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[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 17.646 s
[INFO] Finished at: 2026-01-13T14:01:52Z
[INFO] ------------------------------------------------------------------------
+ source /home/omero/workspace/OMERO-server/.venv3/bin/activate
++ deactivate nondestructive
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ unset VIRTUAL_ENV_PROMPT
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
++ export VIRTUAL_ENV
++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
++ export PATH
++ '[' -n '' ']'
++ '[' -z '' ']'
++ _OLD_VIRTUAL_PS1=
++ PS1='(.venv3) '
++ export PS1
++ VIRTUAL_ENV_PROMPT='(.venv3) '
++ export VIRTUAL_ENV_PROMPT
++ hash -r
+ pip install -U pip
Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
Collecting pip
Using cached pip-25.3-py3-none-any.whl (1.8 MB)
Installing collected packages: pip
Attempting uninstall: pip
Found existing installation: pip 22.3.1
Uninstalling pip-22.3.1:
Successfully uninstalled pip-22.3.1
Successfully installed pip-25.3
+ pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
Collecting zeroc-ice==3.6.5
Downloading https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 22.9 MB/s 0:00:01
Installing collected packages: zeroc-ice
Successfully installed zeroc-ice-3.6.5
+ pip install markdown
Collecting markdown
Using cached markdown-3.10-py3-none-any.whl.metadata (5.1 kB)
Using cached markdown-3.10-py3-none-any.whl (107 kB)
Installing collected packages: markdown
Successfully installed markdown-3.10
+ pip install reportlab
Collecting reportlab
Using cached reportlab-4.4.7-py3-none-any.whl.metadata (1.7 kB)
Collecting pillow>=9.0.0 (from reportlab)
Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
Collecting charset-normalizer (from reportlab)
Using cached charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (37 kB)
Using cached reportlab-4.4.7-py3-none-any.whl (2.0 MB)
Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB)
Using cached charset_normalizer-3.4.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (151 kB)
Installing collected packages: pillow, charset-normalizer, reportlab
Successfully installed charset-normalizer-3.4.4 pillow-12.1.0 reportlab-4.4.7
+ pip install omego
Collecting omego
Using cached omego-0.7.0-py3-none-any.whl
Collecting future (from omego)
Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Collecting yaclifw>=0.1.1 (from omego)
Using cached yaclifw-0.2.0-py3-none-any.whl
Collecting six (from yaclifw>=0.1.1->omego)
Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
Using cached future-1.0.0-py3-none-any.whl (491 kB)
Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
Installing collected packages: six, future, yaclifw, omego
Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
+ pip install tables
Collecting tables
Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
Collecting numpy>=1.20.0 (from tables)
Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
Collecting numexpr>=2.6.2 (from tables)
Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
Collecting packaging (from tables)
Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Collecting py-cpuinfo (from tables)
Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
Collecting blosc2>=2.3.0 (from tables)
Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
Collecting typing-extensions>=4.4.0 (from tables)
Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
Collecting ndindex (from blosc2>=2.3.0->tables)
Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
Collecting msgpack (from blosc2>=2.3.0->tables)
Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
Collecting platformdirs (from blosc2>=2.3.0->tables)
Using cached platformdirs-4.5.1-py3-none-any.whl.metadata (12 kB)
Collecting requests (from blosc2>=2.3.0->tables)
Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.4)
Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB)
Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
Using cached urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB)
Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
Using cached certifi-2026.1.4-py3-none-any.whl.metadata (2.5 kB)
Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.7 MB)
Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB)
Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
Using cached packaging-25.0-py3-none-any.whl (66 kB)
Using cached platformdirs-4.5.1-py3-none-any.whl (18 kB)
Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
Using cached requests-2.32.5-py3-none-any.whl (64 kB)
Using cached idna-3.11-py3-none-any.whl (71 kB)
Using cached urllib3-2.6.3-py3-none-any.whl (131 kB)
Using cached certifi-2026.1.4-py3-none-any.whl (152 kB)
Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
Successfully installed blosc2-3.12.2 certifi-2026.1.4 idna-3.11 msgpack-1.1.2 ndindex-1.10.1 numexpr-2.14.1 numpy-2.4.1 packaging-25.0 platformdirs-4.5.1 py-cpuinfo-9.0.0 requests-2.32.5 tables-3.10.2 typing-extensions-4.15.0 urllib3-2.6.3
+ pip install jinja2
Collecting jinja2
Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
Collecting MarkupSafe>=2.0 (from jinja2)
Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
Installing collected packages: MarkupSafe, jinja2
Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
+ pip install omero-py
Collecting omero-py
Using cached omero_py-5.21.3-py3-none-any.whl.metadata (6.5 kB)
Collecting appdirs (from omero-py)
Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.1.0)
Collecting PyYAML (from omero-py)
Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
Collecting portalocker (from omero-py)
Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.1.4)
Using cached omero_py-5.21.3-py3-none-any.whl (2.8 MB)
Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
Installing collected packages: appdirs, PyYAML, portalocker, omero-py
Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.21.3 portalocker-3.2.0
+ pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
Collecting omero-metadata
Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-xrswld41/omero-metadata_d5ba6d7472b046a99f48cd1381207b64
Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-xrswld41/omero-metadata_d5ba6d7472b046a99f48cd1381207b64
Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit b93d0c4f51c52a2ae3038db29507e3ff5578edb6
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.3)
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
Collecting pandas (from omero-metadata)
Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (12.1.0)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
Collecting pytz>=2020.1 (from pandas->omero-metadata)
Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
Collecting tzdata>=2022.7 (from pandas->omero-metadata)
Using cached tzdata-2025.3-py2.py3-none-any.whl.metadata (1.4 kB)
Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil>=2.8.2->pandas->omero-metadata) (1.17.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.1.4)
Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB)
Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
Using cached tzdata-2025.3-py2.py3-none-any.whl (348 kB)
Building wheels for collected packages: omero-metadata
Building wheel for omero-metadata (pyproject.toml): started
Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=7ce7de4f389547c23b1046e28f818d0cff4e86b7dfcd427d2e9b0c2252b7438e
Stored in directory: /tmp/pip-ephem-wheel-cache-dfj4l0ib/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
Successfully built omero-metadata
Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.3 python-dateutil-2.9.0.post0 pytz-2025.2 tzdata-2025.3
+ pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
Collecting omero-cli-render
Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-j619e31g/omero-cli-render_da124148ac754219b0ab7f721cc8c410
Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-j619e31g/omero-cli-render_da124148ac754219b0ab7f721cc8c410
Running command git checkout -b merge_ci --track origin/merge_ci
Switched to a new branch 'merge_ci'
branch 'merge_ci' set up to track 'origin/merge_ci'.
Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit c0cae4edbf876a5cef9e459c7560575e6e68be3d
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.3)
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (12.1.0)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.1.4)
Building wheels for collected packages: omero-cli-render
Building wheel for omero-cli-render (pyproject.toml): started
Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19840 sha256=6f34dd63d7ee4587aedc0c650d9ecc11c30604166e4d40ca4c091dfbbfde0b2d
Stored in directory: /tmp/pip-ephem-wheel-cache-s7jycj6p/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
Successfully built omero-cli-render
Installing collected packages: omero-cli-render
Successfully installed omero-cli-render-0.8.2.dev0
+ pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
Collecting omero-cli-duplicate
Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-2tk6qhwa/omero-cli-duplicate_167cad1041384f54b078d7562c55600f
Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-2tk6qhwa/omero-cli-duplicate_167cad1041384f54b078d7562c55600f
Running command git checkout -b merge_ci --track origin/merge_ci
Switched to a new branch 'merge_ci'
branch 'merge_ci' set up to track 'origin/merge_ci'.
Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit e187fc15b190a303bf3b81a4cc9b00c3be68ed20
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.3)
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.1.0)
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.1.4)
Building wheels for collected packages: omero-cli-duplicate
Building wheel for omero-cli-duplicate (pyproject.toml): started
Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=86fe690b0132cf8d7991a2d1684fe8f06dbec1bccea3fcfa8e2421271befc00b
Stored in directory: /tmp/pip-ephem-wheel-cache-hdq1_wk7/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
Successfully built omero-cli-duplicate
Installing collected packages: omero-cli-duplicate
Successfully installed omero-cli-duplicate-0.4.1.dev0
+ pip install omero-certificates
Collecting omero-certificates
Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.3)
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.1.0)
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.1.4)
Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
Installing collected packages: omero-certificates
Successfully installed omero-certificates-0.4.0
+ for x in *.tar.gz
+ pip install -U omero_dropbox-5.7.1.dev0.tar.gz
Processing ./omero_dropbox-5.7.1.dev0.tar.gz
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.3)
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.1.0)
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.1.4)
Building wheels for collected packages: omero-dropbox
Building wheel for omero-dropbox (pyproject.toml): started
Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=486d517bf6e39367ddde86492c00fbe17e3be4c34f662c9380b1c8cfc03eaa49
Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
Successfully built omero-dropbox
Installing collected packages: omero-dropbox
Successfully installed omero-dropbox-5.7.1.dev0
+ for x in *.tar.gz
+ pip install -U omero_marshal-0.9.2.dev0.tar.gz
Processing ./omero_marshal-0.9.2.dev0.tar.gz
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: omero_marshal
Building wheel for omero_marshal (pyproject.toml): started
Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88132 sha256=fdf79f9387d7014ef0ce9ba781e52339d997ff89c4d1f9ae280b23705666a4a3
Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
Successfully built omero_marshal
Installing collected packages: omero_marshal
Successfully installed omero_marshal-0.9.2.dev0
+ for x in *.tar.gz
+ pip install -U omero_py-5.22.0.dev0.tar.gz
Processing ./omero_py-5.22.0.dev0.tar.gz
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.0.0)
Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.4.1)
Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (12.1.0)
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (6.0.3)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.32.5)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.2.0)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (2026.1.4)
Building wheels for collected packages: omero-py
Building wheel for omero-py (pyproject.toml): started
Building wheel for omero-py (pyproject.toml): finished with status 'done'
Created wheel for omero-py: filename=omero_py-5.22.0.dev0-py3-none-any.whl size=2785928 sha256=4d72442858f67f1eb3b6128a8a98943cb5fb0bb8c42711727289a516fffb6826
Stored in directory: /home/omero/.cache/pip/wheels/b2/dd/fb/0f3c8a08eddbfe6a2bff7fe7d61ee876973c474d282bc441e3
Successfully built omero-py
Installing collected packages: omero-py
Attempting uninstall: omero-py
Found existing installation: omero-py 5.21.3
Uninstalling omero-py-5.21.3:
Successfully uninstalled omero-py-5.21.3
Successfully installed omero-py-5.22.0.dev0
+ for x in *.tar.gz
+ pip install -U omero_scripts-5.9.2.dev0.tar.gz
Processing ./omero_scripts-5.9.2.dev0.tar.gz
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: omero-scripts
Building wheel for omero-scripts (pyproject.toml): started
Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136991 sha256=ccce030a85825ca152bbcd5ff2320d3e73e320d1b57d1f43e309a3ced69d4aa0
Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
Successfully built omero-scripts
Installing collected packages: omero-scripts
Successfully installed omero-scripts-5.9.2.dev0
+ for x in *.tar.gz
+ pip install -U omero_web-5.30.2.dev0.tar.gz
Processing ./omero_web-5.30.2.dev0.tar.gz
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (5.22.0.dev0)
Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.30.2.dev0)
Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
Collecting Django<5.3,>=5.2.9 (from omero-web==5.30.2.dev0)
Using cached django-5.2.10-py3-none-any.whl.metadata (4.1 kB)
Collecting django-pipeline (from omero-web==5.30.2.dev0)
Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
Collecting django-cors-headers==3.7.0 (from omero-web==5.30.2.dev0)
Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
Collecting whitenoise>=5.3.0 (from omero-web==5.30.2.dev0)
Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
Collecting gunicorn>=19.3 (from omero-web==5.30.2.dev0)
Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
Requirement already satisfied: omero-marshal>=0.9.1 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (0.9.2.dev0)
Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (12.1.0)
Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (2025.2)
Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (3.2.0)
Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (25.0)
Collecting importlib-resources (from omero-web==5.30.2.dev0)
Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
Using cached asgiref-3.11.0-py3-none-any.whl.metadata (9.3 kB)
Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.2.dev0) (1.4.4)
Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.2.dev0) (1.0.0)
Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.2.dev0) (2.4.1)
Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.2.dev0) (6.0.3)
Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.2.dev0) (3.6.5)
Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.30.2.dev0) (2.32.5)
Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.30.2.dev0) (65.5.1)
Collecting wheel (from django-pipeline->omero-web==5.30.2.dev0)
Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.2.dev0) (3.4.4)
Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.2.dev0) (3.11)
Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.2.dev0) (2.6.3)
Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.30.2.dev0) (2026.1.4)
Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
Using cached django-5.2.10-py3-none-any.whl (8.3 MB)
Using cached asgiref-3.11.0-py3-none-any.whl (24 kB)
Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
Building wheels for collected packages: omero-web
Building wheel for omero-web (pyproject.toml): started
Building wheel for omero-web (pyproject.toml): finished with status 'done'
Created wheel for omero-web: filename=omero_web-5.30.2.dev0-py3-none-any.whl size=2819190 sha256=0a07873bc0759575089ae858c93caf63ebc650affac67c10fbfc47d5952de138
Stored in directory: /home/omero/.cache/pip/wheels/22/8a/f9/2aa2b64b8351936989ad8693ee70db658c8360167f1ee574e7
Successfully built omero-web
Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
Successfully installed Django-5.2.10 asgiref-3.11.0 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.30.2.dev0 sqlparse-0.5.5 wheel-0.45.1 whitenoise-6.11.0
+ wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
--2026-01-13 14:02:43-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.108.133, ...
Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 129235 (126K) [text/plain]
Saving to: ‘Figure_To_Pdf.py’
0K .......... .......... .......... .......... .......... 39% 4.05M 0s
50K .......... .......... .......... .......... .......... 79% 5.43M 0s
100K .......... .......... ...... 100% 49.7M=0.02s
2026-01-13 14:02:44 (5.72 MB/s) - ‘Figure_To_Pdf.py’ saved [129235/129235]
+ chmod 755 Figure_To_Pdf.py
+ mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
+ omero config set omero.db.name OMERO-server
+ omero config set omero.db.host pg
+ omero config set omero.db.user postgres
+ omero config set omero.data.dir /home/omero/omero-server-data
+ omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
+ omero config set omero.db.poolsize 25
+ omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
+ omero config set omero.security.trustStorePassword changeit
+ omero config set omero.mail.config true
+ omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
+ omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
+ omero certificates
OpenSSL 3.5.1 1 Jul 2025 (Library: OpenSSL 3.5.1 1 Jul 2025)
certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
+ '[' false = true ']'
+ echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
+ omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
2026-01-13 14:02:58,268 [ omego.db] DEBUG dbcommand => upgrade
2026-01-13 14:02:58,268 [ omego.db] DEBUG dbhost => localhost
2026-01-13 14:02:58,268 [ omego.db] DEBUG dbname => OMERO-server
2026-01-13 14:02:58,268 [ omego.db] DEBUG dbpass => omero
2026-01-13 14:02:58,268 [ omego.db] DEBUG dbuser => omero
2026-01-13 14:02:58,268 [ omego.db] DEBUG rootpass => omero
2026-01-13 14:02:58,268 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
2026-01-13 14:02:58,269 [omego.extern] INFO Executing : omero version
OMERO.py version:
OMERO.server version:
5.6.3-578-31c47ae256-ice36-b17
5.22.0.dev0
2026-01-13 14:02:59,460 [omego.extern] INFO Completed [1.191 s]
2026-01-13 14:02:59,460 [omego.extern] DEBUG Using omero CLI from omero
2026-01-13 14:02:59,460 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
2026-01-13 14:02:59,460 [omego.extern] INFO Running [current environment]: omero config get --show-password
2026-01-13 14:02:59,460 [omego.extern] INFO Executing : omero config get --show-password
2026-01-13 14:03:00,607 [omego.extern] INFO Completed [1.147 s]
2026-01-13 14:03:00,607 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
2026-01-13 14:03:00,608 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
2026-01-13 14:03:00,613 [omego.extern] INFO Completed [0.005 s]
2026-01-13 14:03:00,613 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.11\n'
2026-01-13 14:03:00,613 [ omego.db] INFO psql version: psql (PostgreSQL) 16.11
2026-01-13 14:03:00,613 [omego.extern] INFO Running [current environment]: omero config get --show-password
2026-01-13 14:03:00,613 [omego.extern] INFO Executing : omero config get --show-password
2026-01-13 14:03:01,761 [omego.extern] INFO Completed [1.148 s]
2026-01-13 14:03:01,761 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
2026-01-13 14:03:01,761 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
2026-01-13 14:03:01,771 [omego.extern] INFO Completed [0.009 s]
2026-01-13 14:03:01,771 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.11") at port "5432".\n'
2026-01-13 14:03:01,771 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
2026-01-13 14:03:01,771 [omego.extern] INFO Running [current environment]: omero config get --show-password
2026-01-13 14:03:01,771 [omego.extern] INFO Executing : omero config get --show-password
2026-01-13 14:03:02,911 [omego.extern] INFO Completed [1.141 s]
2026-01-13 14:03:02,911 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
2026-01-13 14:03:02,912 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
2026-01-13 14:03:02,921 [omego.extern] INFO Completed [0.010 s]
2026-01-13 14:03:02,921 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
2026-01-13 14:03:02,921 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
2026-01-13 14:03:02,923 [ omego.db] INFO Database is already at OMERO5.4__0
+ export LANG=en_US.UTF-8
+ LANG=en_US.UTF-8
+ export LANGUAGE=en_US:en
+ LANGUAGE=en_US:en
+ export LC_ALL=en_US.UTF-8
+ LC_ALL=en_US.UTF-8
+ BUILD_ID=DONT_KILL_ME
+ omero admin start
No descriptor given. Using etc/grid/default.xml
Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
Waiting on startup. Use CTRL-C to exit
+ omero admin waitup
Waiting on startup. Use CTRL-C to exit
+ omero admin diagnostics
================================================================================
OMERO Diagnostics (admin)
================================================================================
Commands: java -version 17.0.17 (/usr/bin/java)
Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
Commands: psql --version 16.11 (/usr/bin/psql)
Commands: openssl version 3.5.11 (/usr/bin/openssl)
Component: OMERO.py 5.22.0.dev0
Component: OMERO.server 5.6.3-578-31c47ae256-ice36-b17
Server: icegridnode running
Server: Blitz-0 active (pid = 88531, enabled)
Server: Indexer-0 activating (enabled)
Server: OMERO.Glacier2 active (pid = 88566, enabled)
Server: OMERO.IceStorm active (pid = 88597, enabled)
Server: Processor-0 activating (enabled)
Server: Tables-0 activating (enabled)
Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
Log files: Blitz-0.log 22.7 KB errors=0 warnings=1
Log files: DropBox.log n/a
Log files: FileServer.log n/a
Log files: Indexer-0.log 114 B
Log files: MonitorServer.log n/a
Log files: Processor-0.log 281 B
Log files: Tables-0.log 281 B
Log files: TestDropBox.log n/a
Log files: master.err empty
Log files: master.out 30.5 KB
Log files: Total size 0.05 MB
Environment:OMERO_HOME=(unset)
Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=/opt/ice-3.6.5
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)
OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
JVM settings: Blitz-${index} -Xmx7200m
JVM settings: Indexer-${index} -Xmx4800m
JVM settings: PixelData-${index} -Xmx7200m
JVM settings: Repository-${index} -Xmx4800m
Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 13 January 2026 0d988788af3c196d8fd23672119bd8527c975ae5
Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 13 January 2026 0d988788af3c196d8fd23672119bd8527c975ae5
Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 13 January 2026 0d988788af3c196d8fd23672119bd8527c975ae5
Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3-SNAPSHOT 13 January 2026 88107bf2f599560081918f71ba8a1dd20f6f89be
Jar: lib/server/ome-common.jar OME Common Java 6.1.2-SNAPSHOT 13 January 2026 88107bf2f599560081918f71ba8a1dd20f6f89be
Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 13 January 2026 88107bf2f599560081918f71ba8a1dd20f6f89be
Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 13 January 2026 88107bf2f599560081918f71ba8a1dd20f6f89be
Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 13 January 2026 88107bf2f599560081918f71ba8a1dd20f6f89be
Jar: lib/server/ome-xml.jar OME XML library 6.5.3-SNAPSHOT 13 January 2026 88107bf2f599560081918f71ba8a1dd20f6f89be
Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
Jar: lib/server/omero-gateway.jar jar 5.10.5-SNAPSHOT
Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
+ deactivate
+ '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
+ PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
+ export PATH
+ unset _OLD_VIRTUAL_PATH
+ '[' -n '' ']'
+ hash -r
+ '[' -n '' ']'
+ unset VIRTUAL_ENV
+ unset VIRTUAL_ENV_PROMPT
+ '[' '!' '' = nondestructive ']'
+ unset -f deactivate
Finished: SUCCESS
