Started by timer
Running as SYSTEM
Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/12-Labours-API
[WS-CLEANUP] Deleting project workspace...
[WS-CLEANUP] Deferred wipeout is used...
[WS-CLEANUP] Done
The recommended git tool is: NONE
No credentials specified
Cloning the remote Git repository
Cloning repository https://github.com/ABI-Software/12-labours-api.git
> git init /home/cmiss/Jenkins/workspace/12-Labours-API # timeout=10
Fetching upstream changes from https://github.com/ABI-Software/12-labours-api.git
> git --version # timeout=10
> git --version # 'git version 2.25.1'
> git fetch --tags --force --progress -- https://github.com/ABI-Software/12-labours-api.git +refs/heads/*:refs/remotes/origin/* # timeout=10
> git config remote.origin.url https://github.com/ABI-Software/12-labours-api.git # timeout=10
> git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
> git rev-parse refs/remotes/origin/dev^{commit} # timeout=10
Checking out Revision fed7495860d0492a0d83f51077693f3de98e748d (refs/remotes/origin/dev)
> git config core.sparsecheckout # timeout=10
> git checkout -f fed7495860d0492a0d83f51077693f3de98e748d # timeout=10
Commit message: "Merge pull request #43 from ddjnw1yu/access-control"
> git rev-list --no-walk fed7495860d0492a0d83f51077693f3de98e748d # timeout=10
[12-Labours-API] $ /usr/bin/python3.9 /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenv.py /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9
/home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenv.py:1041: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
import imp
Using base prefix '/usr'
New python executable in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/bin/python3.9
Also creating executable in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/bin/python
Installing setuptools, pip, wheel...done.
[12-Labours-API] $ /bin/sh -xe /tmp/shiningpanda1674815880197003032.sh
+ pwd
+ export PYTHONPATH=/home/cmiss/Jenkins/workspace/12-Labours-API
+ pip install -r requirements.txt
Collecting fastapi==0.80.0 (from -r requirements.txt (line 1))
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Using cached httpcore-0.16.3-py3-none-any.whl (69 kB)
Using cached sniffio-1.3.1-py3-none-any.whl (10 kB)
Using cached idna-3.8-py3-none-any.whl (66 kB)
Downloading marshmallow-3.22.0-py3-none-any.whl (49 kB)
Downloading multidict-6.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (124 kB)
Downloading numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 19.5/19.5 MB 93.7 MB/s eta 0:00:00
Using cached pyrsistent-0.20.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (117 kB)
Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
Downloading PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 737.4/737.4 kB 22.5 MB/s eta 0:00:00
Using cached rfc3986-1.5.0-py2.py3-none-any.whl (31 kB)
Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Using cached typing_inspect-0.9.0-py3-none-any.whl (8.8 kB)
Downloading yarl-1.11.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (453 kB)
Using cached wcwidth-0.2.13-py2.py3-none-any.whl (34 kB)
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Using cached mypy_extensions-1.0.0-py3-none-any.whl (4.7 kB)
Using cached packaging-24.1-py3-none-any.whl (53 kB)
Building wheels for collected packages: indexclient
Building wheel for indexclient (setup.py): started
Building wheel for indexclient (setup.py): finished with status 'done'
Created wheel for indexclient: filename=indexclient-2.3.1-py3-none-any.whl size=17881 sha256=0533cc9d99ab04029f9913bda9ab9efdedc8e82a08247376d85c457e2bee7db3
Stored in directory: /home/cmiss/.cache/pip/wheels/af/04/e4/4a68c4c05e5c98749b463c23c06d0e2e1abebe506bd68ab75b
Successfully built indexclient
Installing collected packages: wcwidth, rfc3986, pytz, cdislogging, asyncio, xmltodict, urllib3, typing-extensions, tqdm, sniffio, six, PyYAML, python-json-logger, python-dotenv, pyrsistent, PyJWT, pydicom, PrettyTable, packaging, numpy, mypy-extensions, idna, humanfriendly, h11, gunicorn, greenlet, graphql-core, frozenlist, fastavro, exceptiongroup, defusedxml, click, charset-normalizer, certifi, backoff, attrs, async-timeout, aiohappyeyeballs, aiofiles, uvicorn, typing-inspect, sqlalchemy, sgqlc, requests, python-irodsclient, python-dateutil, pydantic, multidict, marshmallow, jsonschema, anyio, aiosignal, yarl, starlette, pandas, indexclient, httpcore, dictionaryutils, dataclasses-json, httpx, gen3dictionary, fastapi, aiohttp, pyorthanc, fastapi-utils, drsclient, pypfb, gen3
Successfully installed PrettyTable-3.11.0 PyJWT-2.7.0 PyYAML-6.0.2 aiofiles-0.8.0 aiohappyeyeballs-2.4.0 aiohttp-3.10.5 aiosignal-1.3.1 anyio-4.4.0 async-timeout-4.0.3 asyncio-3.4.3 attrs-24.2.0 backoff-1.11.1 cdislogging-1.1.1 certifi-2024.8.30 charset-normalizer-3.3.2 click-8.1.7 dataclasses-json-0.6.7 defusedxml-0.7.1 dictionaryutils-3.4.10 drsclient-0.2.3 exceptiongroup-1.2.2 fastapi-0.80.0 fastapi-utils-0.2.1 fastavro-1.8.4 frozenlist-1.4.1 gen3-4.19.1 gen3dictionary-2.0.3 graphql-core-3.2.4 greenlet-3.1.0 gunicorn-20.1.0 h11-0.14.0 httpcore-0.16.3 httpx-0.23.3 humanfriendly-10.0 idna-3.8 indexclient-2.3.1 jsonschema-3.2.0 marshmallow-3.22.0 multidict-6.1.0 mypy-extensions-1.0.0 numpy-2.0.2 packaging-24.1 pandas-1.5.3 pydantic-1.10.18 pydicom-2.4.4 pyorthanc-1.11.5 pypfb-0.5.29 pyrsistent-0.20.0 python-dateutil-2.9.0.post0 python-dotenv-0.20.0 python-irodsclient-1.1.8 python-json-logger-0.1.11 pytz-2024.1 requests-2.32.3 rfc3986-1.5.0 sgqlc-16.3 six-1.16.0 sniffio-1.3.1 sqlalchemy-1.4.54 starlette-0.19.1 tqdm-4.66.5 typing-extensions-4.12.2 typing-inspect-0.9.0 urllib3-1.26.20 uvicorn-0.18.2 wcwidth-0.2.13 xmltodict-0.13.0 yarl-1.11.1
+ pip install -r requirements-dev.txt
Collecting pytest==7.1.2 (from -r requirements-dev.txt (line 1))
Using cached pytest-7.1.2-py3-none-any.whl.metadata (7.8 kB)
Collecting pytest-timeout==2.1.0 (from -r requirements-dev.txt (line 2))
Using cached pytest_timeout-2.1.0-py3-none-any.whl.metadata (16 kB)
Collecting anyio==3.6.2 (from -r requirements-dev.txt (line 3))
Using cached anyio-3.6.2-py3-none-any.whl.metadata (4.7 kB)
Requirement already satisfied: attrs>=19.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (24.2.0)
Collecting iniconfig (from pytest==7.1.2->-r requirements-dev.txt (line 1))
Using cached iniconfig-2.0.0-py3-none-any.whl.metadata (2.6 kB)
Requirement already satisfied: packaging in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from pytest==7.1.2->-r requirements-dev.txt (line 1)) (24.1)
Collecting pluggy<2.0,>=0.12 (from pytest==7.1.2->-r requirements-dev.txt (line 1))
Using cached pluggy-1.5.0-py3-none-any.whl.metadata (4.8 kB)
Collecting py>=1.8.2 (from pytest==7.1.2->-r requirements-dev.txt (line 1))
Using cached py-1.11.0-py2.py3-none-any.whl.metadata (2.8 kB)
Collecting tomli>=1.0.0 (from pytest==7.1.2->-r requirements-dev.txt (line 1))
Using cached tomli-2.0.1-py3-none-any.whl.metadata (8.9 kB)
Requirement already satisfied: idna>=2.8 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (3.8)
Requirement already satisfied: sniffio>=1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages (from anyio==3.6.2->-r requirements-dev.txt (line 3)) (1.3.1)
Using cached pytest-7.1.2-py3-none-any.whl (297 kB)
Using cached pytest_timeout-2.1.0-py3-none-any.whl (12 kB)
Using cached anyio-3.6.2-py3-none-any.whl (80 kB)
Using cached pluggy-1.5.0-py3-none-any.whl (20 kB)
Using cached py-1.11.0-py2.py3-none-any.whl (98 kB)
Using cached tomli-2.0.1-py3-none-any.whl (12 kB)
Using cached iniconfig-2.0.0-py3-none-any.whl (5.9 kB)
Installing collected packages: tomli, py, pluggy, iniconfig, anyio, pytest, pytest-timeout
Attempting uninstall: anyio
Found existing installation: anyio 4.4.0
Uninstalling anyio-4.4.0:
Successfully uninstalled anyio-4.4.0
Successfully installed anyio-3.6.2 iniconfig-2.0.0 pluggy-1.5.0 py-1.11.0 pytest-7.1.2 pytest-timeout-2.1.0 tomli-2.0.1
+ pytest
============================= test session starts ==============================
platform linux -- Python 3.9.20, pytest-7.1.2, pluggy-1.5.0
rootdir: /home/cmiss/Jenkins/workspace/12-Labours-API
plugins: anyio-3.6.2, timeout-2.1.0
collected 23 items / 6 errors
==================================== ERRORS ====================================
______________ ERROR collecting tests/test_api/test_access_api.py ______________
tests/test_api/test_access_api.py:4: in <module>
from app.main import app
app/main.py:57: in <module>
from services.external_service import ExternalService
services/external_service.py:7: in <module>
from services.gen3.gen3_service import Gen3Service
services/gen3/gen3_service.py:16: in <module>
from gen3.submission import Gen3Submission
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module>
import pandas as pd
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module>
from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module>
from pandas.compat.numpy import (
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module>
from pandas.util.version import Version
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module>
from pandas.util._decorators import ( # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
_______________ ERROR collecting tests/test_api/test_gen3_api.py _______________
tests/test_api/test_gen3_api.py:4: in <module>
from app.main import app
app/main.py:57: in <module>
from services.external_service import ExternalService
services/external_service.py:7: in <module>
from services.gen3.gen3_service import Gen3Service
services/gen3/gen3_service.py:16: in <module>
from gen3.submission import Gen3Submission
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module>
import pandas as pd
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module>
from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module>
from pandas.compat.numpy import (
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module>
from pandas.util.version import Version
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module>
from pandas.util._decorators import ( # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
______________ ERROR collecting tests/test_api/test_irods_api.py _______________
tests/test_api/test_irods_api.py:4: in <module>
from app.main import app
app/main.py:57: in <module>
from services.external_service import ExternalService
services/external_service.py:7: in <module>
from services.gen3.gen3_service import Gen3Service
services/gen3/gen3_service.py:16: in <module>
from gen3.submission import Gen3Submission
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module>
import pandas as pd
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module>
from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module>
from pandas.compat.numpy import (
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module>
from pandas.util.version import Version
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module>
from pandas.util._decorators import ( # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
_____________ ERROR collecting tests/test_api/test_orthanc_api.py ______________
tests/test_api/test_orthanc_api.py:4: in <module>
from app.main import app
app/main.py:57: in <module>
from services.external_service import ExternalService
services/external_service.py:7: in <module>
from services.gen3.gen3_service import Gen3Service
services/gen3/gen3_service.py:16: in <module>
from gen3.submission import Gen3Submission
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module>
import pandas as pd
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module>
from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module>
from pandas.compat.numpy import (
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module>
from pandas.util.version import Version
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module>
from pandas.util._decorators import ( # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
______________ ERROR collecting tests/test_data/test_gen3_data.py ______________
tests/test_data/test_gen3_data.py:5: in <module>
from app.main import app
app/main.py:57: in <module>
from services.external_service import ExternalService
services/external_service.py:7: in <module>
from services.gen3.gen3_service import Gen3Service
services/gen3/gen3_service.py:16: in <module>
from gen3.submission import Gen3Submission
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module>
import pandas as pd
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module>
from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module>
from pandas.compat.numpy import (
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module>
from pandas.util.version import Version
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module>
from pandas.util._decorators import ( # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
_____________ ERROR collecting tests/test_data/test_irods_data.py ______________
tests/test_data/test_irods_data.py:4: in <module>
from app.main import app
app/main.py:57: in <module>
from services.external_service import ExternalService
services/external_service.py:7: in <module>
from services.gen3.gen3_service import Gen3Service
services/gen3/gen3_service.py:16: in <module>
from gen3.submission import Gen3Submission
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/gen3/submission.py:6: in <module>
import pandas as pd
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/__init__.py:22: in <module>
from pandas.compat import is_numpy_dev as _is_numpy_dev # pyright: ignore # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/__init__.py:18: in <module>
from pandas.compat.numpy import (
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:4: in <module>
from pandas.util.version import Version
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/__init__.py:2: in <module>
from pandas.util._decorators import ( # noqa:F401
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/util/_decorators.py:14: in <module>
from pandas._libs.properties import cache_readonly
../../shiningpanda/jobs/084398e7/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pandas/_libs/__init__.py:13: in <module>
from pandas._libs.interval import Interval
pandas/_libs/interval.pyx:1: in init pandas._libs.interval
???
E ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject
=========================== short test summary info ============================
ERROR tests/test_api/test_access_api.py - ValueError: numpy.dtype size change...
ERROR tests/test_api/test_gen3_api.py - ValueError: numpy.dtype size changed,...
ERROR tests/test_api/test_irods_api.py - ValueError: numpy.dtype size changed...
ERROR tests/test_api/test_orthanc_api.py - ValueError: numpy.dtype size chang...
ERROR tests/test_data/test_gen3_data.py - ValueError: numpy.dtype size change...
ERROR tests/test_data/test_irods_data.py - ValueError: numpy.dtype size chang...
!!!!!!!!!!!!!!!!!!! Interrupted: 6 errors during collection !!!!!!!!!!!!!!!!!!!!
============================== 6 errors in 1.39s ===============================
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #2656 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE