4ubuntu4 [272 kB]
1694s Get:107 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpdemux2 ppc64el 1.4.0-0.1 [14.1 kB]
1694s Get:108 http://ftpmaster.internal/ubuntu plucky/main ppc64el libwebpmux3 ppc64el 1.4.0-0.1 [31.4 kB]
1694s Get:109 http://ftpmaster.internal/ubuntu plucky/main ppc64el libxslt1.1 ppc64el 1.1.39-0exp1ubuntu1 [191 kB]
1694s Get:110 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-packaging all 24.1-1 [41.4 kB]
1694s Get:111 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pyproject-hooks all 1.2.0-1 [10.2 kB]
1694s Get:112 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-toml all 0.10.2-1 [16.5 kB]
1694s Get:113 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-wheel all 0.44.0-1 [54.2 kB]
1694s Get:114 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-build all 1.2.2-1 [31.0 kB]
1694s Get:115 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-installer all 0.7.0+dfsg1-3 [17.4 kB]
1694s Get:116 http://ftpmaster.internal/ubuntu plucky/universe ppc64el pybuild-plugin-pyproject all 6.20241024 [1728 B]
1694s Get:117 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-matplotlib-data all 3.8.3-3 [2928 kB]
1694s Get:118 http://ftpmaster.internal/ubuntu plucky/main ppc64el libjs-mathjax all 2.7.9+dfsg-1 [5665 kB]
1695s Get:119 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python-mdanalysis-doc all 2.7.0-5 [2323 kB]
1695s Get:120 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all ppc64el 3.12.6-0ubuntu1 [888 B]
1695s Get:121 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-dev ppc64el 3.12.7-3 [505 kB]
1695s Get:122 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dev ppc64el 3.12.6-0ubuntu1 [26.7 kB]
1695s Get:123 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-all-dev ppc64el 3.12.6-0ubuntu1 [908 B]
1695s Get:124 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-appdirs all 1.4.4-4 [10.9 kB]
1695s Get:125 http://ftpmaster.internal/ubuntu plucky-proposed/main ppc64el python3-numpy ppc64el 1:1.26.4+ds-11ubuntu1 [5148 kB]
1695s Get:126 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3.12-tk ppc64el 3.12.7-3 [116 kB]
1695s Get:127 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tk ppc64el 3.12.6-1ubuntu1 [9806 B]
1695s Get:128 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pil.imagetk ppc64el 10.4.0-1ubuntu1 [9810 B]
1695s Get:129 http://ftpmaster.internal/ubuntu plucky/main ppc64el libopenjp2-7 ppc64el 2.5.0-2ubuntu1 [246 kB]
1695s Get:130 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-pil ppc64el 10.4.0-1ubuntu1 [581 kB]
1696s Get:131 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-cairo ppc64el 1.26.1-2 [129 kB]
1696s Get:132 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-freetype all 2.5.1-1 [92.3 kB]
1696s Get:133 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-rlpycairo all 0.3.0-3 [9130 B]
1696s Get:134 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-reportlab all 4.2.5-1 [1107 kB]
1696s Get:135 http://ftpmaster.internal/ubuntu plucky/universe ppc64el w3c-sgml-lib all 1.3-3 [280 kB]
1696s Get:136 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-biopython ppc64el 1.84+dfsg-4 [1738 kB]
1696s Get:137 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-brotli ppc64el 1.1.0-2build2 [413 kB]
1696s Get:138 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cftime ppc64el 1.6.4-1 [224 kB]
1696s Get:139 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-lxml ppc64el 5.3.0-1 [1354 kB]
1696s Get:140 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-citeproc all 0.6.0-3 [98.4 kB]
1696s Get:141 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-contourpy ppc64el 1.3.0-2 [217 kB]
1696s Get:142 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-cycler all 0.12.1-1 [9716 B]
1696s Get:143 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-six all 1.16.0-7 [13.1 kB]
1696s Get:144 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-dateutil all 2.9.0-2 [80.3 kB]
1696s Get:145 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-decorator all 5.1.1-5 [10.1 kB]
1696s Get:146 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-defusedxml all 0.7.1-2 [42.0 kB]
1696s Get:147 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-roman all 4.2-1 [10.0 kB]
1696s Get:148 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-docutils all 0.21.2+dfsg-2 [409 kB]
1696s Get:149 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-looseversion all 1.3.0-3 [8354 B]
1696s Get:150 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-duecredit all 0.10.2-2 [66.0 kB]
1696s Get:151 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-monotonic all 1.6-2 [5732 B]
1696s Get:152 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-fasteners all 0.18-2 [12.5 kB]
1696s Get:153 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-scipy ppc64el 1.13.1-5 [18.3 MB]
1698s Get:154 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-ufolib2 all 0.16.1+dfsg1-1 [33.4 kB]
1698s Get:155 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mpmath all 1.3.0-1 [425 kB]
1698s Get:156 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sympy all 1.13.3-1 [4228 kB]
1698s Get:157 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-tz all 2024.1-2 [31.4 kB]
1698s Get:158 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fs all 2.4.16-4 [91.3 kB]
1698s Get:159 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-lz4 ppc64el 4.0.2+dfsg-1build4 [27.8 kB]
1698s Get:160 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-unicodedata2 ppc64el 15.1.0+ds-1build1 [367 kB]
1698s Get:161 http://ftpmaster.internal/ubuntu plucky/universe ppc64el unicode-data all 15.1.0-1 [8878 kB]
1699s Get:162 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-fonttools ppc64el 4.46.0-1build2 [1473 kB]
1699s Get:163 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-rtd-theme-common all 3.0.1+dfsg-1 [1012 kB]
1699s Get:164 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mrcfile all 1.5.3-3 [114 kB]
1699s Get:165 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-griddataformats all 1.0.2-2 [2107 kB]
1699s Get:166 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-gsd ppc64el 3.3.0-1 [211 kB]
1699s Get:167 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py-serial ppc64el 3.11.0-5ubuntu1 [1159 kB]
1699s Get:168 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-h5py all 3.11.0-5ubuntu1 [7974 B]
1699s Get:169 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sortedcontainers all 2.4.0-2 [27.6 kB]
1699s Get:170 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-hypothesis all 6.116.0-1 [326 kB]
1699s Get:171 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-imagesize all 1.4.1-1 [6844 B]
1699s Get:172 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-iniconfig all 1.1.1-2 [6024 B]
1699s Get:173 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-joblib all 1.3.2-5 [206 kB]
1699s Get:174 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-kiwisolver ppc64el 1.4.7-2build1 [72.9 kB]
1699s Get:175 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-latexcodec all 3.0.0-1 [16.6 kB]
1699s Get:176 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-matplotlib ppc64el 3.8.3-3 [4610 kB]
1700s Get:177 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mda-xdrlib all 0.2.0-3 [11.4 kB]
1700s Get:178 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-msgpack ppc64el 1.0.3-3build2 [86.9 kB]
1700s Get:179 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mmtf all 1.1.3-1 [16.2 kB]
1700s Get:180 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-threadpoolctl all 3.1.0-1 [21.3 kB]
1700s Get:181 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-tqdm all 4.67.0-1 [91.6 kB]
1700s Get:182 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-mdanalysis ppc64el 2.7.0-5 [2103 kB]
1700s Get:183 http://ftpmaster.internal/ubuntu plucky/main ppc64el sphinx-common all 7.4.7-4 [775 kB]
1700s Get:184 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-alabaster all 0.7.16-0.1 [18.5 kB]
1700s Get:185 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-snowballstemmer all 2.2.0-4build1 [59.8 kB]
1700s Get:186 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-sphinx all 7.4.7-4 [593 kB]
1700s Get:187 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.jquery all 4.1-5 [6678 B]
1700s Get:188 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-rtd-theme all 3.0.1+dfsg-1 [23.5 kB]
1700s Get:189 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-msmb-theme all 1.2.0-4 [35.4 kB]
1700s Get:190 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-netcdf4 ppc64el 1.7.2-1 [635 kB]
1700s Get:191 http://ftpmaster.internal/ubuntu plucky/main ppc64el python3-networkx all 3.2.1-4ubuntu1 [11.5 MB]
1701s Get:192 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas-lib ppc64el 2.2.3+dfsg-5 [4761 kB]
1702s Get:193 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pandas all 2.2.3+dfsg-5 [3112 kB]
1702s Get:194 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pluggy all 1.5.0-1 [21.0 kB]
1702s Get:195 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pybtex all 0.24.0-4 [70.0 kB]
1702s Get:196 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pybtex-docutils all 1.0.2-1 [7176 B]
1702s Get:197 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-pytest all 8.3.3-1 [251 kB]
1702s Get:198 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-seaborn all 0.13.2-4 [225 kB]
1702s Get:199 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn-lib ppc64el 1.4.2+dfsg-6 [3838 kB]
1702s Get:200 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sklearn all 1.4.2+dfsg-6 [2257 kB]
1702s Get:201 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinx-sitemap all 2.6.0-1 [6674 B]
1702s Get:202 http://ftpmaster.internal/ubuntu plucky/universe ppc64el python3-sphinxcontrib.bibtex all 2.6.2-1 [25.2 kB]
1703s Fetched 203 MB in 14s (14.7 MB/s)
1703s Selecting previously unselected package fonts-lato.
1703s (Reading database ... 
(Reading database ... 5%
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(Reading database ... 25%
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(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%
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(Reading database ... 73773 files and directories currently installed.)
1703s Preparing to unpack .../000-fonts-lato_2.015-1_all.deb ...
1703s Unpacking fonts-lato (2.015-1) ...
1704s Selecting previously unselected package sgml-base.
1704s Preparing to unpack .../001-sgml-base_1.31_all.deb ...
1704s Unpacking sgml-base (1.31) ...
1704s Selecting previously unselected package m4.
1704s Preparing to unpack .../002-m4_1.4.19-4build1_ppc64el.deb ...
1704s Unpacking m4 (1.4.19-4build1) ...
1704s Selecting previously unselected package autoconf.
1704s Preparing to unpack .../003-autoconf_2.72-3_all.deb ...
1704s Unpacking autoconf (2.72-3) ...
1704s Selecting previously unselected package autotools-dev.
1704s Preparing to unpack .../004-autotools-dev_20220109.1_all.deb ...
1704s Unpacking autotools-dev (20220109.1) ...
1704s Selecting previously unselected package automake.
1704s Preparing to unpack .../005-automake_1%3a1.16.5-1.3ubuntu1_all.deb ...
1704s Unpacking automake (1:1.16.5-1.3ubuntu1) ...
1704s Selecting previously unselected package autopoint.
1704s Preparing to unpack .../006-autopoint_0.22.5-2_all.deb ...
1704s Unpacking autopoint (0.22.5-2) ...
1704s Selecting previously unselected package libtcl8.6:ppc64el.
1704s Preparing to unpack .../007-libtcl8.6_8.6.15+dfsg-2_ppc64el.deb ...
1704s Unpacking libtcl8.6:ppc64el (8.6.15+dfsg-2) ...
1704s Selecting previously unselected package fonts-dejavu-mono.
1704s Preparing to unpack .../008-fonts-dejavu-mono_2.37-8_all.deb ...
1704s Unpacking fonts-dejavu-mono (2.37-8) ...
1704s Selecting previously unselected package fonts-dejavu-core.
1704s Preparing to unpack .../009-fonts-dejavu-core_2.37-8_all.deb ...
1704s Unpacking fonts-dejavu-core (2.37-8) ...
1704s Selecting previously unselected package libfontenc1:ppc64el.
1704s Preparing to unpack .../010-libfontenc1_1%3a1.1.8-1build1_ppc64el.deb ...
1704s Unpacking libfontenc1:ppc64el (1:1.1.8-1build1) ...
1704s Selecting previously unselected package x11-common.
1704s Preparing to unpack .../011-x11-common_1%3a7.7+23ubuntu3_all.deb ...
1704s Unpacking x11-common (1:7.7+23ubuntu3) ...
1704s Selecting previously unselected package xfonts-encodings.
1704s Preparing to unpack .../012-xfonts-encodings_1%3a1.0.5-0ubuntu2_all.deb ...
1704s Unpacking xfonts-encodings (1:1.0.5-0ubuntu2) ...
1704s Selecting previously unselected package xfonts-utils.
1704s Preparing to unpack .../013-xfonts-utils_1%3a7.7+7_ppc64el.deb ...
1704s Unpacking xfonts-utils (1:7.7+7) ...
1704s Selecting previously unselected package fonts-urw-base35.
1704s Preparing to unpack .../014-fonts-urw-base35_20200910-8_all.deb ...
1704s Unpacking fonts-urw-base35 (20200910-8) ...
1704s Selecting previously unselected package fontconfig-config.
1704s Preparing to unpack .../015-fontconfig-config_2.15.0-1.1ubuntu2_ppc64el.deb ...
1705s Unpacking fontconfig-config (2.15.0-1.1ubuntu2) ...
1705s Selecting previously unselected package libfontconfig1:ppc64el.
1705s Preparing to unpack .../016-libfontconfig1_2.15.0-1.1ubuntu2_ppc64el.deb ...
1705s Unpacking libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
1705s Selecting previously unselected package libxrender1:ppc64el.
1705s Preparing to unpack .../017-libxrender1_1%3a0.9.10-1.1build1_ppc64el.deb ...
1705s Unpacking libxrender1:ppc64el (1:0.9.10-1.1build1) ...
1705s Selecting previously unselected package libxft2:ppc64el.
1705s Preparing to unpack .../018-libxft2_2.3.6-1build1_ppc64el.deb ...
1705s Unpacking libxft2:ppc64el (2.3.6-1build1) ...
1705s Selecting previously unselected package libxss1:ppc64el.
1705s Preparing to unpack .../019-libxss1_1%3a1.2.3-1build3_ppc64el.deb ...
1705s Unpacking libxss1:ppc64el (1:1.2.3-1build3) ...
1705s Selecting previously unselected package libtk8.6:ppc64el.
1705s Preparing to unpack .../020-libtk8.6_8.6.15-1_ppc64el.deb ...
1705s Unpacking libtk8.6:ppc64el (8.6.15-1) ...
1705s Selecting previously unselected package tk8.6-blt2.5.
1705s Preparing to unpack .../021-tk8.6-blt2.5_2.5.3+dfsg-7build1_ppc64el.deb ...
1705s Unpacking tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
1705s Selecting previously unselected package blt.
1705s Preparing to unpack .../022-blt_2.5.3+dfsg-7build1_ppc64el.deb ...
1705s Unpacking blt (2.5.3+dfsg-7build1) ...
1705s Selecting previously unselected package libisl23:ppc64el.
1705s Preparing to unpack .../023-libisl23_0.27-1_ppc64el.deb ...
1705s Unpacking libisl23:ppc64el (0.27-1) ...
1705s Selecting previously unselected package libmpc3:ppc64el.
1705s Preparing to unpack .../024-libmpc3_1.3.1-1build2_ppc64el.deb ...
1705s Unpacking libmpc3:ppc64el (1.3.1-1build2) ...
1705s Selecting previously unselected package cpp-14-powerpc64le-linux-gnu.
1705s Preparing to unpack .../025-cpp-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ...
1705s Unpacking cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package cpp-14.
1706s Preparing to unpack .../026-cpp-14_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking cpp-14 (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package cpp-powerpc64le-linux-gnu.
1706s Preparing to unpack .../027-cpp-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ...
1706s Unpacking cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ...
1706s Selecting previously unselected package cpp.
1706s Preparing to unpack .../028-cpp_4%3a14.1.0-2ubuntu1_ppc64el.deb ...
1706s Unpacking cpp (4:14.1.0-2ubuntu1) ...
1706s Selecting previously unselected package libcc1-0:ppc64el.
1706s Preparing to unpack .../029-libcc1-0_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libcc1-0:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libgomp1:ppc64el.
1706s Preparing to unpack .../030-libgomp1_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libgomp1:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libitm1:ppc64el.
1706s Preparing to unpack .../031-libitm1_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libitm1:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libasan8:ppc64el.
1706s Preparing to unpack .../032-libasan8_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libasan8:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package liblsan0:ppc64el.
1706s Preparing to unpack .../033-liblsan0_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking liblsan0:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libtsan2:ppc64el.
1706s Preparing to unpack .../034-libtsan2_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libtsan2:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libubsan1:ppc64el.
1706s Preparing to unpack .../035-libubsan1_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libubsan1:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libquadmath0:ppc64el.
1706s Preparing to unpack .../036-libquadmath0_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libquadmath0:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package libgcc-14-dev:ppc64el.
1706s Preparing to unpack .../037-libgcc-14-dev_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ...
1706s Selecting previously unselected package gcc-14-powerpc64le-linux-gnu.
1706s Preparing to unpack .../038-gcc-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ...
1706s Unpacking gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ...
1707s Selecting previously unselected package gcc-14.
1707s Preparing to unpack .../039-gcc-14_14.2.0-8ubuntu1_ppc64el.deb ...
1707s Unpacking gcc-14 (14.2.0-8ubuntu1) ...
1707s Selecting previously unselected package gcc-powerpc64le-linux-gnu.
1707s Preparing to unpack .../040-gcc-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ...
1707s Unpacking gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ...
1707s Selecting previously unselected package gcc.
1707s Preparing to unpack .../041-gcc_4%3a14.1.0-2ubuntu1_ppc64el.deb ...
1707s Unpacking gcc (4:14.1.0-2ubuntu1) ...
1707s Selecting previously unselected package libstdc++-14-dev:ppc64el.
1707s Preparing to unpack .../042-libstdc++-14-dev_14.2.0-8ubuntu1_ppc64el.deb ...
1707s Unpacking libstdc++-14-dev:ppc64el (14.2.0-8ubuntu1) ...
1707s Selecting previously unselected package g++-14-powerpc64le-linux-gnu.
1707s Preparing to unpack .../043-g++-14-powerpc64le-linux-gnu_14.2.0-8ubuntu1_ppc64el.deb ...
1707s Unpacking g++-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ...
1707s Selecting previously unselected package g++-14.
1707s Preparing to unpack .../044-g++-14_14.2.0-8ubuntu1_ppc64el.deb ...
1707s Unpacking g++-14 (14.2.0-8ubuntu1) ...
1707s Selecting previously unselected package g++-powerpc64le-linux-gnu.
1707s Preparing to unpack .../045-g++-powerpc64le-linux-gnu_4%3a14.1.0-2ubuntu1_ppc64el.deb ...
1707s Unpacking g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ...
1707s Selecting previously unselected package g++.
1707s Preparing to unpack .../046-g++_4%3a14.1.0-2ubuntu1_ppc64el.deb ...
1707s Unpacking g++ (4:14.1.0-2ubuntu1) ...
1707s Selecting previously unselected package build-essential.
1707s Preparing to unpack .../047-build-essential_12.10ubuntu1_ppc64el.deb ...
1707s Unpacking build-essential (12.10ubuntu1) ...
1707s Selecting previously unselected package cython3.
1707s Preparing to unpack .../048-cython3_3.0.11+dfsg-1ubuntu1_ppc64el.deb ...
1707s Unpacking cython3 (3.0.11+dfsg-1ubuntu1) ...
1707s Selecting previously unselected package libdebhelper-perl.
1707s Preparing to unpack .../049-libdebhelper-perl_13.20ubuntu1_all.deb ...
1707s Unpacking libdebhelper-perl (13.20ubuntu1) ...
1707s Selecting previously unselected package libtool.
1707s Preparing to unpack .../050-libtool_2.4.7-7build1_all.deb ...
1707s Unpacking libtool (2.4.7-7build1) ...
1707s Selecting previously unselected package dh-autoreconf.
1707s Preparing to unpack .../051-dh-autoreconf_20_all.deb ...
1707s Unpacking dh-autoreconf (20) ...
1707s Selecting previously unselected package libarchive-zip-perl.
1707s Preparing to unpack .../052-libarchive-zip-perl_1.68-1_all.deb ...
1707s Unpacking libarchive-zip-perl (1.68-1) ...
1707s Selecting previously unselected package libfile-stripnondeterminism-perl.
1707s Preparing to unpack .../053-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ...
1707s Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ...
1707s Selecting previously unselected package dh-strip-nondeterminism.
1707s Preparing to unpack .../054-dh-strip-nondeterminism_1.14.0-1_all.deb ...
1707s Unpacking dh-strip-nondeterminism (1.14.0-1) ...
1708s Selecting previously unselected package debugedit.
1708s Preparing to unpack .../055-debugedit_1%3a5.1-1_ppc64el.deb ...
1708s Unpacking debugedit (1:5.1-1) ...
1708s Selecting previously unselected package dwz.
1708s Preparing to unpack .../056-dwz_0.15-1build6_ppc64el.deb ...
1708s Unpacking dwz (0.15-1build6) ...
1708s Selecting previously unselected package gettext.
1708s Preparing to unpack .../057-gettext_0.22.5-2_ppc64el.deb ...
1708s Unpacking gettext (0.22.5-2) ...
1708s Selecting previously unselected package intltool-debian.
1708s Preparing to unpack .../058-intltool-debian_0.35.0+20060710.6_all.deb ...
1708s Unpacking intltool-debian (0.35.0+20060710.6) ...
1708s Selecting previously unselected package po-debconf.
1708s Preparing to unpack .../059-po-debconf_1.0.21+nmu1_all.deb ...
1708s Unpacking po-debconf (1.0.21+nmu1) ...
1708s Selecting previously unselected package debhelper.
1708s Preparing to unpack .../060-debhelper_13.20ubuntu1_all.deb ...
1708s Unpacking debhelper (13.20ubuntu1) ...
1708s Selecting previously unselected package dh-python.
1708s Preparing to unpack .../061-dh-python_6.20241024_all.deb ...
1708s Unpacking dh-python (6.20241024) ...
1708s Selecting previously unselected package xml-core.
1708s Preparing to unpack .../062-xml-core_0.19_all.deb ...
1708s Unpacking xml-core (0.19) ...
1708s Selecting previously unselected package docutils-common.
1708s Preparing to unpack .../063-docutils-common_0.21.2+dfsg-2_all.deb ...
1708s Unpacking docutils-common (0.21.2+dfsg-2) ...
1708s Selecting previously unselected package fonts-font-awesome.
1708s Preparing to unpack .../064-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ...
1708s Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
1708s Selecting previously unselected package fonts-lyx.
1708s Preparing to unpack .../065-fonts-lyx_2.4.2.1-1_all.deb ...
1708s Unpacking fonts-lyx (2.4.2.1-1) ...
1708s Selecting previously unselected package fonts-mathjax.
1708s Preparing to unpack .../066-fonts-mathjax_2.7.9+dfsg-1_all.deb ...
1708s Unpacking fonts-mathjax (2.7.9+dfsg-1) ...
1708s Selecting previously unselected package libaec0:ppc64el.
1708s Preparing to unpack .../067-libaec0_1.1.3-1_ppc64el.deb ...
1708s Unpacking libaec0:ppc64el (1.1.3-1) ...
1708s Selecting previously unselected package libblas3:ppc64el.
1708s Preparing to unpack .../068-libblas3_3.12.0-3build2_ppc64el.deb ...
1708s Unpacking libblas3:ppc64el (3.12.0-3build2) ...
1708s Selecting previously unselected package libpixman-1-0:ppc64el.
1708s Preparing to unpack .../069-libpixman-1-0_0.44.0-3_ppc64el.deb ...
1708s Unpacking libpixman-1-0:ppc64el (0.44.0-3) ...
1708s Selecting previously unselected package libxcb-render0:ppc64el.
1708s Preparing to unpack .../070-libxcb-render0_1.17.0-2_ppc64el.deb ...
1708s Unpacking libxcb-render0:ppc64el (1.17.0-2) ...
1708s Selecting previously unselected package libxcb-shm0:ppc64el.
1708s Preparing to unpack .../071-libxcb-shm0_1.17.0-2_ppc64el.deb ...
1708s Unpacking libxcb-shm0:ppc64el (1.17.0-2) ...
1708s Selecting previously unselected package libcairo2:ppc64el.
1708s Preparing to unpack .../072-libcairo2_1.18.2-2_ppc64el.deb ...
1708s Unpacking libcairo2:ppc64el (1.18.2-2) ...
1709s Selecting previously unselected package libdeflate0:ppc64el.
1709s Preparing to unpack .../073-libdeflate0_1.22-1_ppc64el.deb ...
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1709s Selecting previously unselected package libexpat1-dev:ppc64el.
1709s Preparing to unpack .../074-libexpat1-dev_2.6.2-2_ppc64el.deb ...
1709s Unpacking libexpat1-dev:ppc64el (2.6.2-2) ...
1709s Selecting previously unselected package libgfortran5:ppc64el.
1709s Preparing to unpack .../075-libgfortran5_14.2.0-8ubuntu1_ppc64el.deb ...
1709s Unpacking libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
1709s Selecting previously unselected package libgraphite2-3:ppc64el.
1709s Preparing to unpack .../076-libgraphite2-3_1.3.14-2ubuntu1_ppc64el.deb ...
1709s Unpacking libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ...
1709s Selecting previously unselected package libharfbuzz0b:ppc64el.
1709s Preparing to unpack .../077-libharfbuzz0b_10.0.1-1_ppc64el.deb ...
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1709s Selecting previously unselected package libsz2:ppc64el.
1709s Preparing to unpack .../078-libsz2_1.1.3-1_ppc64el.deb ...
1709s Unpacking libsz2:ppc64el (1.1.3-1) ...
1709s Selecting previously unselected package libhdf5-103-1t64:ppc64el.
1709s Preparing to unpack .../079-libhdf5-103-1t64_1.10.10+repack-4ubuntu3_ppc64el.deb ...
1709s Unpacking libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
1709s Selecting previously unselected package libhdf5-hl-100t64:ppc64el.
1709s Preparing to unpack .../080-libhdf5-hl-100t64_1.10.10+repack-4ubuntu3_ppc64el.deb ...
1709s Unpacking libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ...
1709s Selecting previously unselected package libimagequant0:ppc64el.
1709s Preparing to unpack .../081-libimagequant0_2.18.0-1build1_ppc64el.deb ...
1709s Unpacking libimagequant0:ppc64el (2.18.0-1build1) ...
1709s Selecting previously unselected package libjpeg-turbo8:ppc64el.
1709s Preparing to unpack .../082-libjpeg-turbo8_2.1.5-2ubuntu2_ppc64el.deb ...
1709s Unpacking libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ...
1709s Selecting previously unselected package libjpeg8:ppc64el.
1709s Preparing to unpack .../083-libjpeg8_8c-2ubuntu11_ppc64el.deb ...
1709s Unpacking libjpeg8:ppc64el (8c-2ubuntu11) ...
1709s Selecting previously unselected package libjs-jquery.
1709s Preparing to unpack .../084-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ...
1709s Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1709s Selecting previously unselected package libjs-jquery-ui.
1709s Preparing to unpack .../085-libjs-jquery-ui_1.13.2+dfsg-1_all.deb ...
1709s Unpacking libjs-jquery-ui (1.13.2+dfsg-1) ...
1709s Selecting previously unselected package libjs-underscore.
1709s Preparing to unpack .../086-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ...
1709s Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
1709s Selecting previously unselected package libjs-sphinxdoc.
1709s Preparing to unpack .../087-libjs-sphinxdoc_7.4.7-4_all.deb ...
1709s Unpacking libjs-sphinxdoc (7.4.7-4) ...
1709s Selecting previously unselected package libjson-perl.
1709s Preparing to unpack .../088-libjson-perl_4.10000-1_all.deb ...
1709s Unpacking libjson-perl (4.10000-1) ...
1709s Selecting previously unselected package liblapack3:ppc64el.
1709s Preparing to unpack .../089-liblapack3_3.12.0-3build2_ppc64el.deb ...
1709s Unpacking liblapack3:ppc64el (3.12.0-3build2) ...
1709s Selecting previously unselected package liblbfgsb0:ppc64el.
1709s Preparing to unpack .../090-liblbfgsb0_3.0+dfsg.4-1build1_ppc64el.deb ...
1709s Unpacking liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ...
1709s Selecting previously unselected package liblcms2-2:ppc64el.
1709s Preparing to unpack .../091-liblcms2-2_2.16-2_ppc64el.deb ...
1709s Unpacking liblcms2-2:ppc64el (2.16-2) ...
1709s Selecting previously unselected package liblerc4:ppc64el.
1709s Preparing to unpack .../092-liblerc4_4.0.0+ds-4ubuntu2_ppc64el.deb ...
1709s Unpacking liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ...
1709s Selecting previously unselected package liblzf1:ppc64el.
1709s Preparing to unpack .../093-liblzf1_3.6-4_ppc64el.deb ...
1709s Unpacking liblzf1:ppc64el (3.6-4) ...
1709s Selecting previously unselected package libnetcdf19t64:ppc64el.
1709s Preparing to unpack .../094-libnetcdf19t64_1%3a4.9.2-6ubuntu1_ppc64el.deb ...
1709s Unpacking libnetcdf19t64:ppc64el (1:4.9.2-6ubuntu1) ...
1709s Selecting previously unselected package zlib1g-dev:ppc64el.
1709s Preparing to unpack .../095-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1ubuntu1_ppc64el.deb ...
1709s Unpacking zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
1709s Selecting previously unselected package libpython3.12-dev:ppc64el.
1709s Preparing to unpack .../096-libpython3.12-dev_3.12.7-3_ppc64el.deb ...
1709s Unpacking libpython3.12-dev:ppc64el (3.12.7-3) ...
1710s Selecting previously unselected package libpython3-dev:ppc64el.
1710s Preparing to unpack .../097-libpython3-dev_3.12.6-0ubuntu1_ppc64el.deb ...
1710s Unpacking libpython3-dev:ppc64el (3.12.6-0ubuntu1) ...
1710s Selecting previously unselected package libpython3-all-dev:ppc64el.
1710s Preparing to unpack .../098-libpython3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ...
1710s Unpacking libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ...
1710s Selecting previously unselected package libqhull-r8.0:ppc64el.
1710s Preparing to unpack .../099-libqhull-r8.0_2020.2-6build1_ppc64el.deb ...
1710s Unpacking libqhull-r8.0:ppc64el (2020.2-6build1) ...
1710s Selecting previously unselected package libraqm0:ppc64el.
1710s Preparing to unpack .../100-libraqm0_0.10.1-1build1_ppc64el.deb ...
1710s Unpacking libraqm0:ppc64el (0.10.1-1build1) ...
1710s Selecting previously unselected package libsharpyuv0:ppc64el.
1710s Preparing to unpack .../101-libsharpyuv0_1.4.0-0.1_ppc64el.deb ...
1710s Unpacking libsharpyuv0:ppc64el (1.4.0-0.1) ...
1710s Selecting previously unselected package libjbig0:ppc64el.
1710s Preparing to unpack .../102-libjbig0_2.1-6.1ubuntu2_ppc64el.deb ...
1710s Unpacking libjbig0:ppc64el (2.1-6.1ubuntu2) ...
1710s Selecting previously unselected package libwebp7:ppc64el.
1710s Preparing to unpack .../103-libwebp7_1.4.0-0.1_ppc64el.deb ...
1710s Unpacking libwebp7:ppc64el (1.4.0-0.1) ...
1710s Selecting previously unselected package libtiff6:ppc64el.
1710s Preparing to unpack .../104-libtiff6_4.5.1+git230720-4ubuntu4_ppc64el.deb ...
1710s Unpacking libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
1710s Selecting previously unselected package libwebpdemux2:ppc64el.
1710s Preparing to unpack .../105-libwebpdemux2_1.4.0-0.1_ppc64el.deb ...
1710s Unpacking libwebpdemux2:ppc64el (1.4.0-0.1) ...
1710s Selecting previously unselected package libwebpmux3:ppc64el.
1710s Preparing to unpack .../106-libwebpmux3_1.4.0-0.1_ppc64el.deb ...
1710s Unpacking libwebpmux3:ppc64el (1.4.0-0.1) ...
1710s Selecting previously unselected package libxslt1.1:ppc64el.
1710s Preparing to unpack .../107-libxslt1.1_1.1.39-0exp1ubuntu1_ppc64el.deb ...
1710s Unpacking libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ...
1710s Selecting previously unselected package python3-packaging.
1710s Preparing to unpack .../108-python3-packaging_24.1-1_all.deb ...
1710s Unpacking python3-packaging (24.1-1) ...
1710s Selecting previously unselected package python3-pyproject-hooks.
1710s Preparing to unpack .../109-python3-pyproject-hooks_1.2.0-1_all.deb ...
1710s Unpacking python3-pyproject-hooks (1.2.0-1) ...
1710s Selecting previously unselected package python3-toml.
1710s Preparing to unpack .../110-python3-toml_0.10.2-1_all.deb ...
1710s Unpacking python3-toml (0.10.2-1) ...
1710s Selecting previously unselected package python3-wheel.
1710s Preparing to unpack .../111-python3-wheel_0.44.0-1_all.deb ...
1710s Unpacking python3-wheel (0.44.0-1) ...
1710s Selecting previously unselected package python3-build.
1710s Preparing to unpack .../112-python3-build_1.2.2-1_all.deb ...
1710s Unpacking python3-build (1.2.2-1) ...
1710s Selecting previously unselected package python3-installer.
1710s Preparing to unpack .../113-python3-installer_0.7.0+dfsg1-3_all.deb ...
1710s Unpacking python3-installer (0.7.0+dfsg1-3) ...
1710s Selecting previously unselected package pybuild-plugin-pyproject.
1710s Preparing to unpack .../114-pybuild-plugin-pyproject_6.20241024_all.deb ...
1710s Unpacking pybuild-plugin-pyproject (6.20241024) ...
1710s Selecting previously unselected package python-matplotlib-data.
1710s Preparing to unpack .../115-python-matplotlib-data_3.8.3-3_all.deb ...
1710s Unpacking python-matplotlib-data (3.8.3-3) ...
1710s Selecting previously unselected package libjs-mathjax.
1710s Preparing to unpack .../116-libjs-mathjax_2.7.9+dfsg-1_all.deb ...
1710s Unpacking libjs-mathjax (2.7.9+dfsg-1) ...
1711s Selecting previously unselected package python-mdanalysis-doc.
1711s Preparing to unpack .../117-python-mdanalysis-doc_2.7.0-5_all.deb ...
1711s Unpacking python-mdanalysis-doc (2.7.0-5) ...
1711s Selecting previously unselected package python3-all.
1711s Preparing to unpack .../118-python3-all_3.12.6-0ubuntu1_ppc64el.deb ...
1711s Unpacking python3-all (3.12.6-0ubuntu1) ...
1711s Selecting previously unselected package python3.12-dev.
1711s Preparing to unpack .../119-python3.12-dev_3.12.7-3_ppc64el.deb ...
1711s Unpacking python3.12-dev (3.12.7-3) ...
1711s Selecting previously unselected package python3-dev.
1711s Preparing to unpack .../120-python3-dev_3.12.6-0ubuntu1_ppc64el.deb ...
1711s Unpacking python3-dev (3.12.6-0ubuntu1) ...
1711s Selecting previously unselected package python3-all-dev.
1711s Preparing to unpack .../121-python3-all-dev_3.12.6-0ubuntu1_ppc64el.deb ...
1711s Unpacking python3-all-dev (3.12.6-0ubuntu1) ...
1711s Selecting previously unselected package python3-appdirs.
1711s Preparing to unpack .../122-python3-appdirs_1.4.4-4_all.deb ...
1711s Unpacking python3-appdirs (1.4.4-4) ...
1711s Selecting previously unselected package python3-numpy.
1711s Preparing to unpack .../123-python3-numpy_1%3a1.26.4+ds-11ubuntu1_ppc64el.deb ...
1711s Unpacking python3-numpy (1:1.26.4+ds-11ubuntu1) ...
1712s Selecting previously unselected package python3.12-tk.
1712s Preparing to unpack .../124-python3.12-tk_3.12.7-3_ppc64el.deb ...
1712s Unpacking python3.12-tk (3.12.7-3) ...
1712s Selecting previously unselected package python3-tk:ppc64el.
1712s Preparing to unpack .../125-python3-tk_3.12.6-1ubuntu1_ppc64el.deb ...
1712s Unpacking python3-tk:ppc64el (3.12.6-1ubuntu1) ...
1712s Selecting previously unselected package python3-pil.imagetk:ppc64el.
1712s Preparing to unpack .../126-python3-pil.imagetk_10.4.0-1ubuntu1_ppc64el.deb ...
1712s Unpacking python3-pil.imagetk:ppc64el (10.4.0-1ubuntu1) ...
1712s Selecting previously unselected package libopenjp2-7:ppc64el.
1712s Preparing to unpack .../127-libopenjp2-7_2.5.0-2ubuntu1_ppc64el.deb ...
1712s Unpacking libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ...
1712s Selecting previously unselected package python3-pil:ppc64el.
1712s Preparing to unpack .../128-python3-pil_10.4.0-1ubuntu1_ppc64el.deb ...
1712s Unpacking python3-pil:ppc64el (10.4.0-1ubuntu1) ...
1712s Selecting previously unselected package python3-cairo.
1712s Preparing to unpack .../129-python3-cairo_1.26.1-2_ppc64el.deb ...
1712s Unpacking python3-cairo (1.26.1-2) ...
1712s Selecting previously unselected package python3-freetype.
1712s Preparing to unpack .../130-python3-freetype_2.5.1-1_all.deb ...
1712s Unpacking python3-freetype (2.5.1-1) ...
1712s Selecting previously unselected package python3-rlpycairo.
1712s Preparing to unpack .../131-python3-rlpycairo_0.3.0-3_all.deb ...
1712s Unpacking python3-rlpycairo (0.3.0-3) ...
1712s Selecting previously unselected package python3-reportlab.
1712s Preparing to unpack .../132-python3-reportlab_4.2.5-1_all.deb ...
1712s Unpacking python3-reportlab (4.2.5-1) ...
1712s Selecting previously unselected package w3c-sgml-lib.
1712s Preparing to unpack .../133-w3c-sgml-lib_1.3-3_all.deb ...
1712s Unpacking w3c-sgml-lib (1.3-3) ...
1712s Selecting previously unselected package python3-biopython.
1712s Preparing to unpack .../134-python3-biopython_1.84+dfsg-4_ppc64el.deb ...
1712s Unpacking python3-biopython (1.84+dfsg-4) ...
1712s Selecting previously unselected package python3-brotli.
1712s Preparing to unpack .../135-python3-brotli_1.1.0-2build2_ppc64el.deb ...
1712s Unpacking python3-brotli (1.1.0-2build2) ...
1712s Selecting previously unselected package python3-cftime.
1712s Preparing to unpack .../136-python3-cftime_1.6.4-1_ppc64el.deb ...
1712s Unpacking python3-cftime (1.6.4-1) ...
1712s Selecting previously unselected package python3-lxml:ppc64el.
1712s Preparing to unpack .../137-python3-lxml_5.3.0-1_ppc64el.deb ...
1712s Unpacking python3-lxml:ppc64el (5.3.0-1) ...
1712s Selecting previously unselected package python3-citeproc.
1712s Preparing to unpack .../138-python3-citeproc_0.6.0-3_all.deb ...
1712s Unpacking python3-citeproc (0.6.0-3) ...
1713s Selecting previously unselected package python3-contourpy.
1713s Preparing to unpack .../139-python3-contourpy_1.3.0-2_ppc64el.deb ...
1713s Unpacking python3-contourpy (1.3.0-2) ...
1713s Selecting previously unselected package python3-cycler.
1713s Preparing to unpack .../140-python3-cycler_0.12.1-1_all.deb ...
1713s Unpacking python3-cycler (0.12.1-1) ...
1713s Selecting previously unselected package python3-six.
1713s Preparing to unpack .../141-python3-six_1.16.0-7_all.deb ...
1713s Unpacking python3-six (1.16.0-7) ...
1713s Selecting previously unselected package python3-dateutil.
1713s Preparing to unpack .../142-python3-dateutil_2.9.0-2_all.deb ...
1713s Unpacking python3-dateutil (2.9.0-2) ...
1713s Selecting previously unselected package python3-decorator.
1713s Preparing to unpack .../143-python3-decorator_5.1.1-5_all.deb ...
1713s Unpacking python3-decorator (5.1.1-5) ...
1713s Selecting previously unselected package python3-defusedxml.
1713s Preparing to unpack .../144-python3-defusedxml_0.7.1-2_all.deb ...
1713s Unpacking python3-defusedxml (0.7.1-2) ...
1713s Selecting previously unselected package python3-roman.
1713s Preparing to unpack .../145-python3-roman_4.2-1_all.deb ...
1713s Unpacking python3-roman (4.2-1) ...
1713s Selecting previously unselected package python3-docutils.
1713s Preparing to unpack .../146-python3-docutils_0.21.2+dfsg-2_all.deb ...
1713s Unpacking python3-docutils (0.21.2+dfsg-2) ...
1713s Selecting previously unselected package python3-looseversion.
1713s Preparing to unpack .../147-python3-looseversion_1.3.0-3_all.deb ...
1713s Unpacking python3-looseversion (1.3.0-3) ...
1713s Selecting previously unselected package python3-duecredit.
1713s Preparing to unpack .../148-python3-duecredit_0.10.2-2_all.deb ...
1713s Unpacking python3-duecredit (0.10.2-2) ...
1713s Selecting previously unselected package python3-monotonic.
1713s Preparing to unpack .../149-python3-monotonic_1.6-2_all.deb ...
1713s Unpacking python3-monotonic (1.6-2) ...
1713s Selecting previously unselected package python3-fasteners.
1713s Preparing to unpack .../150-python3-fasteners_0.18-2_all.deb ...
1713s Unpacking python3-fasteners (0.18-2) ...
1713s Selecting previously unselected package python3-scipy.
1713s Preparing to unpack .../151-python3-scipy_1.13.1-5_ppc64el.deb ...
1713s Unpacking python3-scipy (1.13.1-5) ...
1714s Selecting previously unselected package python3-ufolib2.
1714s Preparing to unpack .../152-python3-ufolib2_0.16.1+dfsg1-1_all.deb ...
1714s Unpacking python3-ufolib2 (0.16.1+dfsg1-1) ...
1714s Selecting previously unselected package python3-mpmath.
1714s Preparing to unpack .../153-python3-mpmath_1.3.0-1_all.deb ...
1714s Unpacking python3-mpmath (1.3.0-1) ...
1714s Selecting previously unselected package python3-sympy.
1714s Preparing to unpack .../154-python3-sympy_1.13.3-1_all.deb ...
1714s Unpacking python3-sympy (1.13.3-1) ...
1714s Selecting previously unselected package python3-tz.
1714s Preparing to unpack .../155-python3-tz_2024.1-2_all.deb ...
1714s Unpacking python3-tz (2024.1-2) ...
1714s Selecting previously unselected package python3-fs.
1714s Preparing to unpack .../156-python3-fs_2.4.16-4_all.deb ...
1714s Unpacking python3-fs (2.4.16-4) ...
1714s Selecting previously unselected package python3-lz4.
1714s Preparing to unpack .../157-python3-lz4_4.0.2+dfsg-1build4_ppc64el.deb ...
1714s Unpacking python3-lz4 (4.0.2+dfsg-1build4) ...
1714s Selecting previously unselected package python3-unicodedata2.
1714s Preparing to unpack .../158-python3-unicodedata2_15.1.0+ds-1build1_ppc64el.deb ...
1714s Unpacking python3-unicodedata2 (15.1.0+ds-1build1) ...
1714s Selecting previously unselected package unicode-data.
1714s Preparing to unpack .../159-unicode-data_15.1.0-1_all.deb ...
1714s Unpacking unicode-data (15.1.0-1) ...
1715s Selecting previously unselected package python3-fonttools.
1715s Preparing to unpack .../160-python3-fonttools_4.46.0-1build2_ppc64el.deb ...
1715s Unpacking python3-fonttools (4.46.0-1build2) ...
1715s Selecting previously unselected package sphinx-rtd-theme-common.
1715s Preparing to unpack .../161-sphinx-rtd-theme-common_3.0.1+dfsg-1_all.deb ...
1715s Unpacking sphinx-rtd-theme-common (3.0.1+dfsg-1) ...
1715s Selecting previously unselected package python3-mrcfile.
1715s Preparing to unpack .../162-python3-mrcfile_1.5.3-3_all.deb ...
1715s Unpacking python3-mrcfile (1.5.3-3) ...
1715s Selecting previously unselected package python3-griddataformats.
1715s Preparing to unpack .../163-python3-griddataformats_1.0.2-2_all.deb ...
1715s Unpacking python3-griddataformats (1.0.2-2) ...
1715s Selecting previously unselected package python3-gsd.
1715s Preparing to unpack .../164-python3-gsd_3.3.0-1_ppc64el.deb ...
1715s Unpacking python3-gsd (3.3.0-1) ...
1715s Selecting previously unselected package python3-h5py-serial.
1715s Preparing to unpack .../165-python3-h5py-serial_3.11.0-5ubuntu1_ppc64el.deb ...
1715s Unpacking python3-h5py-serial (3.11.0-5ubuntu1) ...
1715s Selecting previously unselected package python3-h5py.
1715s Preparing to unpack .../166-python3-h5py_3.11.0-5ubuntu1_all.deb ...
1715s Unpacking python3-h5py (3.11.0-5ubuntu1) ...
1715s Selecting previously unselected package python3-sortedcontainers.
1715s Preparing to unpack .../167-python3-sortedcontainers_2.4.0-2_all.deb ...
1715s Unpacking python3-sortedcontainers (2.4.0-2) ...
1715s Selecting previously unselected package python3-hypothesis.
1715s Preparing to unpack .../168-python3-hypothesis_6.116.0-1_all.deb ...
1715s Unpacking python3-hypothesis (6.116.0-1) ...
1715s Selecting previously unselected package python3-imagesize.
1715s Preparing to unpack .../169-python3-imagesize_1.4.1-1_all.deb ...
1715s Unpacking python3-imagesize (1.4.1-1) ...
1715s Selecting previously unselected package python3-iniconfig.
1715s Preparing to unpack .../170-python3-iniconfig_1.1.1-2_all.deb ...
1715s Unpacking python3-iniconfig (1.1.1-2) ...
1715s Selecting previously unselected package python3-joblib.
1715s Preparing to unpack .../171-python3-joblib_1.3.2-5_all.deb ...
1715s Unpacking python3-joblib (1.3.2-5) ...
1715s Selecting previously unselected package python3-kiwisolver.
1715s Preparing to unpack .../172-python3-kiwisolver_1.4.7-2build1_ppc64el.deb ...
1715s Unpacking python3-kiwisolver (1.4.7-2build1) ...
1715s Selecting previously unselected package python3-latexcodec.
1715s Preparing to unpack .../173-python3-latexcodec_3.0.0-1_all.deb ...
1715s Unpacking python3-latexcodec (3.0.0-1) ...
1715s Selecting previously unselected package python3-matplotlib.
1715s Preparing to unpack .../174-python3-matplotlib_3.8.3-3_ppc64el.deb ...
1715s Unpacking python3-matplotlib (3.8.3-3) ...
1715s Selecting previously unselected package python3-mda-xdrlib.
1715s Preparing to unpack .../175-python3-mda-xdrlib_0.2.0-3_all.deb ...
1715s Unpacking python3-mda-xdrlib (0.2.0-3) ...
1715s Selecting previously unselected package python3-msgpack.
1715s Preparing to unpack .../176-python3-msgpack_1.0.3-3build2_ppc64el.deb ...
1715s Unpacking python3-msgpack (1.0.3-3build2) ...
1715s Selecting previously unselected package python3-mmtf.
1715s Preparing to unpack .../177-python3-mmtf_1.1.3-1_all.deb ...
1715s Unpacking python3-mmtf (1.1.3-1) ...
1715s Selecting previously unselected package python3-threadpoolctl.
1715s Preparing to unpack .../178-python3-threadpoolctl_3.1.0-1_all.deb ...
1715s Unpacking python3-threadpoolctl (3.1.0-1) ...
1715s Selecting previously unselected package python3-tqdm.
1715s Preparing to unpack .../179-python3-tqdm_4.67.0-1_all.deb ...
1715s Unpacking python3-tqdm (4.67.0-1) ...
1715s Selecting previously unselected package python3-mdanalysis.
1716s Preparing to unpack .../180-python3-mdanalysis_2.7.0-5_ppc64el.deb ...
1716s Unpacking python3-mdanalysis (2.7.0-5) ...
1716s Selecting previously unselected package sphinx-common.
1716s Preparing to unpack .../181-sphinx-common_7.4.7-4_all.deb ...
1716s Unpacking sphinx-common (7.4.7-4) ...
1716s Selecting previously unselected package python3-alabaster.
1716s Preparing to unpack .../182-python3-alabaster_0.7.16-0.1_all.deb ...
1716s Unpacking python3-alabaster (0.7.16-0.1) ...
1716s Selecting previously unselected package python3-snowballstemmer.
1716s Preparing to unpack .../183-python3-snowballstemmer_2.2.0-4build1_all.deb ...
1716s Unpacking python3-snowballstemmer (2.2.0-4build1) ...
1716s Selecting previously unselected package python3-sphinx.
1716s Preparing to unpack .../184-python3-sphinx_7.4.7-4_all.deb ...
1716s Unpacking python3-sphinx (7.4.7-4) ...
1716s Selecting previously unselected package python3-sphinxcontrib.jquery.
1716s Preparing to unpack .../185-python3-sphinxcontrib.jquery_4.1-5_all.deb ...
1716s Unpacking python3-sphinxcontrib.jquery (4.1-5) ...
1716s Selecting previously unselected package python3-sphinx-rtd-theme.
1716s Preparing to unpack .../186-python3-sphinx-rtd-theme_3.0.1+dfsg-1_all.deb ...
1716s Unpacking python3-sphinx-rtd-theme (3.0.1+dfsg-1) ...
1716s Selecting previously unselected package python3-msmb-theme.
1716s Preparing to unpack .../187-python3-msmb-theme_1.2.0-4_all.deb ...
1716s Unpacking python3-msmb-theme (1.2.0-4) ...
1716s Selecting previously unselected package python3-netcdf4.
1716s Preparing to unpack .../188-python3-netcdf4_1.7.2-1_ppc64el.deb ...
1716s Unpacking python3-netcdf4 (1.7.2-1) ...
1716s Selecting previously unselected package python3-networkx.
1716s Preparing to unpack .../189-python3-networkx_3.2.1-4ubuntu1_all.deb ...
1716s Unpacking python3-networkx (3.2.1-4ubuntu1) ...
1717s Selecting previously unselected package python3-pandas-lib:ppc64el.
1717s Preparing to unpack .../190-python3-pandas-lib_2.2.3+dfsg-5_ppc64el.deb ...
1717s Unpacking python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ...
1717s Selecting previously unselected package python3-pandas.
1717s Preparing to unpack .../191-python3-pandas_2.2.3+dfsg-5_all.deb ...
1717s Unpacking python3-pandas (2.2.3+dfsg-5) ...
1717s Selecting previously unselected package python3-pluggy.
1717s Preparing to unpack .../192-python3-pluggy_1.5.0-1_all.deb ...
1717s Unpacking python3-pluggy (1.5.0-1) ...
1717s Selecting previously unselected package python3-pybtex.
1717s Preparing to unpack .../193-python3-pybtex_0.24.0-4_all.deb ...
1717s Unpacking python3-pybtex (0.24.0-4) ...
1717s Selecting previously unselected package python3-pybtex-docutils.
1717s Preparing to unpack .../194-python3-pybtex-docutils_1.0.2-1_all.deb ...
1717s Unpacking python3-pybtex-docutils (1.0.2-1) ...
1717s Selecting previously unselected package python3-pytest.
1717s Preparing to unpack .../195-python3-pytest_8.3.3-1_all.deb ...
1717s Unpacking python3-pytest (8.3.3-1) ...
1718s Selecting previously unselected package python3-seaborn.
1718s Preparing to unpack .../196-python3-seaborn_0.13.2-4_all.deb ...
1718s Unpacking python3-seaborn (0.13.2-4) ...
1718s Selecting previously unselected package python3-sklearn-lib:ppc64el.
1718s Preparing to unpack .../197-python3-sklearn-lib_1.4.2+dfsg-6_ppc64el.deb ...
1718s Unpacking python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ...
1718s Selecting previously unselected package python3-sklearn.
1718s Preparing to unpack .../198-python3-sklearn_1.4.2+dfsg-6_all.deb ...
1718s Unpacking python3-sklearn (1.4.2+dfsg-6) ...
1718s Selecting previously unselected package python3-sphinx-sitemap.
1718s Preparing to unpack .../199-python3-sphinx-sitemap_2.6.0-1_all.deb ...
1718s Unpacking python3-sphinx-sitemap (2.6.0-1) ...
1718s Selecting previously unselected package python3-sphinxcontrib.bibtex.
1718s Preparing to unpack .../200-python3-sphinxcontrib.bibtex_2.6.2-1_all.deb ...
1718s Unpacking python3-sphinxcontrib.bibtex (2.6.2-1) ...
1718s Selecting previously unselected package autopkgtest-satdep.
1718s Preparing to unpack .../201-1-autopkgtest-satdep.deb ...
1718s Unpacking autopkgtest-satdep (0) ...
1718s Setting up dh-python (6.20241024) ...
1718s Setting up libgraphite2-3:ppc64el (1.3.14-2ubuntu1) ...
1718s Setting up liblcms2-2:ppc64el (2.16-2) ...
1718s Setting up python3-iniconfig (1.1.1-2) ...
1718s Setting up libpixman-1-0:ppc64el (0.44.0-3) ...
1718s Setting up libsharpyuv0:ppc64el (1.4.0-0.1) ...
1718s Setting up fonts-lato (2.015-1) ...
1718s Setting up fonts-mathjax (2.7.9+dfsg-1) ...
1718s Setting up liblerc4:ppc64el (4.0.0+ds-4ubuntu2) ...
1718s Setting up libjs-mathjax (2.7.9+dfsg-1) ...
1718s Setting up libxrender1:ppc64el (1:0.9.10-1.1build1) ...
1719s Setting up python3-joblib (1.3.2-5) ...
1719s Setting up python3-lz4 (4.0.2+dfsg-1build4) ...
1719s Setting up libxcb-render0:ppc64el (1.17.0-2) ...
1719s Setting up python3-defusedxml (0.7.1-2) ...
1719s Setting up libarchive-zip-perl (1.68-1) ...
1719s Setting up python3-alabaster (0.7.16-0.1) ...
1719s Setting up python3-unicodedata2 (15.1.0+ds-1build1) ...
1719s Setting up fonts-lyx (2.4.2.1-1) ...
1719s Setting up libdebhelper-perl (13.20ubuntu1) ...
1719s Setting up python3-tqdm (4.67.0-1) ...
1720s Setting up python3-threadpoolctl (3.1.0-1) ...
1720s Setting up x11-common (1:7.7+23ubuntu3) ...
1720s Setting up libdeflate0:ppc64el (1.22-1) ...
1720s Setting up m4 (1.4.19-4build1) ...
1720s Setting up python3-latexcodec (3.0.0-1) ...
1720s Setting up libqhull-r8.0:ppc64el (2020.2-6build1) ...
1720s Setting up python3-all (3.12.6-0ubuntu1) ...
1720s Setting up libxcb-shm0:ppc64el (1.17.0-2) ...
1720s Setting up python3-sortedcontainers (2.4.0-2) ...
1721s Setting up libgomp1:ppc64el (14.2.0-8ubuntu1) ...
1721s Setting up python3-freetype (2.5.1-1) ...
1721s Setting up python3-networkx (3.2.1-4ubuntu1) ...
1723s Setting up python3-wheel (0.44.0-1) ...
1723s Setting up libjbig0:ppc64el (2.1-6.1ubuntu2) ...
1723s Setting up python3-mda-xdrlib (0.2.0-3) ...
1723s Setting up libaec0:ppc64el (1.1.3-1) ...
1723s Setting up python3-tz (2024.1-2) ...
1723s Setting up python3-monotonic (1.6-2) ...
1723s Setting up unicode-data (15.1.0-1) ...
1723s Setting up python3-six (1.16.0-7) ...
1724s Setting up python3-roman (4.2-1) ...
1724s Setting up python3-decorator (5.1.1-5) ...
1724s Setting up libfontenc1:ppc64el (1:1.1.8-1build1) ...
1724s Setting up autotools-dev (20220109.1) ...
1724s Setting up libblas3:ppc64el (3.12.0-3build2) ...
1724s 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
1724s Setting up python3-packaging (24.1-1) ...
1724s Setting up libexpat1-dev:ppc64el (2.6.2-2) ...
1724s Setting up python3-pyproject-hooks (1.2.0-1) ...
1724s Setting up python3-snowballstemmer (2.2.0-4build1) ...
1725s Setting up python3-brotli (1.1.0-2build2) ...
1725s Setting up liblzf1:ppc64el (3.6-4) ...
1725s Setting up xfonts-encodings (1:1.0.5-0ubuntu2) ...
1725s Setting up libquadmath0:ppc64el (14.2.0-8ubuntu1) ...
1725s Setting up python3-cycler (0.12.1-1) ...
1725s Setting up libimagequant0:ppc64el (2.18.0-1build1) ...
1725s Setting up fonts-dejavu-mono (2.37-8) ...
1725s Setting up python3-kiwisolver (1.4.7-2build1) ...
1725s Setting up libmpc3:ppc64el (1.3.1-1build2) ...
1725s Setting up cython3 (3.0.11+dfsg-1ubuntu1) ...
1727s Setting up libtcl8.6:ppc64el (8.6.15+dfsg-2) ...
1727s Setting up autopoint (0.22.5-2) ...
1727s Setting up fonts-dejavu-core (2.37-8) ...
1727s Setting up python3-fasteners (0.18-2) ...
1727s Setting up libjpeg-turbo8:ppc64el (2.1.5-2ubuntu2) ...
1727s Setting up python3-toml (0.10.2-1) ...
1727s Setting up python3-installer (0.7.0+dfsg1-3) ...
1727s Setting up libgfortran5:ppc64el (14.2.0-8ubuntu1) ...
1727s Setting up autoconf (2.72-3) ...
1727s Setting up python3-pluggy (1.5.0-1) ...
1727s Setting up libwebp7:ppc64el (1.4.0-0.1) ...
1727s Setting up python3-pybtex (0.24.0-4) ...
1727s Setting up libubsan1:ppc64el (14.2.0-8ubuntu1) ...
1727s Setting up zlib1g-dev:ppc64el (1:1.3.dfsg+really1.3.1-1ubuntu1) ...
1728s Setting up dwz (0.15-1build6) ...
1728s Setting up python3-looseversion (1.3.0-3) ...
1728s Setting up libasan8:ppc64el (14.2.0-8ubuntu1) ...
1728s Setting up libjson-perl (4.10000-1) ...
1728s Setting up libxslt1.1:ppc64el (1.1.39-0exp1ubuntu1) ...
1728s Setting up debugedit (1:5.1-1) ...
1728s Setting up libopenjp2-7:ppc64el (2.5.0-2ubuntu1) ...
1728s Setting up libharfbuzz0b:ppc64el (10.0.1-1) ...
1728s Setting up python3-dateutil (2.9.0-2) ...
1728s Setting up sgml-base (1.31) ...
1728s Setting up python3-msgpack (1.0.3-3build2) ...
1728s Setting up libxss1:ppc64el (1:1.2.3-1build3) ...
1728s Setting up libtsan2:ppc64el (14.2.0-8ubuntu1) ...
1728s Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ...
1728s Setting up python3-mpmath (1.3.0-1) ...
1729s Setting up libisl23:ppc64el (0.27-1) ...
1729s Setting up python3-build (1.2.2-1) ...
1729s Setting up python-matplotlib-data (3.8.3-3) ...
1729s Setting up libwebpmux3:ppc64el (1.4.0-0.1) ...
1729s Setting up python3-appdirs (1.4.4-4) ...
1729s Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ...
1729s Setting up sphinx-rtd-theme-common (3.0.1+dfsg-1) ...
1729s Setting up libcc1-0:ppc64el (14.2.0-8ubuntu1) ...
1729s Setting up liblsan0:ppc64el (14.2.0-8ubuntu1) ...
1729s Setting up libsz2:ppc64el (1.1.3-1) ...
1729s Setting up libitm1:ppc64el (14.2.0-8ubuntu1) ...
1729s Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ...
1729s Setting up python3-imagesize (1.4.1-1) ...
1729s Setting up libjpeg8:ppc64el (8c-2ubuntu11) ...
1729s Setting up automake (1:1.16.5-1.3ubuntu1) ...
1729s update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
1729s Setting up libfile-stripnondeterminism-perl (1.14.0-1) ...
1729s Setting up python3-sympy (1.13.3-1) ...
1738s Setting up liblapack3:ppc64el (3.12.0-3build2) ...
1738s 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
1738s Setting up gettext (0.22.5-2) ...
1738s Setting up pybuild-plugin-pyproject (6.20241024) ...
1738s Setting up fontconfig-config (2.15.0-1.1ubuntu2) ...
1739s Setting up python3-pytest (8.3.3-1) ...
1739s Setting up libwebpdemux2:ppc64el (1.4.0-0.1) ...
1739s Setting up python3-hypothesis (6.116.0-1) ...
1740s Setting up libpython3.12-dev:ppc64el (3.12.7-3) ...
1740s Setting up xfonts-utils (1:7.7+7) ...
1740s Setting up intltool-debian (0.35.0+20060710.6) ...
1740s Setting up python3-fs (2.4.16-4) ...
1740s Setting up libjs-jquery-ui (1.13.2+dfsg-1) ...
1740s Setting up libraqm0:ppc64el (0.10.1-1build1) ...
1740s Setting up python3.12-dev (3.12.7-3) ...
1740s Setting up cpp-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ...
1740s Setting up python3-numpy (1:1.26.4+ds-11ubuntu1) ...
1742s Setting up libjs-sphinxdoc (7.4.7-4) ...
1742s Setting up cpp-14 (14.2.0-8ubuntu1) ...
1742s Setting up dh-strip-nondeterminism (1.14.0-1) ...
1742s Setting up python3-lxml:ppc64el (5.3.0-1) ...
1742s Setting up libtiff6:ppc64el (4.5.1+git230720-4ubuntu4) ...
1742s Setting up xml-core (0.19) ...
1743s Setting up python3-contourpy (1.3.0-2) ...
1743s Setting up libfontconfig1:ppc64el (2.15.0-1.1ubuntu2) ...
1743s Setting up libgcc-14-dev:ppc64el (14.2.0-8ubuntu1) ...
1743s Setting up libhdf5-103-1t64:ppc64el (1.10.10+repack-4ubuntu3) ...
1743s Setting up libstdc++-14-dev:ppc64el (14.2.0-8ubuntu1) ...
1743s Setting up cpp-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ...
1743s Setting up gcc-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ...
1743s Setting up liblbfgsb0:ppc64el (3.0+dfsg.4-1build1) ...
1743s Setting up python3-mrcfile (1.5.3-3) ...
1743s Setting up libhdf5-hl-100t64:ppc64el (1.10.10+repack-4ubuntu3) ...
1743s Setting up libnetcdf19t64:ppc64el (1:4.9.2-6ubuntu1) ...
1743s Setting up libxft2:ppc64el (2.3.6-1build1) ...
1743s Setting up python3-scipy (1.13.1-5) ...
1748s Setting up libpython3-dev:ppc64el (3.12.6-0ubuntu1) ...
1748s Setting up g++-14-powerpc64le-linux-gnu (14.2.0-8ubuntu1) ...
1748s Setting up python3-citeproc (0.6.0-3) ...
1748s Setting up po-debconf (1.0.21+nmu1) ...
1748s Setting up libtk8.6:ppc64el (8.6.15-1) ...
1748s Setting up python3-pandas-lib:ppc64el (2.2.3+dfsg-5) ...
1748s Setting up python3.12-tk (3.12.7-3) ...
1748s Setting up python3-sklearn-lib:ppc64el (1.4.2+dfsg-6) ...
1748s Setting up python3-h5py-serial (3.11.0-5ubuntu1) ...
1749s Setting up python3-gsd (3.3.0-1) ...
1749s Setting up python3-mmtf (1.1.3-1) ...
1749s Setting up fonts-urw-base35 (20200910-8) ...
1749s Setting up libcairo2:ppc64el (1.18.2-2) ...
1749s Setting up python-mdanalysis-doc (2.7.0-5) ...
1750s Setting up gcc-14 (14.2.0-8ubuntu1) ...
1750s Setting up python3-pil:ppc64el (10.4.0-1ubuntu1) ...
1750s Setting up python3-griddataformats (1.0.2-2) ...
1750s Setting up python3-pandas (2.2.3+dfsg-5) ...
1758s Setting up gcc-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ...
1758s Setting up libpython3-all-dev:ppc64el (3.12.6-0ubuntu1) ...
1758s Setting up sphinx-common (7.4.7-4) ...
1758s Setting up python3-dev (3.12.6-0ubuntu1) ...
1758s Setting up python3-h5py (3.11.0-5ubuntu1) ...
1758s Setting up python3-sklearn (1.4.2+dfsg-6) ...
1761s Setting up python3-cftime (1.6.4-1) ...
1761s Setting up cpp (4:14.1.0-2ubuntu1) ...
1761s Setting up g++-14 (14.2.0-8ubuntu1) ...
1761s Setting up python3-netcdf4 (1.7.2-1) ...
1761s Setting up g++-powerpc64le-linux-gnu (4:14.1.0-2ubuntu1) ...
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1761s Setting up tk8.6-blt2.5 (2.5.3+dfsg-7build1) ...
1761s Setting up python3-cairo (1.26.1-2) ...
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1761s Setting up blt (2.5.3+dfsg-7build1) ...
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1821s autopkgtest [19:37:07]: test test-mdanalysis: [-----------------------
1822s skipping tests with SKIP_TEST_LIST=
1833s ============================= test session starts ==============================
1833s platform linux -- Python 3.12.7, pytest-8.3.3, pluggy-1.5.0
1833s rootdir: /tmp/autopkgtest.elFkPf/build.zZp/src
1833s plugins: typeguard-4.4.1, hypothesis-6.116.0
1833s collected 19229 items / 6 skipped
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2563s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py .......... [ 85%]
2591s .......................................                                  [ 85%]
2591s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py .... [ 85%]
2591s ....                                                                     [ 85%]
2592s testsuite/MDAnalysisTests/test_api.py ............................       [ 86%]
2601s testsuite/MDAnalysisTests/topology/test_altloc.py ...                    [ 86%]
2602s testsuite/MDAnalysisTests/topology/test_crd.py ........                  [ 86%]
2602s testsuite/MDAnalysisTests/topology/test_dlpoly.py ...................... [ 86%]
2602s ..........................................                               [ 86%]
2604s testsuite/MDAnalysisTests/topology/test_dms.py ....................      [ 86%]
2604s testsuite/MDAnalysisTests/topology/test_fhiaims.py ............          [ 86%]
2604s testsuite/MDAnalysisTests/topology/test_gms.py ......................... [ 86%]
2604s .....                                                                    [ 86%]
2608s testsuite/MDAnalysisTests/topology/test_gro.py ...............           [ 86%]
2608s testsuite/MDAnalysisTests/topology/test_gsd.py ......................... [ 86%]
2608s ......                                                                   [ 86%]
2608s testsuite/MDAnalysisTests/topology/test_guessers.py .................... [ 87%]
2609s ..............ssssssssss                                                 [ 87%]
2609s testsuite/MDAnalysisTests/topology/test_hoomdxml.py ..................   [ 87%]
2609s testsuite/MDAnalysisTests/topology/test_itp.py ......................... [ 87%]
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2614s testsuite/MDAnalysisTests/topology/test_lammpsdata.py .................. [ 88%]
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2616s testsuite/MDAnalysisTests/topology/test_minimal.py ..................... [ 88%]
2616s ...........                                                              [ 88%]
2616s testsuite/MDAnalysisTests/topology/test_mmtf.py ........................ [ 88%]
2616s ......................................................                   [ 89%]
2617s testsuite/MDAnalysisTests/topology/test_mol2.py ........................ [ 89%]
2617s .......                                                                  [ 89%]
2622s testsuite/MDAnalysisTests/topology/test_pdb.py ......................... [ 89%]
2622s ..........................                                               [ 89%]
2622s testsuite/MDAnalysisTests/topology/test_pdbqt.py .........               [ 89%]
2623s testsuite/MDAnalysisTests/topology/test_pqr.py ....................      [ 89%]
2630s testsuite/MDAnalysisTests/topology/test_psf.py ......................... [ 89%]
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2635s testsuite/MDAnalysisTests/topology/test_top.py ......................... [ 90%]
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2640s ...........                                                              [ 91%]
2640s testsuite/MDAnalysisTests/topology/test_topology_base.py ...             [ 91%]
2640s testsuite/MDAnalysisTests/topology/test_topology_str_types.py .......... [ 91%]
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2651s ..................                                                       [ 91%]
2657s testsuite/MDAnalysisTests/topology/test_tprparser.py ................... [ 91%]
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2704s testsuite/MDAnalysisTests/topology/test_txyz.py ......................   [ 96%]
2704s testsuite/MDAnalysisTests/topology/test_xpdb.py ........                 [ 96%]
2704s testsuite/MDAnalysisTests/topology/test_xyz.py ........................  [ 96%]
2704s testsuite/MDAnalysisTests/transformations/test_base.py .....             [ 96%]
2704s testsuite/MDAnalysisTests/transformations/test_boxdimensions.py ........ [ 96%]
2704s ......                                                                   [ 96%]
2705s testsuite/MDAnalysisTests/transformations/test_fit.py .................. [ 96%]
2705s .........................................                                [ 96%]
2706s testsuite/MDAnalysisTests/transformations/test_nojump.py ............    [ 96%]
2707s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py .... [ 96%]
2707s .                                                                        [ 96%]
2707s testsuite/MDAnalysisTests/transformations/test_rotate.py ............... [ 96%]
2707s ............................                                             [ 97%]
2707s testsuite/MDAnalysisTests/transformations/test_translate.py ............ [ 97%]
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2717s .......                                                                  [ 97%]
2717s testsuite/MDAnalysisTests/utils/test_authors.py .                        [ 97%]
2717s testsuite/MDAnalysisTests/utils/test_datafiles.py ....                   [ 97%]
2717s testsuite/MDAnalysisTests/utils/test_duecredit.py ..............         [ 97%]
2717s testsuite/MDAnalysisTests/utils/test_failure.py .                        [ 97%]
2717s testsuite/MDAnalysisTests/utils/test_imports.py ........................ [ 97%]
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2718s testsuite/MDAnalysisTests/utils/test_log.py .                            [ 98%]
2718s testsuite/MDAnalysisTests/utils/test_meta.py ....                        [ 98%]
2719s testsuite/MDAnalysisTests/utils/test_modelling.py .............          [ 98%]
2720s testsuite/MDAnalysisTests/utils/test_persistence.py .......              [ 98%]
2742s testsuite/MDAnalysisTests/utils/test_pickleio.py ....................... [ 98%]
2742s ..............ss..                                                       [ 98%]
2742s testsuite/MDAnalysisTests/utils/test_qcprot.py ......                    [ 98%]
2745s testsuite/MDAnalysisTests/utils/test_selections.py ..................... [ 98%]
2745s                                                                          [ 98%]
2745s testsuite/MDAnalysisTests/utils/test_streamio.py ....................... [ 98%]
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2746s testsuite/MDAnalysisTests/utils/test_units.py .......................... [ 99%]
2746s .......                                                                  [ 99%]
2747s testsuite/MDAnalysisTests/visualization/test_streamlines.py ...          [100%]
2747s 
2747s =============================== warnings summary ===============================
2747s ../../../../usr/lib/python3/dist-packages/Bio/Application/__init__.py:39
2747s   /usr/lib/python3/dist-packages/Bio/Application/__init__.py:39: BiopythonDeprecationWarning: The Bio.Application modules and modules relying on it have been deprecated.
2747s   
2747s   Due to the on going maintenance burden of keeping command line application
2747s   wrappers up to date, we have decided to deprecate and eventually remove these
2747s   modules.
2747s   
2747s   We instead now recommend building your command line and invoking it directly
2747s   with the subprocess module.
2747s     warnings.warn(
2747s 
2747s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: 2 warnings
2747s testsuite/MDAnalysisTests/analysis/test_align.py: 77 warnings
2747s testsuite/MDAnalysisTests/analysis/test_base.py: 3 warnings
2747s testsuite/MDAnalysisTests/analysis/test_bat.py: 2 warnings
2747s testsuite/MDAnalysisTests/analysis/test_contacts.py: 21 warnings
2747s testsuite/MDAnalysisTests/analysis/test_dielectric.py: 6 warnings
2747s testsuite/MDAnalysisTests/analysis/test_encore.py: 10 warnings
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 7 warnings
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py: 6 warnings
2747s testsuite/MDAnalysisTests/analysis/test_lineardensity.py: 6 warnings
2747s testsuite/MDAnalysisTests/analysis/test_msd.py: 2 warnings
2747s testsuite/MDAnalysisTests/analysis/test_pca.py: 12 warnings
2747s testsuite/MDAnalysisTests/analysis/test_psa.py: 124 warnings
2747s testsuite/MDAnalysisTests/analysis/test_rms.py: 38 warnings
2747s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 72 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 112 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_memory.py: 88 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 7 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
2747s testsuite/MDAnalysisTests/core/test_accumulate.py: 48 warnings
2747s testsuite/MDAnalysisTests/core/test_atom.py: 15 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 170 warnings
2747s testsuite/MDAnalysisTests/core/test_atomselections.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_copying.py: 6 warnings
2747s testsuite/MDAnalysisTests/core/test_groups.py: 11 warnings
2747s testsuite/MDAnalysisTests/core/test_residue.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_residuegroup.py: 23 warnings
2747s testsuite/MDAnalysisTests/core/test_segmentgroup.py: 9 warnings
2747s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 8 warnings
2747s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 31 warnings
2747s testsuite/MDAnalysisTests/lib/test_distances.py: 46 warnings
2747s testsuite/MDAnalysisTests/lib/test_neighborsearch.py: 2 warnings
2747s testsuite/MDAnalysisTests/lib/test_qcprot.py: 2 warnings
2747s testsuite/MDAnalysisTests/lib/test_util.py: 67 warnings
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 3 warnings
2747s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py: 8 warnings
2747s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_minimal.py: 2 warnings
2747s testsuite/MDAnalysisTests/transformations/test_base.py: 1 warning
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 3 warnings
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
2747s testsuite/MDAnalysisTests/utils/test_selections.py: 20 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:165: DeprecationWarning: DCDReader currently makes independent timesteps by copying self.ts while other readers update self.ts inplace. This behavior will be changed in 3.0 to be the same as other readers. Read more at https://github.com/MDAnalysis/mdanalysis/issues/3889 to learn if this change in behavior might affect you.
2747s     warnings.warn("DCDReader currently makes independent timesteps"
2747s 
2747s ../../../../usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hbonds/hbond_autocorrel.py:52: DeprecationWarning: This module was moved to MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel; hbonds.hbond_autocorrel will be removed in 3.0.0.
2747s     warnings.warn(wmsg, category=DeprecationWarning)
2747s 
2747s ../../../../usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[ChemfilesWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[ChemfilesWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[ChemfilesWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chemfiles.py:122: UserWarning: chemfiles package not found, try installing it with 'pip install chemfiles'
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_align.py: 8 warnings
2747s testsuite/MDAnalysisTests/analysis/test_psa.py: 20 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 8 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 13 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:463: UserWarning: No dimensions set for current frame, zeroed unitcell will be written
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_align.py: 5 warnings
2747s testsuite/MDAnalysisTests/analysis/test_encore.py: 203 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_memory.py: 9 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 17 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/memory.py:535: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_align.py: 2 warnings
2747s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
2747s testsuite/MDAnalysisTests/core/test_universe.py: 46 warnings
2747s testsuite/MDAnalysisTests/core/test_updating_atomgroup.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_psf.py: 4 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/adk.psf. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/MOL2Parser.py:234: UserWarning: Unknown elements found for some atoms: {'h1', 'ho', 'c3', 'hc', 'oh'}. These have been given an empty element record.
2747s     warnings.warn("Unknown elements found for some "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_bat.py: 9 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_mol2.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_mol2.py: 3 warnings
2747s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: 
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_bat.py: 7 warnings
2747s testsuite/MDAnalysisTests/analysis/test_contacts.py: 2 warnings
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_nucleicacids.py: 3 warnings
2747s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 9 warnings
2747s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/base.py:447: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     self.times[i] = ts.time
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_bat.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_dlpoly.py: 31 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 4 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 6 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_tng.py: 1 warning
2747s testsuite/MDAnalysisTests/core/test_atom.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 5 warnings
2747s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
2747s testsuite/MDAnalysisTests/topology/test_dlpoly.py: 45 warnings
2747s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 20 warnings
2747s testsuite/MDAnalysisTests/topology/test_xyz.py: 8 warnings
2747s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: A
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_folded
2747s testsuite/MDAnalysisTests/analysis/test_contacts.py::TestContacts::test_villin_unfolded
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_contacts.py:160: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     results.append((ts.time, x.sum() / mask.sum()))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_shape
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_type
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_gridcenter_missing
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_type
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_ValueError_userdefn_xdim_nanvalue
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/density.py:423: UserWarning: Box padding (currently set at 2.0) is not used in user defined grids.
2747s     warnings.warn(msg)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_neqbox
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_userdefn_boxshape
2747s testsuite/MDAnalysisTests/analysis/test_density.py::TestDensityAnalysis::test_warn_userdefn_padding
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/density.py:556: UserWarning: Atom selection does not fit grid --- you may want to define a larger box
2747s     warnings.warn(msg)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_diffusionmap.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
2747s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 8 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 16 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 6 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 21 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 80 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trc.py: 8 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 17 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
2747s testsuite/MDAnalysisTests/core/test_atomselections.py: 2 warnings
2747s testsuite/MDAnalysisTests/core/test_copying.py: 1 warning
2747s testsuite/MDAnalysisTests/core/test_group_traj_access.py: 9 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 11 warnings
2747s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 3 warnings
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 6 warnings
2747s testsuite/MDAnalysisTests/topology/test_pdb.py: 19 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
2747s testsuite/MDAnalysisTests/topology/test_xpdb.py: 8 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_persistence.py: 7 warnings
2747s testsuite/MDAnalysisTests/utils/test_streamio.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:331: UserWarning: Element information is missing, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers.
2747s     warnings.warn("Element information is missing, elements attribute "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_single_frame
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_residue_selections
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestRamachandran::test_ramachandran_attr_warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:400: UserWarning: Cannot determine phi and psi angles for the first or last residues
2747s     warnings.warn("Cannot determine phi and psi angles for the first "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_tpr
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_single_frame
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_plot
2747s testsuite/MDAnalysisTests/analysis/test_dihedrals.py::TestJanin::test_janin_attr_warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/dihedrals.py:582: UserWarning: All residues selected with 'resname ALA CYS* GLY PRO SER THR VAL' have been removed from the selection.
2747s     warnings.warn(f"All residues selected with '{select_remove}' "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_encore.py: 5 warnings
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 34 warnings
2747s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 3 warnings
2747s   /usr/lib/python3.12/multiprocessing/popen_fork.py:66: DeprecationWarning: This process (pid=6868) is multi-threaded, use of fork() may lead to deadlocks in the child.
2747s     self.pid = os.fork()
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_plane_circle
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_ortho_circle
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py::test_local_screw_angles_parallel_axes
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:181: RuntimeWarning: invalid value encountered in divide
2747s     cos = cos_perp, cos_ortho = np.matmul(refs, proj_plane.T)/norms
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 30 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/helix_analysis.py:262: RuntimeWarning: invalid value encountered in divide
2747s     local_axes = (cross_bi.T / mdamath.pnorm(cross_bi)).T  # (n_res-3, 3)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
2747s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:206: RuntimeWarning: Degrees of freedom <= 0 for slice
2747s     ret = _var(a, axis=axis, dtype=dtype, out=out, ddof=ddof,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
2747s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:195: RuntimeWarning: invalid value encountered in divide
2747s     ret = um.true_divide(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_helix_analysis.py: 16 warnings
2747s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:198: RuntimeWarning: invalid value encountered in scalar divide
2747s     ret = ret.dtype.type(ret / rcount)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 15 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 14 warnings
2747s testsuite/MDAnalysisTests/core/test_atomselections.py: 1 warning
2747s testsuite/MDAnalysisTests/core/test_topologyattrs.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_pdb.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:453: UserWarning: 1 A^3 CRYST1 record, this is usually a placeholder. Unit cell dimensions will be set to None.
2747s     warnings.warn("1 A^3 CRYST1 record,"
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 23 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:777: UserWarning: Unit cell dimensions not found. CRYST1 record set to unitary values.
2747s     warnings.warn("Unit cell dimensions not found. "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 22 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'elements' Using default value of ' '
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hole2.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 32 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/topology/test_altloc.py: 1 warning
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 3 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'formalcharges' Using default value of '0'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 13 warnings
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 14 warnings
2747s testsuite/MDAnalysisTests/analysis/test_persistencelength.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 18 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 5 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 39 warnings
2747s testsuite/MDAnalysisTests/core/test_atomselections.py: 14 warnings
2747s testsuite/MDAnalysisTests/core/test_topologyobjects.py: 1 warning
2747s testsuite/MDAnalysisTests/core/test_universe.py: 3 warnings
2747s testsuite/MDAnalysisTests/core/test_wrap.py: 13 warnings
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_minimal.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:119: DeprecationWarning: The TRZ reader is deprecated and will be removed in MDAnalysis version 3.0.0
2747s     warnings.warn(wmsg, DeprecationWarning)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel.py: 9 warnings
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py: 10 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py:377: RuntimeWarning: Desired number of sample points too high, using 6
2747s     warnings.warn("Desired number of sample points too high, using {0}"
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:62: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_continuous_excl
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:79: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:99: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_timecut
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:117: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_intermittent_excl
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:135: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_continuous
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:156: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_intermittent
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:181: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_wronglength_DA
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:210: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_exclusions
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:225: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_bond_type_VE
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:236: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_solve_before_run_VE
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:247: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_unslicable_traj_VE
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:262: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     HBAC(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::TestHydrogenBondAutocorrel::test_repr
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:272: DeprecationWarning: `HydrogenBondAutoCorrel` is deprecated!
2747s   `HydrogenBondAutoCorrel` will be removed in release 3.0.0.
2747s   The class was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbond = HBAC(u,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_find_donors
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:300: DeprecationWarning: `find_hydrogen_donors` is deprecated!
2747s   `find_hydrogen_donors` will be removed in release 3.0.0.
2747s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     D = hbonds.find_hydrogen_donors(H)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py::test_donors_nobonds
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/analysis/test_hydrogenbondautocorrel_deprecated.py:312: DeprecationWarning: `find_hydrogen_donors` is deprecated!
2747s   `find_hydrogen_donors` will be removed in release 3.0.0.
2747s   The function was moved to MDAnalysis.analysis.hbonds.hbond_autocorrel.
2747s     hbonds.find_hydrogen_donors(u.atoms)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, name O, and Acceptor, name O.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_count_by_type
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, name O, and Acceptor, name O.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
2747s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
2747s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:3504: RuntimeWarning: Mean of empty slice.
2747s     return _methods._mean(a, axis=axis, dtype=dtype,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisIdeal::test_logging_step_not_1
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_logging_step_not_1
2747s testsuite/MDAnalysisTests/analysis/test_waterdynamics.py::test_SurvivalProbability_zeroMolecules
2747s   /usr/lib/python3/dist-packages/numpy/core/_methods.py:129: RuntimeWarning: invalid value encountered in scalar divide
2747s     ret = ret.dtype.type(ret / rcount)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_no_hydrogen_bonds
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, type O, and Acceptor, type O.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisNoRes::test_count_by_type
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, type O, and Acceptor, type O.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, None, and Acceptor, name OH2.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisTIP3P_GuessAcceptors_GuessHydrogens_UseTopology_::test_no_hydrogens
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 120.0 between Donor, None, and Acceptor, name OH2.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: donors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection.
2747s     warnings.warn(msg.format(sel))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: hydrogens_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection.
2747s     warnings.warn(msg.format(sel))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:355: UserWarning: acceptors_sel is an empty selection string - no hydrogen bonds will be found. This may be intended, but please check your selection.
2747s     warnings.warn(msg.format(sel))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:3218: UserWarning: Empty string to select atoms, empty group returned.
2747s     warnings.warn("Empty string to select atoms, empty group returned.",
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:733: UserWarning: No hydrogen bonds were found given d-a cutoff of 3.0 between Donor, , and Acceptor, .
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_hydrogenbonds_analysis.py::TestHydrogenBondAnalysisEmptySelections::test_hbond_analysis
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py:765: UserWarning: No hydrogen bonds were found given angle of 150 between Donor, , and Acceptor, .
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
2747s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
2747s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
2747s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: G
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_leaflet.py: 12 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
2747s testsuite/MDAnalysisTests/lib/test_nsgrid.py: 1 warning
2747s testsuite/MDAnalysisTests/visualization/test_streamlines.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: R
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_msd.py::TestMSDSimple::test_random_walk_u_simple
2747s testsuite/MDAnalysisTests/analysis/test_pca.py::test_cosine_content
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element X found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers.
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_msd.py: 1 warning
2747s testsuite/MDAnalysisTests/analysis/test_pca.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_guessers.py: 1 warning
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: X
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
2747s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-9-3.16497]
2747s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
2747s testsuite/MDAnalysisTests/analysis/test_nuclinfo.py::test_phase_cp[RNAA-21-22.07721]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/nuclinfo.py:302: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.)
2747s     phase_ang = (atan2(D, C) + (pi / 2.)) * 180. / pi
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_psa.py::TestPSAnalysis::test_dist_mat_to_vec_i_greater_j
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/psa.py:733: UserWarning: Column index entered (j = 3 is smaller than row index (i = 4). Using symmetric element in upper triangle of distance matrix instead: i --> j, j --> i
2747s     warnings.warn("Column index entered (j = {:d} is smaller than row "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_rdf.py: 20 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:658: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     dt=self.trajectory.ts.dt * step,
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[residue-8]
2747s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[segment-0]
2747s testsuite/MDAnalysisTests/analysis/test_rdf.py::test_ignore_same_residues[chain-8]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/rdf.py:347: DeprecationWarning: The `rdf` attribute was deprecated in MDAnalysis 2.0.0 and will be removed in MDAnalysis 3.0.0. Please use `results.rdf` instead
2747s     warnings.warn(wmsg, DeprecationWarning)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_amber_inpcrd.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
2747s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: D
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_rdf_s.py: 13 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/rdf.py:554: DeprecationWarning: The `u` attribute is superflous and will be removed in MDAnalysis 3.0.0.
2747s     warnings.warn("The `u` attribute is superflous and will be removed "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_density[True-0.021915460340071267]
2747s testsuite/MDAnalysisTests/analysis/test_rdf_s.py::test_overwrite_norm
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/rdf.py:567: DeprecationWarning: The `density` attribute was deprecated in MDAnalysis 2.3.0 and will be removed in MDAnalysis 3.0.0. Please use `norm=density` instead.
2747s     warnings.warn("The `density` attribute was deprecated in "
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_wbridge.py::TestWaterBridgeAnalysis::test_nodata
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1782: MissingDataWarning: No data computed, do run() first.
2747s     warnings.warn(msg, category=MissingDataWarning)
2747s 
2747s testsuite/MDAnalysisTests/analysis/test_wbridge.py: 36 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py:1248: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     self.timesteps.append(self._ts.time)
2747s 
2747s testsuite/MDAnalysisTests/auxiliary/test_core.py: 1 warning
2747s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 16 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:175: UserWarning: AuxStep does not support time selection. Reverting to default
2747s     warnings.warn("{} does not support time selection. Reverting to "
2747s 
2747s testsuite/MDAnalysisTests/auxiliary/test_xvg.py: 20 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:211: UserWarning: AuxStep does not support data selection. Reverting to default
2747s     warnings.warn("{} does not support data selection. Reverting to "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 24 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 7 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gms.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 12 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 1 warning
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 4 warnings
2747s testsuite/MDAnalysisTests/utils/test_persistence.py: 5 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:725: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     return self.ts.dt
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 34 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 1 warning
2747s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 4 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/LAMMPS.py:598: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     ts.data['time'] = step_num * ts.dt
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderFormats::test_set_all_formats
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_ts_time[universe0]
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 597, in close
2747s       self._apply('close')
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py", line 504, in _apply
2747s       return [reader.__getattribute__(method)(**kwargs) for reader in self.readers]
2747s                                                                       ^^^^^^^^^^^^
2747s   AttributeError: 'ChainReader' object has no attribute 'readers'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_chainreader.py::TestChainReaderContinuous::test_missing
2747s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderVacuumBox::test_initial_frame_is_0
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/chain.py:349: UserWarning: Missing frame in continuous chain
2747s     warnings.warn("Missing frame in continuous chain", UserWarning)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 103 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:595: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     time_frame_0 = ts.time - ts.frame*ts.dt  # assumes ts.dt is constant
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 215 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 151 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 300 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:597: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     frame_index = int(math.floor((time_step-time_frame_0+ts.dt/2.)/ts.dt))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 161 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 59 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 124 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:622: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     step = int(math.floor((ts.time-ts.dt/2-self.initial_time)/self.dt))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_copying.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 152 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 136 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:457: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     self._add_step_to_frame_data(ts.time)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resnames]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, tempfactors. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AL
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 3 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: BE
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[resids]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resids, tempfactors. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[names]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: names, tempfactors. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_crd.py::TestCRDWriterMissingAttrs::test_write[tempfactors]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: tempfactors, tempfactors. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 23 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 7 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 24 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/base.py:749: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     if not np.allclose(A.time, B.time):
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1]
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 2]
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_asel_shape[index 1 to 3]
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_empty_asel
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_timeseries_atomgroup_asel_mutex
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices0]
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices1]
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_timeseries_atomindices[indices2]
2747s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_filename_array
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py:326: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDReader::test_empty_dcd
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 181, in close
2747s       self._file.close()
2747s       ^^^^^^^^^^
2747s   AttributeError: 'DCDReader' object has no attribute '_file'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::TestDCDWriter::test_no_container
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py::test_write_no_natoms
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_time_unit
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDWriterClass::test_wrong_unit
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function DCDWriter.__del__ at 0x6a674ee065c0>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 482, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/DCD.py", line 479, in close
2747s       self._file.close()
2747s       ^^^^^^^^^^
2747s   AttributeError: 'DCDWriter' object has no attribute '_file'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_dcd.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 102 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trj.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_windows.py: 2 warnings
2747s testsuite/MDAnalysisTests/core/test_atomselections.py: 3 warnings
2747s testsuite/MDAnalysisTests/topology/test_top.py: 63 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 10 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/TOPParser.py:299: UserWarning: ATOMIC_NUMBER record not found, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers.
2747s     warnings.warn(msg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_dms.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_namdbin.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:754: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     return self.ts.time
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_fhiaims.py::TestFHIAIMSWriter::test_writer_no_atom_names
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[FHIAIMSWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[FHIAIMSWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/FHIAIMS.py:281: UserWarning: Supplied AtomGroup was missing the following attributes: names, ids. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_ts_dt_matches_reader
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_ts_dt_matches_reader
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_ts_dt_matches_reader
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_ts_dt_matches_reader
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_ts_dt_matches_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_ts_dt_matches_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_ts_dt_matches_reader
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/base.py:261: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     assert_equal(reader.ts.dt, reader.dt)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 6 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/auxiliary/base.py:601: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     time_frame = time_frame_0 + frame_index*ts.dt
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReader::test_pickle_reader
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderNoConversion::test_pickle_reader
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROReaderIncompleteVelocities::test_pickle_reader
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROBZ2Reader::test_pickle_reader
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_reader
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/base.py:442: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     reader_p = pickle.loads(pickle.dumps(reader))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 20 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 5 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py: 10 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py: 10 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py:1034: DeprecationWarning: asel argument to timeseries will be renamed to'atomgroup' in 3.0, see #3911
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resnames
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 4 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 2 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:479: UserWarning: missing dimension - setting unit cell to zeroed box [0., 0., 0.]
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 3 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 8 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:228: UserWarning: Empty box [0., 0., 0.] found - treating as missing unit cell. Dimensions set to `None`.
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_write_no_resids
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: resids. These will be written with default values. Alternatively these can be supplied as keyword arguments.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::TestGROWriter::test_writer_no_atom_names
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names. These will be written with default values. Alternatively these can be supplied as keyword arguments.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py: 55 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:216: UserWarning: Not all velocities were present.  Unset velocities set to zero.
2747s     warnings.warn("Not all velocities were present.  "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_gro.py::test_growriter_resid_truncation
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames. These will be written with default values. Alternatively these can be supplied as keyword arguments.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_next_ts_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_next_ts_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_next_ts_reader
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/base.py:604: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     reader_p = pickle.loads(pickle.dumps(reader))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderBaseAPI::test_pickle_last_ts_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::TestXYZReader::test_pickle_last_ts_reader
2747s testsuite/MDAnalysisTests/coordinates/test_xyz.py::Test_XYZBZReader::test_pickle_last_ts_reader
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/base.py:612: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     reader_p = pickle.loads(pickle.dumps(reader))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5MDReaderWithRealTrajectory::test_wrong_driver
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/H5MD.py", line 739, in close
2747s       self._file.close()
2747s       ^^^^^^^^^^
2747s   AttributeError: 'H5MDReader' object has no attribute '_file'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'altLocs' Using default value of ' '
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'icodes' Using default value of ' '
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'occupancies' Using default value of '1.0'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 17 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'tempfactors' Using default value of '0.0'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py: 3 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 16 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'record_types' Using default value of 'ATOM'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_h5md.py::TestH5PYNotInstalled::test_reader_no_h5py
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
2747s       for aux in self.aux_list:
2747s                  ^^^^^^^^^^^^^
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
2747s       return self._auxs.keys()
2747s              ^^^^^^^^^^
2747s   AttributeError: 'H5MDReader' object has no attribute '_auxs'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py: 33 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_windows.py: 20 warnings
2747s testsuite/MDAnalysisTests/topology/test_lammpsdata.py: 18 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/LAMMPSParser.py:632: UserWarning: Guessed all Masses to 1.0
2747s     warnings.warn('Guessed all Masses to 1.0')
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_time_unit
2747s testsuite/MDAnalysisTests/coordinates/test_lammps.py::TestLAMMPSDCDReader::test_wrong_unit
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
2747s       for aux in self.aux_list:
2747s                  ^^^^^^^^^^^^^
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
2747s       return self._auxs.keys()
2747s              ^^^^^^^^^^
2747s   AttributeError: 'DCDReader' object has no attribute '_auxs'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_memory.py::TestMemoryReader::test_timeseries_subarray_view
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/memory.py:545: DeprecationWarning: MemoryReader.timeseries inclusive `stop` indexing will be removed in 3.0 in favour of exclusive indexing
2747s     warnings.warn("MemoryReader.timeseries inclusive `stop` "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_namdbin.py::TestNAMDBINReader::test_pickle_singleframe_reader
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBReader::test_pickle_singleframe_reader
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestExtendedPDBReader::test_pickle_singleframe_reader
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_CRDReader::test_pickle_singleframe_reader
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPSF_PDBReader::test_pickle_singleframe_reader
2747s testsuite/MDAnalysisTests/coordinates/test_pqr.py::TestPQRReader::test_pickle_singleframe_reader
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/base.py:124: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     reader_p = pickle.loads(pickle.dumps(reader))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:554: UserWarning: NCDF trajectory does not contain `time` information; `time` will be set as an increasing index
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_warn_user_no_time_information
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:667: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     ts.time)  # in-place ! (hope this works...)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_chain_times
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:316: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     time_list = [ts.time for ts in u.trajectory]
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFReader4::test_dt
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:322: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     assert u.trajectory.ts.dt == pytest.approx(ref)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netCDF4
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netCDF4
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:700: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
2747s     return self._test_write_trajectory(universe, outfile)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_factors_default
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[-2.0--2.0--2.0--2.0--2.0--2.0]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[1.0-1.0-1.0-1.0-1.0-1.0]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestScipyScaleFactors::test_write_read_write[2.0-4.0-8.0-16.0-32.0-64.0]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:969: UserWarning: Could not find netCDF4 module. Falling back to MUCH slower scipy.io.netcdf implementation for writing.
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriter::test_write_trajectory_netcdf
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterTZ2::test_write_trajectory_netcdf
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_netcdf.py:711: RuntimeWarning: Cannot close a netcdf_file opened with mmap=True, when netcdf_variables or arrays referring to its data still exist. All data arrays obtained from such files refer directly to data on disk, and must be copied before the file can be cleanly closed. (See netcdf_file docstring for more information on mmap.)
2747s     return self._test_write_trajectory(universe, outfile)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 19 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'chainIDs' Using default value of ''
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py: 2 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 28 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py: 1 warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 15 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s testsuite/MDAnalysisTests/utils/test_modelling.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1200: UserWarning: Found missing chainIDs. Corresponding atoms will use value of 'X'
2747s     warnings.warn("Found missing chainIDs."
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[coordinates-angstrom]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[time-picosecond]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_lengths-angstrom]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[cell_angles-degree]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[velocities-angstrom/picosecond]
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterUnits::test_writer_units[forces-kilocalorie/mole/angstrom]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py:1134: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     time = ts.time
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_netcdf.py::TestNCDFWriterErrorsWarnings::test_zero_atoms_VE
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0x6a674eddff60>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 1184, in close
2747s       if self.trjfile is not None:
2747s          ^^^^^^^^^^^^
2747s   AttributeError: 'NCDFWriter' object has no attribute 'trjfile'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resnames
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resnames' Using default value of 'UNK'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 8 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'segids' Using default value of ' '
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_writer_no_resids
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[MultiPDBWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[MultiPDBWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBWriter]
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_iterate_twice
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'resids' Using default value of '1'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py: 6 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py: 4 warnings
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1153: UserWarning: Found no information for attr: 'names' Using default value of 'X'
2747s     warnings.warn("Found no information for attr: '{}'"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[@]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1196: UserWarning: Found chainIDs using unnaccepted character. Corresponding atoms will use value of 'X'
2747s     warnings.warn("Found chainIDs using unnaccepted character."
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBWriter::test_chainid_validated[AA]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDB.py:1192: UserWarning: Found chainIDs with invalid length. Corresponding atoms will use value of 'X'
2747s     warnings.warn("Found chainIDs with invalid length."
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:304: UserWarning: Serial numbers went over 100,000.  Higher serials have been guessed
2747s     warnings.warn("Serial numbers went over 100,000.  "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:423: UserWarning: Invalid atom serials were present, bonds will not be parsed
2747s     warnings.warn("Invalid atom serials were present, bonds will not"
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestPDBXLSerial::test_load
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:215: UserWarning: Invalid atom serials were present, bonds will not be parsed
2747s     warnings.warn("Invalid atom serials were present, "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdb.py::TestWriterAlignments::test_atomname_alignment
2747s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:348: UserWarning: Unknown element  found for some atoms. These have been given an empty element record. If needed they can be guessed using MDAnalysis.topology.guessers.
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
2747s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py: 13 warnings
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 2 warnings
2747s testsuite/MDAnalysisTests/topology/test_pdbqt.py: 9 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s testsuite/MDAnalysisTests/utils/test_streamio.py: 1 warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OA
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_charges
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Ty
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_pdbqt.py::TestPDBQTWriter::test_write_no_chainids_with_segids
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, occupancies, tempfactors. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_dt
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:306: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     assert_equal(ts.dt, 1.0)  # default value
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py::TestTimestep::test_delete_time
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:327: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     assert_equal(ts.time, 0.0)  # default to 1.0 (dt) * 0 (frame)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_timestep_api.py: 13 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/coordinates/test_timestep_api.py:686: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     assert_equal(universe.trajectory.dt, universe.trajectory.ts.dt)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_tng.py::test_pytng_not_present_raises
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1530, in __del__
2747s       for aux in self.aux_list:
2747s                  ^^^^^^^^^^^^^
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1170, in aux_list
2747s       return self._auxs.keys()
2747s              ^^^^^^^^^^
2747s   AttributeError: 'TNGReader' object has no attribute '_auxs'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTriclinicBox::test_trc_n_atoms
2747s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCReaderTruncOctBox::test_universe
2747s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxOrigin::test_universe
2747s testsuite/MDAnalysisTests/coordinates/test_trc.py::TestTRCGenboxEuler::test_universe
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRC.py:265: UserWarning: The trajectory does not contain TIMESTEP blocks!
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trj.py::test_trj_no_natoms
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function ReaderBase.__del__ at 0x6a674eddfc40>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1532, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRJ.py", line 352, in close
2747s       if self.trjfile is None:
2747s          ^^^^^^^^^^^^
2747s   AttributeError: 'TRJReader' object has no attribute 'trjfile'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:546: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     data['time'] = ts.time
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:551: UserWarning: Timestep didn't have the following attributes: 'pressure, pressure_tensor, total_energy, potential_energy, kinetic_energy, temperature, step', these will be set to 0 in the output trajectory
2747s     warnings.warn("Timestep didn't have the following attributes: '{0}', "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::test_deprecated_trz_writer
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_no_box_warning
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_writer_trz_from_other
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter2::test_no_dt_warning
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:567: UserWarning: Timestep didn't have velocity information, this will be set to zero in output trajectory. 
2747s     warnings.warn("Timestep didn't have velocity information, "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZReader::test_read_zero_box
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:559: UserWarning: Timestep didn't have dimensions information, box will be written as all zero values
2747s     warnings.warn("Timestep didn't have dimensions information, "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_trz.py::TestTRZWriter::test_long_title
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function WriterBase.__del__ at 0x6a674eddff60>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/base.py", line 1612, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py", line 605, in close
2747s       if self.trzfile is None:
2747s          ^^^^^^^^^^^^
2747s   AttributeError: 'TRZWriter' object has no attribute 'trzfile'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
2747s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
2747s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
2747s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
2747s testsuite/MDAnalysisTests/topology/test_txyz.py::test_missing_elements_noattribute
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CH3
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_arcpbc_traj_length
2747s testsuite/MDAnalysisTests/coordinates/test_txyz.py::test_pbc_boxsize
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/TXYZParser.py:139: UserWarning: Element information is missing, elements attribute will not be populated. If needed these can be guessed using MDAnalysis.topology.guessers.
2747s     warnings.warn("Element information is missing, elements attribute "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_ts_error[TRZWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[TRZWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[TRZWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRZ.py:428: DeprecationWarning: The TRZ writer is deprecated and will be removed in MDAnalysis version 3.0.0
2747s     warnings.warn(wmsg, DeprecationWarning)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[CRDWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[CRDWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/CRD.py:248: UserWarning: Supplied AtomGroup was missing the following attributes: resnames, resids, names, tempfactors, tempfactors. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[GROWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[GROWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/GRO.py:421: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids. These will be written with default values. Alternatively these can be supplied as keyword arguments.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PDBQTWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PDBQTWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PDBQT.py:296: UserWarning: Supplied AtomGroup was missing the following attributes: altLocs, charges, icodes, names, occupancies, resids, resnames, tempfactors, types, chainids. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[PQRWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[PQRWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/PQR.py:301: UserWarning: Supplied AtomGroup was missing the following attributes: names, resnames, resids, charges, radii. These will be written with default values. 
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_atomgroup[XYZWriter]
2747s testsuite/MDAnalysisTests/coordinates/test_writer_api.py::test_write_with_universe[XYZWriter]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XYZ.py:193: UserWarning: Input AtomGroup or Universe does not have atom elements or names attributes, writer will default atom names to 'X'
2747s     warnings.warn(wmsg)
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_GRO
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_PDB
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriterSingleFrame::test_single_frame_CRD
2747s testsuite/MDAnalysisTests/visualization/test_streamlines.py::test_streamplot_2D
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XTC.py:105: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     time = ts.time
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_GRO
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_PDB
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriterSingleFrame::test_single_frame_CRD
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/TRR.py:116: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     time = ts.time
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCWriter_2::test_no_container
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0x6a674a65c9a0>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
2747s       self._xdr.close()
2747s       ^^^^^^^^^
2747s   AttributeError: 'XTCWriter' object has no attribute '_xdr'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRWriter_2::test_no_container
2747s   /usr/lib/python3/dist-packages/_pytest/unraisableexception.py:85: PytestUnraisableExceptionWarning: Exception ignored in: <function XDRBaseWriter.__del__ at 0x6a674a65c9a0>
2747s   
2747s   Traceback (most recent call last):
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 324, in __del__
2747s       self.close()
2747s     File "/usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py", line 321, in close
2747s       self._xdr.close()
2747s       ^^^^^^^^^
2747s   AttributeError: 'TRRWriter' object has no attribute '_xdr'
2747s   
2747s     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-ubuntu/pytest-0/xtc0/.adk_oplsaa.xtc_offsets.npz failed, reading offsets from trajectory instead.
2747s   Consider setting 'refresh_offsets=True' when loading your Universe.
2747s     warnings.warn(f"Reading offsets from {fname} failed, "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestXTCReader_offsets::test_persistent_offsets_readonly
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-ubuntu/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.xtc. Using slow offset calculation.
2747s     warnings.warn(f"Cannot write lock/offset file in same location as "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_io_fails
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_reload_offsets_if_offsets_readin_value_fails
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:222: UserWarning: Reading offsets from /tmp/pytest-of-ubuntu/pytest-0/xtc1/.adk_oplsaa.trr_offsets.npz failed, reading offsets from trajectory instead.
2747s   Consider setting 'refresh_offsets=True' when loading your Universe.
2747s     warnings.warn(f"Reading offsets from {fname} failed, "
2747s 
2747s testsuite/MDAnalysisTests/coordinates/test_xdr.py::TestTRRReader_offsets::test_persistent_offsets_readonly
2747s   /usr/lib/python3/dist-packages/MDAnalysis/coordinates/XDR.py:202: UserWarning: Cannot write lock/offset file in same location as /tmp/pytest-of-ubuntu/pytest-0/test_persistent_offsets_readon0/adk_oplsaa.trr. Using slow offset calculation.
2747s     warnings.warn(f"Cannot write lock/offset file in same location as "
2747s 
2747s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[atoms]
2747s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[residues]
2747s testsuite/MDAnalysisTests/core/test_accumulate.py::TestAccumulate::test_accumulate_different_func[segments]
2747s   /usr/lib/python3/dist-packages/numpy/core/fromnumeric.py:88: RuntimeWarning: overflow encountered in reduce
2747s     return ufunc.reduce(obj, axis, dtype, out, **passkwargs)
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CB
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CD2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CE2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CG2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: CZ
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HA2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HB3
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD11
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD12
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD13
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD21
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD22
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD23
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HD3
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE21
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE22
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HE3
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG11
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG12
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG13
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG21
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG22
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HG23
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH11
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH12
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH21
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HH22
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HN
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HT3
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: HZ3
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: ND2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NE2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NH2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: NZ
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OD2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OE2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OG1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OH
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT1
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: OT2
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SD
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.gz-xyz]
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py::TestAtomGroupWriting::test_write_frame_none[.bz2-xyz]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: SG
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 17 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 2 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:833: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead.
2747s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 20 warnings
2747s testsuite/MDAnalysisTests/core/test_universe.py: 4 warnings
2747s testsuite/MDAnalysisTests/topology/test_mmtf.py: 3 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/topologyattrs.py:295: DeprecationWarning: The bfactor topology attribute is only provided as an alias to the tempfactor attribute. It will be removed in 3.0. Please use the tempfactor attribute instead.
2747s     warnings.warn(BFACTOR_WARNING, DeprecationWarning)
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
2747s testsuite/MDAnalysisTests/core/test_atomselections.py: 27 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py: 3 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/adk_oplsaa.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 7 warnings
2747s testsuite/MDAnalysisTests/core/test_wrap.py: 3 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1074: RuntimeWarning: invalid value encountered in divide
2747s     return np.einsum('ij,ij->j',coords,weights[:, None]) / weights.sum()
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomgroup.py: 19 warnings
2747s testsuite/MDAnalysisTests/core/test_wrap.py: 12 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:1104: RuntimeWarning: invalid value encountered in divide
2747s     _centers /= _weights.sum(axis=1)[:, None]
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::TestSelectionsNucleicAcids::test_nucleic
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -11.0 to -9.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
2747s     warnings.warn(msg, category=SelectionWarning)
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass -10 -3-0-selkwargs11]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -4.0 to -2.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
2747s     warnings.warn(msg, category=SelectionWarning)
2747s 
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs12]
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-5-selkwargs13]
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-5-selkwargs15]
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-5-selkwargs16]
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3-10-selkwargs17]
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.30000000000000004-10-selkwargs18]
2747s testsuite/MDAnalysisTests/core/test_atomselections.py::test_mass_sel[mass 0.3 0.30000000000000001-10-selkwargs19]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'mass -0.7 to 1.3'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
2747s     warnings.warn(msg, category=SelectionWarning)
2747s 
2747s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-fragments]
2747s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-molecules]
2747s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-residues]
2747s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-group]
2747s testsuite/MDAnalysisTests/core/test_groups.py::TestDecorator::test_wrap_and_unwrap_deprecation[True-True-segments]
2747s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_cog_pbc
2747s testsuite/MDAnalysisTests/transformations/test_rotate.py::test_rotateby_atomgroup_com_pbc
2747s testsuite/MDAnalysisTests/transformations/test_translate.py::test_center_in_box_coords_all_options
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/groups.py:445: DeprecationWarning: The 'pbc' kwarg has been deprecated and will be removed in version 3.0., please use 'wrap' instead
2747s     warnings.warn("The 'pbc' kwarg has been deprecated and will be "
2747s 
2747s testsuite/MDAnalysisTests/core/test_topologyattrs.py::TestDeprecateBFactor::test_deprecate_bfactor_sel
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/selection.py:988: SelectionWarning: Using float equality to select atoms is not recommended because of inherent limitations in representing numbers on computers (see https://docs.python.org/3.8/tutorial/floatingpoint.html for more). Instead, we recommend using a range to select, e.g. 'bfactor 2.0 to 4.0'. If you still want to compare floats, use the `atol` and `rtol` keywords to modify the tolerance for `np.isclose`.
2747s     warnings.warn(msg, category=SelectionWarning)
2747s 
2747s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[serial]
2747s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_angles[openmp]
2747s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[serial]
2747s testsuite/MDAnalysisTests/lib/test_distances.py::TestCythonFunctions::test_numpy_compliance_dihedrals[openmp]
2747s testsuite/MDAnalysisTests/lib/test_util.py::TestGeometryFunctions::test_vectors[x_axis5-y_axis5-nan]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:156: RuntimeWarning: invalid value encountered in scalar divide
2747s     x = np.dot(a, b) / (norm(a) * norm(b))
2747s 
2747s testsuite/MDAnalysisTests/lib/test_nsgrid.py::test_issue_2345
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: AG
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 48 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/lib/test_util.py:293: RuntimeWarning: invalid value encountered in sqrt
2747s     ref[2, 2] = np.sqrt(z * z - ref[2, 0] ** 2 - ref[2, 1] ** 2)
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 53 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/lib/mdamath.py:392: RuntimeWarning: invalid value encountered in sqrt
2747s     box_matrix[2, 2] = np.sqrt(lz * lz - box_matrix[2, 0] ** 2 -
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 339 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/lib/test_util.py:324: RuntimeWarning: invalid value encountered in scalar divide
2747s     a = np.rad2deg(np.arccos(np.dot(tri_vecs[1], tri_vecs[2]) / (y * z)))
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 363 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/lib/test_util.py:325: RuntimeWarning: invalid value encountered in scalar divide
2747s     b = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[2]) / (x * z)))
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 756 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/lib/test_util.py:326: RuntimeWarning: invalid value encountered in scalar divide
2747s     c = np.rad2deg(np.arccos(np.dot(tri_vecs[0], tri_vecs[1]) / (x * y)))
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 43 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: invalid value encountered in scalar divide
2747s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 17 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/lib/test_util.py:315: RuntimeWarning: divide by zero encountered in scalar divide
2747s     ref[2, 1] = z * (cos_a - cos_b * cos_c) / sin_c
2747s 
2747s testsuite/MDAnalysisTests/lib/test_util.py: 14 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: E
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u2]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u3]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u4]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u5]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u6]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u7]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u10]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u11]
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py::test_multiprocess_COG[u14]
2747s   /usr/lib/python3.12/multiprocessing/reduction.py:51: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     cls(buf, protocol).dump(obj)
2747s 
2747s testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py: 23 warnings
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/parallelism/test_multiprocessing.py:216: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     ps = pickle.dumps(ref_reader)
2747s 
2747s testsuite/MDAnalysisTests/parallelism/test_pickle_transformation.py::test_add_PositionAverager_pickle[u0]
2747s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_fwd
2747s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_bwd
2747s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_reset
2747s testsuite/MDAnalysisTests/transformations/test_positionaveraging.py::test_posavging_specific
2747s   /usr/lib/python3/dist-packages/MDAnalysis/transformations/positionaveraging.py:193: Warning: Cannot average position for non sequentialiterations. Averager will be reset.
2747s     warnings.warn('Cannot average position for non sequential'
2747s 
2747s testsuite/MDAnalysisTests/topology/test_guessers.py::TestGuessMasses::test_guess_masses_miss
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: Z
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/topology/test_hoomdxml.py::TestHoomdXMLParser::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-name]
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-resname]
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-type]
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-segid]
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py::test_str_types[XML-/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2-moltype]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/C12x64.xml.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py: 10 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/gromacs_ala10.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoMass::test_mass_guess
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/itp_nomass.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_charge_parse
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPAtomtypes::test_mass_parse_or_guess
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/atomtypes_charge.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_bonds_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestDifferentDirectivesITP::test_dihedrals_identity
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/edited_itp.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPNoKeywords::test_whether_settles_types
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestITPKeywords::test_whether_settles_types
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tip5p.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestNestedIfs::test_heavy_atom
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/spce.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestReadTop::test_sequential
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/gromacs_ala10.top. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relstring
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relpath
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../sub1/test.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_itp.py::TestRelativePath::test_relative_path
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for ../test.itp. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_pdb.py::test_PDB_no_resid
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/PDBParser.py:290: UserWarning: PDB file is missing resid information.  Defaulted to '1'
2747s     warnings.warn("PDB file is missing resid information.  "
2747s 
2747s testsuite/MDAnalysisTests/topology/test_pdb.py::test_wrong_elements_warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/guessers.py:146: UserWarning: Failed to guess the mass for the following atom types: XX
2747s     warnings.warn("Failed to guess the mass for the following atom types: {}".format(atom_type))
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_creates_universe[bz2]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_creates_universe_bz2_0/file.psf.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_bonds_atom_counts[bz2]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_bonds_atom_counts_bz2_0/file.psf.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_angles_atom_counts[bz2]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_angles_atom_counts_bz2_0/file.psf.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser::test_dihedrals_atom_counts[bz2]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/pytest-of-ubuntu/pytest-0/test_dihedrals_atom_counts_bz20/file.psf.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestNAMDPSFParser::test_creates_universe
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/namd_cgenff.psf. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParser2::test_creates_universe
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/2r9r-1b.psf. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::TestPSFParserNoTop::test_creates_universe
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/adk_notop.psf. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_psf.py::test_psf_nosegid
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/nosegid.psf. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/ache.prmtop. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_bonds_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_angles_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_dihedrals_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_impropers_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMChainidParser::test_chainIDs
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/ache_chainid.prmtop.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/anti.top. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py: 5 warnings
2747s testsuite/MDAnalysisTests/topology/test_topology_str_types.py: 5 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/tz2.truncoct.parm7.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_bonds_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_angles_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_dihedrals_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRM2::test_impropers_atom_counts
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/capped-ala.prmtop. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_bonds_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_angles_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_dihedrals_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST::test_impropers_atom_counts
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.parm7. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py: 42 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/topology/TOPParser.py:306: UserWarning: Unknown ATOMIC_NUMBER value found for some atoms, these have been given an empty element record. If needed these can be guessed using MDAnalysis.topology.guessers.
2747s     warnings.warn(msg)
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_bonds_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_angles_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_dihedrals_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMNCRST_negative::test_impropers_atom_counts
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/ace_mbondi3.negative.parm7. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_creates_universe
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_bonds_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_angles_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_dihedrals_atom_counts
2747s testsuite/MDAnalysisTests/topology/test_top.py::TestPRMEP::test_impropers_atom_counts
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/Amber/ala.ff19SB.OPC.parm7.bz2. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.2.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.3.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.4.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.5.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.6.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.0.7.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.1.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.2.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.3.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.4.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_4.5.5.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.2.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.4.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.0.5.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_5.1.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2018.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2019-beta3.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2020_double.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2021_double.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2022-rc1.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRGromacsVersions::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2023.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPRDouble::test_creates_universe
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/drew_gmx_4.5.5.double.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/topology/test_tprparser.py::TestTPR46x::test_creates_universe[/tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/core/universe.py:147: UserWarning: No coordinate reader found for /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/data/tprs/ab42_gmx_4.6.1.tpr. Skipping this file.
2747s     warnings.warn('No coordinate reader found for {}. Skipping '
2747s 
2747s testsuite/MDAnalysisTests/transformations/test_fit.py::test_fit_translation_no_masses
2747s   /usr/lib/python3/dist-packages/MDAnalysis/analysis/align.py:1509: SelectionWarning: Atoms could not be matched since they don't contain masses.
2747s     warnings.warn(msg, category=SelectionWarning)
2747s 
2747s testsuite/MDAnalysisTests/transformations/test_nojump.py::test_nojump_constantvel_stride_2
2747s   /usr/lib/python3/dist-packages/MDAnalysis/transformations/nojump.py:139: UserWarning: NoJump detected that the interval between frames is unequal.We are resetting the reference frame to the current timestep.
2747s     warnings.warn(
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:60: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     return pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_pickle_unpickle_empty
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:86: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     pickle_str = pickle.dumps(ag, protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_two_ag
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:65: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     return pickle.dumps((ag, ag_2), protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe_f
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:70: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     return pickle.dumps((universe, ag), protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestAtomGroupPickle::test_unpickle_ag_with_universe
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:75: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     return pickle.dumps((ag, universe), protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:123: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     pickle_str = pickle.dumps(uag, protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_persistence.py::TestPicklingUpdatingAtomGroups::test_pickling_uag_of_uag
2747s   /tmp/autopkgtest.elFkPf/build.zZp/src/testsuite/MDAnalysisTests/utils/test_persistence.py:131: UserWarning: Reader has no dt information, set to 1.0 ps
2747s     pickle_str = pickle.dumps(uag2, protocol=pickle.HIGHEST_PROTOCOL)
2747s 
2747s testsuite/MDAnalysisTests/utils/test_streamio.py: 10 warnings
2747s   /usr/lib/python3/dist-packages/MDAnalysis/lib/util.py:676: RuntimeWarning: Constructed NamedStream from a NamedStream
2747s     warnings.warn("Constructed NamedStream from a NamedStream",
2747s 
2747s testsuite/MDAnalysisTests/utils/test_units.py::TestConstants::test_constant[Boltzman_constant-0.008314462159]
2747s   /usr/lib/python3/dist-packages/MDAnalysis/units.py:183: DeprecationWarning: Please use 'Boltzmann_constant' henceforth. The key 'Boltzman_constant' was a typo and will be removed in MDAnalysis 2.8.0.
2747s     warnings.warn(wmsg, DeprecationWarning)
2747s 
2747s -- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
2747s = 18632 passed, 594 skipped, 7 xfailed, 2 xpassed, 8130 warnings in 924.84s (0:15:24) =
2771s 
2771s DueCredit Report:
2771s - Molecular simulation analysis library / MDAnalysis (v 2.7.0) [1, 2]
2771s   - Bond-Angle-Torsions Coordinate Transformation / MDAnalysis.analysis.bat.BAT (v 2.7.0) [3]
2771s   - Dielectric analysis / MDAnalysis.analysis.dielectric (v 2.7.0) [4]
2771s   - ENCORE Ensemble Comparison / MDAnalysis.analysis.encore (v 2.7.0) [5]
2771s   - HOLE program, HOLE trajectory analysis with orderparameters / MDAnalysis.analysis.hole2 (v 2.7.0) [6, 7, 8]
2771s   - Hydrogen bond analysis implementation / MDAnalysis.analysis.hydrogenbonds.hbond_analysis (v 2.7.0) [9]
2771s   - Hydrogen bonding autocorrelation time / MDAnalysis.analysis.hydrogenbonds.hbond_autocorrel (v 2.7.0) [10]
2771s   - LeafletFinder algorithm / MDAnalysis.analysis.leaflet (v 2.7.0) [2]
2771s   - FCA fast correlation algorithm, Mean Squared Displacements with tidynamics / MDAnalysis.analysis.msd (v 2.7.0) [11, 12]
2771s   - Cumulative overlap / MDAnalysis.analysis.pca (v 2.7.0) [13]
2771s   - Path Similarity Analysis algorithm and implementation / MDAnalysis.analysis.psa (v 2.7.0) [14]
2771s   - Specifications of the H5MD standard, MDAnalysis trajectory reader/writer of the H5MDformat / MDAnalysis.coordinates.H5MD (v 1.1, 2.7.0) [15, 16]
2771s   - MMTF Reader / MDAnalysis.coordinates.MMTF (v 2.7.0) [17]
2771s   - The TNG paper / MDAnalysis.coordinates.TNG (v 2.7.0) [18]
2771s   - QCProt implementation / MDAnalysis.lib.qcprot (v 2.7.0) [19, 20]
2771s   - MMTF Parser / MDAnalysis.topology.MMTFParser (v 2.7.0) [17]
2771s   - Works through the orthogonal case for unwrapping, and proposes the non-orthogonal approach. / MDAnalysis.transformations.nojump (v 2.7.0) [21]
2771s - Scientific tools library / numpy (v 1.26.4) [22]
2771s 
2771s 2 packages cited
2771s 16 modules cited
2771s 0 functions cited
2771s 
2771s References
2771s ----------
2771s 
2771s [1] Gowers, R. et al., 2016. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the 15th Python in Science Conference. SciPy.  SciPy, pp. 98–105.
2771s [2] Michaud‐Agrawal, N. et al., 2011. MDAnalysis: A toolkit for the analysis of molecular dynamics simulations. Journal of Computational Chemistry, 32(10), pp.2319–2327.
2771s [3] Minh, D.D.L., 2019. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors. Journal of Computational Chemistry, 41(7), pp.715–730.
2771s [4] Neumann, M., 1983. Dipole moment fluctuation formulas in computer simulations of polar systems. Molecular Physics, 50(4), pp.841–858.
2771s [5] Tiberti, M. et al., 2015. ENCORE: Software for Quantitative Ensemble Comparison B. L. de Groot, ed.. PLOS Computational Biology, 11(10), p.1004415.
2771s [6] Smart, O.S., Goodfellow, J.M. & Wallace, B.A., 1993. The pore dimensions of gramicidin A. Biophysical Journal, 65(6), pp.2455–2460.
2771s [7] Smart, O.S. et al., 1996. HOLE: A program for the analysis of the pore dimensions of ion channel structural models. Journal of Molecular Graphics, 14(6), pp.354–360.
2771s [8] Stelzl, L.S. et al., 2014. Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY. Journal of Molecular Biology, 426(3), pp.735–751.
2771s [9] Smith, P. et al., 2019. On the interaction of hyaluronic acid with synovial fluid lipid membranes. Physical Chemistry Chemical Physics, 21(19), pp.9845–9857.
2771s [10] Gowers, R.J. & Carbone, P., 2015. A multiscale approach to model hydrogen bonding: The case of polyamide. The Journal of Chemical Physics, 142(22).
2771s [11] de Buyl, P., 2018. tidynamics: A tiny package to compute the dynamics of stochastic and molecular simulations. Journal of Open Source Software, 3(28), p.877.
2771s [12] Calandrini, V. et al., 2011. nMoldyn - Interfacing spectroscopic experiments, molecular dynamics simulations and models for time correlation functions. École thématique de la Société Française de la Neutronique, 12, pp.201–232.
2771s [13] Yang, L. et al., 2008. Close Correspondence between the Motions from Principal Component Analysis of Multiple HIV-1 Protease Structures and Elastic Network Modes. Structure, 16(2), pp.321–330.
2771s [14] Seyler, S.L. et al., 2015. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways E. Tajkhorshid, ed.. PLOS Computational Biology, 11(10), p.1004568.
2771s [15] Jakupovic, E. & Beckstein, O., 2021. MPI-parallel Molecular Dynamics Trajectory Analysis with the H5MD Format in the MDAnalysis Python Package. In Proceedings of the 20th Python in Science Conference. SciPy.  SciPy, pp. 40–48.
2771s [16] de Buyl, P., Colberg, P.H. & Höfling, F., 2014. H5MD: A structured, efficient, and portable file format for molecular data. Computer Physics Communications, 185(6), pp.1546–1553.
2771s [17] Bradley, A.R. et al., 2017. MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures D. Schneidman, ed.. PLOS Computational Biology, 13(6), p.1005575.
2771s [18] Lundborg, M. et al., 2013. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations. Journal of Computational Chemistry, 35(3), pp.260–269.
2771s [19] Theobald, D.L., 2005. Rapid calculation of RMSDs using a quaternion-based characteristic polynomial. Acta Crystallographica Section A Foundations of Crystallography, 61(4), pp.478–480.
2771s [20] Liu, P., Agrafiotis, D.K. & Theobald, D.L., Fast determination of the optimal rotational matrix for macromolecular superpositions. Journal of Computational Chemistry, 31(7), pp.1561–1563.
2771s [21] Kulke, M. & Vermaas, J.V., 2022. Reversible Unwrapping Algorithm for Constant-Pressure Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 18(10), pp.6161–6171.
2771s [22] Van Der Walt, S., Colbert, S.C. & Varoquaux, G., 2011. The NumPy array: a structure for efficient numerical computation. Computing in Science & Engineering, 13(2), pp.22–30.
2773s autopkgtest [19:52:59]: test test-mdanalysis: -----------------------]
2773s autopkgtest [19:52:59]: test test-mdanalysis:  - - - - - - - - - - results - - - - - - - - - -
2773s test-mdanalysis      PASS
2774s autopkgtest [19:53:00]: @@@@@@@@@@@@@@@@@@@@ summary
2774s test-mdanalysis      PASS