Console

01:44:36 Started by upstream project "Trigger" build number 21
01:44:36 originally caused by:
01:44:36  Started by timer
01:44:36 Running as SYSTEM
01:44:36 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
01:44:36 [OMERO-server] $ /bin/bash -xe /tmp/jenkins2948705059894083748.sh
01:44:36 + source /home/settings.env
01:44:36 ++ OMERO_DB_HOST=pg
01:44:36 ++ OMERO_DB_USER=postgres
01:44:36 ++ OMERO_DB_PASS=
01:44:36 ++ OMERO_ROOT_PASS=omero
01:44:36 ++ OMERO_DATA_DIR=/OMERO
01:44:36 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
01:44:36 + OMERO_DB_NAME=OMERO-server
01:44:36 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
01:44:36 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:44:36 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:44:36 + OMERO_DATA_DIR=/home/omero/omero-server-data
01:44:36 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
01:44:36 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
01:44:36 ++ deactivate nondestructive
01:44:36 ++ '[' -n '' ']'
01:44:36 ++ '[' -n '' ']'
01:44:36 ++ hash -r
01:44:36 ++ '[' -n '' ']'
01:44:36 ++ unset VIRTUAL_ENV
01:44:36 ++ unset VIRTUAL_ENV_PROMPT
01:44:36 ++ '[' '!' nondestructive = nondestructive ']'
01:44:36 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
01:44:36 ++ export VIRTUAL_ENV
01:44:36 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:44:36 ++ 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
01:44:36 ++ export PATH
01:44:36 ++ '[' -n '' ']'
01:44:36 ++ '[' -z '' ']'
01:44:36 ++ _OLD_VIRTUAL_PS1=
01:44:36 ++ PS1='(.venv3) '
01:44:36 ++ export PS1
01:44:36 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
01:44:36 ++ export VIRTUAL_ENV_PROMPT
01:44:36 ++ hash -r
01:44:36 + omero admin stop
01:44:49 Waiting on shutdown. Use CTRL-C to exit
01:44:49 .+ sleep 5
01:45:04 + deactivate
01:45:04 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
01:45:04 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:45:04 + export PATH
01:45:04 + unset _OLD_VIRTUAL_PATH
01:45:04 + '[' -n '' ']'
01:45:04 + hash -r
01:45:04 + '[' -n '' ']'
01:45:04 + unset VIRTUAL_ENV
01:45:04 + unset VIRTUAL_ENV_PROMPT
01:45:04 + '[' '!' '' = nondestructive ']'
01:45:04 + unset -f deactivate
01:45:04 + rm -rf /home/omero/workspace/OMERO-server/.venv3
01:47:21 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
01:47:41 + '[' false = true ']'
01:47:41 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
01:47:41 Skipping PURGE_DATA:CleanDbAndRepo
01:47:41 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.6-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.22.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.10.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.32.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
01:47:46 Copied 1 artifact from "OMERO-build" build number 13
01:47:46 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 12
01:47:46 Copied 2 artifacts from "OMERO-build-build" build number 23
01:47:46 [OMERO-server] $ /bin/bash -xe /tmp/jenkins6426590739669369182.sh
01:47:46 + source /home/settings.env
01:47:46 ++ OMERO_DB_HOST=pg
01:47:46 ++ OMERO_DB_USER=postgres
01:47:46 ++ OMERO_DB_PASS=
01:47:46 ++ OMERO_ROOT_PASS=omero
01:47:46 ++ OMERO_DATA_DIR=/OMERO
01:47:46 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
01:47:46 + OMERO_DB_NAME=OMERO-server
01:47:46 + OMERO_DATA_DIR=/home/omero/omero-server-data
01:47:46 + mkdir -p /home/omero/omero-server-data
01:47:46 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
01:47:46 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:47:46 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:47:46 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
01:47:46 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
01:47:46 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
01:47:46 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
01:47:46 ++ ls OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13.zip
01:47:46 + ZIP=OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13.zip
01:47:46 + '[' '!' -z '' ']'
01:47:46 + DIST=OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13
01:47:46 + unzip OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13.zip
01:47:46 Archive:  OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13.zip
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/blitz/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/grid/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/profiles/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/error/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/grid/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/luts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/luts/janelia/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/luts/matplotlib/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/luts/ncsa_paledit/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/luts/seaborn/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/luts/wcif/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/analysis_scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/annotation_scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/export_scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/figure_scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/import_scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/scripts/omero/util_scripts/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/server/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/share/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/share/licenses/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/misc/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__1/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__10/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__11/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__2/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__3/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__4/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__5/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__6/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__7/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__8/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__9/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__4/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__5/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__6/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__7/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.1__0/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.2__0/
01:47:46    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.2__0/t/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.3__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.4__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.0__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.1__1/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.2__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4DEV__1/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4DEV__2/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4DEV__3/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/var/
01:47:47    creating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/var/tmp/
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/LICENSE.txt  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/backup.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/blitz/mail-senders.example  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/blitz/mail-server.example  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/build.properties  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/env.bat  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/env.sh  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/hibernate.properties  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/ice.config  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/logback-cli.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/logback-indexing-cli.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/logback-indexing.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/logback.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/mime.types  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/node1.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/node2.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/omero.properties  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/profiles/psql  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/rollover.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/Windows.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/error/maintainance.html  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/grid/README  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/grid/default.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/grid/templates.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/grid/windefault.xml  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/ice.config  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/internal.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/master.cfg  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/templates/robot.template  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/etc/testdropbox.config  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/history.rst  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/OMEZarrReader.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/accessors-smart.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/activation.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/aggdesigner-algorithm.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/aircompressor.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/antlr.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/aopalliance.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/apiguardian-api.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/asm.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/avatica-core.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/avatica-metrics.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/aws-java-sdk-core.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/aws-java-sdk-kms.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/aws-java-sdk-s3.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/base.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-anim.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-awt-util.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-bridge.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-codec.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-constants.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-css.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-dom.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-ext.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-gvt.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-i18n.jar  
01:47:47   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-parser.jar  
01:47:48   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/lib/client/batik-script.jar  
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01:47:59   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/misc/enums.py  
01:47:59   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__1/OMERO3__7.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__10/OMERO3A__9.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__11/OMERO3A__10.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__11/OMERO3A__5.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__2/OMERO3A__1.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__3/OMERO3A__2.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__3/OMERO3__5.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__4/OMERO3A__3.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__4/OMERO3__5.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__5/OMERO3A__4.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__6/OMERO3A__5.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__7/OMERO3A__6.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__8/OMERO3A__6.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3A__9/OMERO3A__8.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__4/OMERO3__1.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__5/OMERO3__4.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__6/OMERO3__5.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO3__7/OMERO3__6.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.1__0/OMERO4__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.2__0/OMERO4.1__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.3__0/OMERO4.2__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4.4__0/OMERO4.1__0.sql  
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01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO4__0/OMERO3A__11.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.0__0/OMERO4.4__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.1__1/OMERO5.0__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.1__1/OMERO5.1__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.2__0/OMERO5.1__1.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/OMERO5.2__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/delete-ns-orphans.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/OMERO5.3__0.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/OMERO5.3__1.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/psql-footer.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/psql-header.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/schema.sql  
01:48:00   inflating: OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13/sql/psql/OMERO5.4__0/views.sql  
01:48:00 + rm -f OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13.zip
01:48:00 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-627-05c9d1bf8e-ice36-b13 /home/omero/workspace/OMERO-server/OMERO.server
01:48:00 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
01:48:00 ++ deactivate nondestructive
01:48:00 ++ '[' -n '' ']'
01:48:00 ++ '[' -n '' ']'
01:48:00 ++ hash -r
01:48:00 ++ '[' -n '' ']'
01:48:00 ++ unset VIRTUAL_ENV
01:48:00 ++ unset VIRTUAL_ENV_PROMPT
01:48:00 ++ '[' '!' nondestructive = nondestructive ']'
01:48:00 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
01:48:00 ++ export VIRTUAL_ENV
01:48:00 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:48:00 ++ 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
01:48:00 ++ export PATH
01:48:00 ++ '[' -n '' ']'
01:48:00 ++ '[' -z '' ']'
01:48:00 ++ _OLD_VIRTUAL_PS1=
01:48:00 ++ PS1='(.venv3) '
01:48:00 ++ export PS1
01:48:00 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
01:48:00 ++ export VIRTUAL_ENV_PROMPT
01:48:00 ++ hash -r
01:48:00 + pip install -U pip
01:48:01 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
01:48:02 Collecting pip
01:48:02   Using cached pip-26.1.2-py3-none-any.whl (1.8 MB)
01:48:02 Installing collected packages: pip
01:48:02   Attempting uninstall: pip
01:48:02     Found existing installation: pip 22.3.1
01:48:02     Uninstalling pip-22.3.1:
01:48:03       Successfully uninstalled pip-22.3.1
01:48:15 Successfully installed pip-26.1.2
01:48:15 + 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
01:48:16 Collecting zeroc-ice==3.6.5
01:48:17   Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
01:48:19      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 13.7 MB/s  0:00:02
01:48:20 Installing collected packages: zeroc-ice
01:48:23 Successfully installed zeroc-ice-3.6.5
01:48:23 + pip install markdown
01:48:24 Collecting markdown
01:48:24   Using cached markdown-3.10.2-py3-none-any.whl.metadata (5.1 kB)
01:48:24 Using cached markdown-3.10.2-py3-none-any.whl (108 kB)
01:48:24 Installing collected packages: markdown
01:48:25 Successfully installed markdown-3.10.2
01:48:25 + pip install reportlab
01:48:26 Collecting reportlab
01:48:26   Using cached reportlab-5.0.0-py3-none-any.whl.metadata (1.6 kB)
01:48:26 Collecting pillow>=9.0.0 (from reportlab)
01:48:26   Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
01:48:27 Collecting charset-normalizer (from reportlab)
01:48:27   Using cached charset_normalizer-3.4.9-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (41 kB)
01:48:27 Using cached reportlab-5.0.0-py3-none-any.whl (2.0 MB)
01:48:27 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
01:48:27 Using cached charset_normalizer-3.4.9-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (221 kB)
01:48:27 Installing collected packages: pillow, charset-normalizer, reportlab
01:48:35 
01:48:35 Successfully installed charset-normalizer-3.4.9 pillow-12.3.0 reportlab-5.0.0
01:48:35 + pip install omego
01:48:36 Collecting omego
01:48:36   Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
01:48:36 Collecting future (from omego)
01:48:36   Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
01:48:36 Collecting yaclifw>=0.1.1 (from omego)
01:48:36   Using cached yaclifw-0.2.0-py3-none-any.whl
01:48:36 Collecting six (from yaclifw>=0.1.1->omego)
01:48:36   Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
01:48:37 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
01:48:37 Using cached future-1.0.0-py3-none-any.whl (491 kB)
01:48:37 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
01:48:37 Installing collected packages: six, future, yaclifw, omego
01:48:42 
01:48:42 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
01:48:42 + pip install tables
01:48:43 Collecting tables
01:48:43   Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.1 kB)
01:48:43 Collecting numpy>=1.20.0 (from tables)
01:48:43   Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
01:48:44 Collecting numexpr>=2.6.2 (from tables)
01:48:44   Downloading numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
01:48:44 Collecting packaging (from tables)
01:48:44   Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
01:48:44 Collecting py-cpuinfo (from tables)
01:48:44   Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
01:48:44 Collecting blosc2>=2.3.0 (from tables)
01:48:44   Using cached blosc2-4.9.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (7.8 kB)
01:48:45 Collecting ndindex (from blosc2>=2.3.0->tables)
01:48:45   Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
01:48:45 Collecting msgpack (from blosc2>=2.3.0->tables)
01:48:45   Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
01:48:45 Collecting pydantic (from blosc2>=2.3.0->tables)
01:48:45   Using cached pydantic-2.13.4-py3-none-any.whl.metadata (109 kB)
01:48:45 Collecting httpx[http2] (from blosc2>=2.3.0->tables)
01:48:45   Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
01:48:46 Collecting rich (from blosc2>=2.3.0->tables)
01:48:46   Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
01:48:46 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
01:48:46   Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
01:48:46 Collecting anyio (from httpx[http2]->blosc2>=2.3.0->tables)
01:48:46   Using cached anyio-4.14.2-py3-none-any.whl.metadata (4.6 kB)
01:48:46 Collecting certifi (from httpx[http2]->blosc2>=2.3.0->tables)
01:48:46   Using cached certifi-2026.6.17-py3-none-any.whl.metadata (2.5 kB)
01:48:46 Collecting httpcore==1.* (from httpx[http2]->blosc2>=2.3.0->tables)
01:48:46   Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB)
01:48:46 Collecting idna (from httpx[http2]->blosc2>=2.3.0->tables)
01:48:46   Using cached idna-3.18-py3-none-any.whl.metadata (6.1 kB)
01:48:46 Collecting h2<5,>=3 (from httpx[http2]->blosc2>=2.3.0->tables)
01:48:46   Using cached h2-4.3.0-py3-none-any.whl.metadata (5.1 kB)
01:48:47 Collecting hyperframe<7,>=6.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
01:48:47   Using cached hyperframe-6.1.0-py3-none-any.whl.metadata (4.3 kB)
01:48:47 Collecting hpack<5,>=4.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
01:48:47   Using cached hpack-4.2.0-py3-none-any.whl.metadata (3.3 kB)
01:48:47 Collecting h11>=0.16 (from httpcore==1.*->httpx[http2]->blosc2>=2.3.0->tables)
01:48:47   Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB)
01:48:47 Collecting typing_extensions>=4.5 (from anyio->httpx[http2]->blosc2>=2.3.0->tables)
01:48:47   Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
01:48:47 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
01:48:47   Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)
01:48:48 Collecting pydantic-core==2.46.4 (from pydantic->blosc2>=2.3.0->tables)
01:48:48   Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
01:48:48 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
01:48:48   Using cached typing_inspection-0.4.2-py3-none-any.whl.metadata (2.6 kB)
01:48:48 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
01:48:48   Using cached markdown_it_py-4.2.0-py3-none-any.whl.metadata (7.4 kB)
01:48:48 Collecting pygments<3.0.0,>=2.13.0 (from rich->blosc2>=2.3.0->tables)
01:48:48   Using cached pygments-2.20.0-py3-none-any.whl.metadata (2.5 kB)
01:48:48 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
01:48:48   Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
01:48:48 Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (7.2 MB)
01:48:49 Using cached blosc2-4.9.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.3 MB)
01:48:49 Downloading numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (443 kB)
01:48:49 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
01:48:49 Using cached httpx-0.28.1-py3-none-any.whl (73 kB)
01:48:49 Using cached h2-4.3.0-py3-none-any.whl (61 kB)
01:48:49 Using cached hpack-4.2.0-py3-none-any.whl (34 kB)
01:48:49 Using cached httpcore-1.0.9-py3-none-any.whl (78 kB)
01:48:49 Using cached hyperframe-6.1.0-py3-none-any.whl (13 kB)
01:48:49 Using cached h11-0.16.0-py3-none-any.whl (37 kB)
01:48:49 Using cached anyio-4.14.2-py3-none-any.whl (125 kB)
01:48:49 Using cached idna-3.18-py3-none-any.whl (65 kB)
01:48:49 Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB)
01:48:49 Using cached certifi-2026.6.17-py3-none-any.whl (133 kB)
01:48:49 Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (423 kB)
01:48:49 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
01:48:49 Using cached packaging-26.2-py3-none-any.whl (100 kB)
01:48:49 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
01:48:49 Using cached pydantic-2.13.4-py3-none-any.whl (472 kB)
01:48:49 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
01:48:49 Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB)
01:48:49 Using cached typing_inspection-0.4.2-py3-none-any.whl (14 kB)
01:48:49 Using cached rich-15.0.0-py3-none-any.whl (310 kB)
01:48:49 Using cached pygments-2.20.0-py3-none-any.whl (1.2 MB)
01:48:49 Using cached markdown_it_py-4.2.0-py3-none-any.whl (91 kB)
01:48:49 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
01:48:49 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
01:48:50 Installing collected packages: py-cpuinfo, typing_extensions, threadpoolctl, pygments, packaging, numpy, ndindex, msgpack, mdurl, idna, hyperframe, hpack, h11, certifi, annotated-types, typing-inspection, pydantic-core, numexpr, markdown-it-py, httpcore, h2, anyio, rich, pydantic, httpx, blosc2, tables
01:49:34 
01:49:34 Successfully installed annotated-types-0.7.0 anyio-4.14.2 blosc2-4.9.1 certifi-2026.6.17 h11-0.16.0 h2-4.3.0 hpack-4.2.0 httpcore-1.0.9 httpx-0.28.1 hyperframe-6.1.0 idna-3.18 markdown-it-py-4.2.0 mdurl-0.1.2 msgpack-1.2.1 ndindex-1.10.1 numexpr-2.14.2 numpy-2.4.6 packaging-26.2 py-cpuinfo-9.0.0 pydantic-2.13.4 pydantic-core-2.46.4 pygments-2.20.0 rich-15.0.0 tables-3.11.1 threadpoolctl-3.6.0 typing-inspection-0.4.2 typing_extensions-4.16.0
01:49:34 + pip install jinja2
01:49:35 Collecting jinja2
01:49:35   Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
01:49:36 Collecting MarkupSafe>=2.0 (from jinja2)
01:49:36   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)
01:49:36 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
01:49:36 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
01:49:36 Installing collected packages: MarkupSafe, jinja2
01:49:36 
01:49:37 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
01:49:37 + pip install omero-py
01:49:37 Collecting omero-py
01:49:37   Using cached omero_py-5.22.1-py3-none-any.whl.metadata (6.5 kB)
01:49:37 Collecting appdirs (from omero-py)
01:49:37   Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
01:49:37 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
01:49:37 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
01:49:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
01:49:38 Collecting PyYAML (from omero-py)
01:49:38   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)
01:49:38 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
01:49:38 Collecting requests (from omero-py)
01:49:38   Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
01:49:38 Collecting portalocker (from omero-py)
01:49:38   Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
01:49:38 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.9)
01:49:38 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.18)
01:49:38 Collecting urllib3<3,>=1.26 (from requests->omero-py)
01:49:38   Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
01:49:38 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.6.17)
01:49:38 Using cached omero_py-5.22.1-py3-none-any.whl (2.8 MB)
01:49:38 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
01:49:38 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
01:49:38 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
01:49:38 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
01:49:38 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
01:49:38 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, requests, omero-py
01:49:54 
01:49:55 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.22.1 portalocker-3.2.0 requests-2.34.2 urllib3-2.7.0
01:49:55 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
01:49:55 Collecting omero-metadata
01:49:55   Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-mkfreebh/omero-metadata_b2d163b5d2924ff7b2d3d3a1a934535c
01:49:55   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-mkfreebh/omero-metadata_b2d163b5d2924ff7b2d3d3a1a934535c
01:49:56   Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit ba41e15256279ba472d06b9a2898e13cfdc7d17f
01:49:56   Installing build dependencies: started
01:49:58   Installing build dependencies: finished with status 'done'
01:49:58   Getting requirements to build wheel: started
01:49:58   Getting requirements to build wheel: finished with status 'done'
01:49:58   Preparing metadata (pyproject.toml): started
01:49:58   Preparing metadata (pyproject.toml): finished with status 'done'
01:49:58 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.22.1)
01:49:58 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
01:49:58 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
01:49:59 Collecting pandas (from omero-metadata)
01:49:59   Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
01:49:59 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
01:49:59 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
01:49:59 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.6)
01:49:59 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (12.3.0)
01:49:59 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)
01:49:59 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
01:49:59 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
01:49:59 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
01:49:59 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
01:49:59   Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
01:49:59 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)
01:49:59 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.9)
01:49:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.18)
01:49:59 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.7.0)
01:49:59 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.6.17)
01:49:59 Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.3 MB)
01:49:59 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
01:49:59 Building wheels for collected packages: omero-metadata
01:49:59   Building wheel for omero-metadata (pyproject.toml): started
01:49:59   Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
01:49:59   Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=a819f15423e9d7b10435ffea304ce9545d6d6d0ede0ad2ccb6f3f4d70be0df7e
01:49:59   Stored in directory: /tmp/pip-ephem-wheel-cache-u7khfghv/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
01:49:59 Successfully built omero-metadata
01:49:59 Installing collected packages: python-dateutil, pandas, omero-metadata
01:50:38 
01:50:38 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.3 python-dateutil-2.9.0.post0
01:50:38 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
01:50:39 Collecting omero-cli-render
01:50:39   Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-6u45tf8s/omero-cli-render_d48d9f3f15574c9ca0bad7e7f1a481be
01:50:39   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-6u45tf8s/omero-cli-render_d48d9f3f15574c9ca0bad7e7f1a481be
01:50:40   Running command git checkout -b merge_ci --track origin/merge_ci
01:50:40   Switched to a new branch 'merge_ci'
01:50:40   branch 'merge_ci' set up to track 'origin/merge_ci'.
01:50:40   Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 91ecc1154b1ec8564a37240ea0550078a9b86357
01:50:40   Installing build dependencies: started
01:50:41   Installing build dependencies: finished with status 'done'
01:50:41   Getting requirements to build wheel: started
01:50:42   Getting requirements to build wheel: finished with status 'done'
01:50:42   Preparing metadata (pyproject.toml): started
01:50:42   Preparing metadata (pyproject.toml): finished with status 'done'
01:50:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
01:50:42 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.22.1)
01:50:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
01:50:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
01:50:42 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.6)
01:50:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (12.3.0)
01:50:42 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)
01:50:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
01:50:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
01:50:42 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.9)
01:50:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.18)
01:50:42 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.7.0)
01:50:42 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.6.17)
01:50:42 Building wheels for collected packages: omero-cli-render
01:50:42   Building wheel for omero-cli-render (pyproject.toml): started
01:50:42   Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
01:50:42   Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19838 sha256=bb839c01ec1d4c2e50b675e06b7acc4ad4d84ae437a5dc6e98b0a38214bc6f19
01:50:42   Stored in directory: /tmp/pip-ephem-wheel-cache-4rjmwyj0/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
01:50:42 Successfully built omero-cli-render
01:50:42 Installing collected packages: omero-cli-render
01:50:42 Successfully installed omero-cli-render-0.8.2.dev0
01:50:43 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
01:50:43 Collecting omero-cli-duplicate
01:50:43   Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-0sn7n2r2/omero-cli-duplicate_9ad960628a9a42d2ab2b361c2344d5f9
01:50:43   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-0sn7n2r2/omero-cli-duplicate_9ad960628a9a42d2ab2b361c2344d5f9
01:50:44   Running command git checkout -b merge_ci --track origin/merge_ci
01:50:45   Switched to a new branch 'merge_ci'
01:50:45   branch 'merge_ci' set up to track 'origin/merge_ci'.
01:50:45   Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit cecb8d50dea2afef2e49f720cf8ce790cd6d731f
01:50:45   Installing build dependencies: started
01:50:46   Installing build dependencies: finished with status 'done'
01:50:46   Getting requirements to build wheel: started
01:50:46   Getting requirements to build wheel: finished with status 'done'
01:50:46   Preparing metadata (pyproject.toml): started
01:50:46   Preparing metadata (pyproject.toml): finished with status 'done'
01:50:46 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.22.1)
01:50:46 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
01:50:46 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
01:50:46 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
01:50:46 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.3.0)
01:50:46 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
01:50:46 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)
01:50:46 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.34.2)
01:50:46 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
01:50:46 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.9)
01:50:46 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.18)
01:50:46 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.7.0)
01:50:46 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.6.17)
01:50:46 Building wheels for collected packages: omero-cli-duplicate
01:50:46   Building wheel for omero-cli-duplicate (pyproject.toml): started
01:50:47   Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
01:50:47   Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=f67fe60320c443b90c3a5d61264c98ee2f0724431f17f1203730f6139953bec3
01:50:47   Stored in directory: /tmp/pip-ephem-wheel-cache-etrunhcy/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
01:50:47 Successfully built omero-cli-duplicate
01:50:47 Installing collected packages: omero-cli-duplicate
01:50:47 Successfully installed omero-cli-duplicate-0.4.1.dev0
01:50:47 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
01:50:48 Collecting omero-cli-zarr
01:50:48   Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-4sa9rucq/omero-cli-zarr_52fffb56d0274d458062147ef1dc1077
01:50:48   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-4sa9rucq/omero-cli-zarr_52fffb56d0274d458062147ef1dc1077
01:50:49   Running command git checkout -b merge_ci --track origin/merge_ci
01:50:49   Switched to a new branch 'merge_ci'
01:50:49   branch 'merge_ci' set up to track 'origin/merge_ci'.
01:50:49   Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit d93d4cdac0ae629acfd41bdb3d9d74080b95fd9b
01:50:49   Installing build dependencies: started
01:50:50   Installing build dependencies: finished with status 'done'
01:50:50   Getting requirements to build wheel: started
01:50:51   Getting requirements to build wheel: finished with status 'done'
01:50:51   Installing backend dependencies: started
01:50:52   Installing backend dependencies: finished with status 'done'
01:50:52   Preparing metadata (pyproject.toml): started
01:50:52   Preparing metadata (pyproject.toml): finished with status 'done'
01:50:52 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.22.1)
01:50:53 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
01:50:53   Using cached ome_zarr-0.18.0-py3-none-any.whl.metadata (2.9 kB)
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01:50:55 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:55 Collecting importlib_metadata>=4.13.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:56 Collecting pydantic-core==2.41.5 (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:56 Collecting locket (from partd>=1.4.0->dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:57 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
01:50:57   Using cached jmespath-1.1.0-py3-none-any.whl.metadata (7.6 kB)
01:50:57 Collecting multidict<7.0.0,>=6.0.0 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
01:50:57   Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
01:50:57 Collecting wrapt<3.0.0,>=1.10.10 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:58 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:58 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:58 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:58 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:59 Collecting scipy>=1.11.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:50:59 Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:51:00 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
01:51:00 Building wheels for collected packages: omero-cli-zarr
01:51:00   Building wheel for omero-cli-zarr (pyproject.toml): started
01:51:01   Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
01:51:01   Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev162+gd93d4cd-py3-none-any.whl size=38286 sha256=2205a6bcacc83e39b631f8679c136b952abb5761904a07629b35451b6a03cbf2
01:51:01   Stored in directory: /tmp/pip-ephem-wheel-cache-rdmntq9p/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
01:51:01 Successfully built omero-cli-zarr
01:51:01 Installing collected packages: rangehttpserver, zipp, wrapt, toolz, tifffile, scipy, pydantic-core, propcache, numcodecs, networkx, multidict, locket, lazy-loader, jmespath, imageio, google-crc32c, fsspec, frozenlist, donfig, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, zarr, yarl, scikit-image, pydantic, partd, importlib_metadata, Deprecated, botocore, aiosignal, pydantic-zarr, dask, aiohttp, ome-zarr-models, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
01:51:33   Attempting uninstall: pydantic-core
01:51:33     Found existing installation: pydantic_core 2.46.4
01:51:33     Uninstalling pydantic_core-2.46.4:
01:51:33       Successfully uninstalled pydantic_core-2.46.4
01:52:03   Attempting uninstall: pydantic
01:52:03     Found existing installation: pydantic 2.13.4
01:52:03     Uninstalling pydantic-2.13.4:
01:52:04       Successfully uninstalled pydantic-2.13.4
01:52:40 
01:52:40 Successfully installed Deprecated-1.3.1 aiobotocore-3.8.0 aiohappyeyeballs-2.7.1 aiohttp-3.14.1 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.46 click-8.4.2 cloudpickle-3.1.2 dask-2026.7.1 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.6.0 google-crc32c-1.8.0 imageio-2.37.3 importlib_metadata-9.0.0 jmespath-1.1.0 lazy-loader-0.5 locket-1.0.0 multidict-6.7.1 networkx-3.6.1 numcodecs-0.16.5 ome-zarr-0.18.0 ome-zarr-models-1.7 omero-cli-zarr-0.5.5.dev162+gd93d4cd partd-1.4.2 propcache-0.5.2 pydantic-2.12.5 pydantic-core-2.41.5 pydantic-zarr-0.9.2 rangehttpserver-1.4.0 s3fs-2026.6.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 wrapt-2.2.2 yarl-1.24.2 zarr-3.1.6 zipp-4.1.0
01:52:40 + pip install omero-certificates
01:52:42 Collecting omero-certificates
01:52:42   Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
01:52:42 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.22.1)
01:52:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
01:52:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
01:52:42 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.6)
01:52:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.3.0)
01:52:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
01:52:42 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)
01:52:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.34.2)
01:52:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
01:52:42 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.9)
01:52:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.18)
01:52:42 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.7.0)
01:52:42 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.6.17)
01:52:42 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
01:52:42 Installing collected packages: omero-certificates
01:52:42 Successfully installed omero-certificates-0.4.0
01:52:42 + for x in *.tar.gz
01:52:42 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
01:52:43 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
01:52:43   Installing build dependencies: started
01:52:45   Installing build dependencies: finished with status 'done'
01:52:45   Getting requirements to build wheel: started
01:52:45   Getting requirements to build wheel: finished with status 'done'
01:52:45   Preparing metadata (pyproject.toml): started
01:52:45   Preparing metadata (pyproject.toml): finished with status 'done'
01:52:45 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.22.1)
01:52:45 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
01:52:45 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
01:52:45 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.6)
01:52:45 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.3.0)
01:52:45 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
01:52:45 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)
01:52:45 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
01:52:45 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
01:52:45 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.9)
01:52:45 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.18)
01:52:45 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.7.0)
01:52:45 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.6.17)
01:52:45 Building wheels for collected packages: omero-dropbox
01:52:45   Building wheel for omero-dropbox (pyproject.toml): started
01:52:45   Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
01:52:45   Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49153 sha256=dd56c678f880bb4131a7129058c0d24b097cc606e94032c73f016c42664e61f8
01:52:45   Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
01:52:46 Successfully built omero-dropbox
01:52:46 Installing collected packages: omero-dropbox
01:52:46 Successfully installed omero-dropbox-5.7.1.dev0
01:52:46 + for x in *.tar.gz
01:52:46 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
01:52:47 Processing ./omero_marshal-0.9.2.dev0.tar.gz
01:52:47   Installing build dependencies: started
01:52:48   Installing build dependencies: finished with status 'done'
01:52:48   Getting requirements to build wheel: started
01:52:49   Getting requirements to build wheel: finished with status 'done'
01:52:49   Preparing metadata (pyproject.toml): started
01:52:49   Preparing metadata (pyproject.toml): finished with status 'done'
01:52:49 Building wheels for collected packages: omero_marshal
01:52:49   Building wheel for omero_marshal (pyproject.toml): started
01:52:50   Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
01:52:50   Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88129 sha256=c2995d6a0e50a8b975052a7ec3907678102f6312465b0cd90bc9c7e69662d85e
01:52:50   Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
01:52:50 Successfully built omero_marshal
01:52:50 Installing collected packages: omero_marshal
01:52:52 Successfully installed omero_marshal-0.9.2.dev0
01:52:52 + for x in *.tar.gz
01:52:52 + pip install -U omero_py-5.22.2.dev0.tar.gz
01:52:53 Processing ./omero_py-5.22.2.dev0.tar.gz
01:52:53   Installing build dependencies: started
01:52:54   Installing build dependencies: finished with status 'done'
01:52:54   Getting requirements to build wheel: started
01:52:55   Getting requirements to build wheel: finished with status 'done'
01:52:55   Preparing metadata (pyproject.toml): started
01:52:55   Preparing metadata (pyproject.toml): finished with status 'done'
01:52:55 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.4.4)
01:52:55 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.0.0)
01:52:55 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.4.6)
01:52:55 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (12.3.0)
01:52:55 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (6.0.3)
01:52:55 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.6.5)
01:52:55 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.34.2)
01:52:55 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.2.0)
01:52:55 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.4.9)
01:52:55 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.18)
01:52:55 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2.7.0)
01:52:55 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2026.6.17)
01:52:55 Building wheels for collected packages: omero-py
01:52:55   Building wheel for omero-py (pyproject.toml): started
01:52:56   Building wheel for omero-py (pyproject.toml): finished with status 'done'
01:52:56   Created wheel for omero-py: filename=omero_py-5.22.2.dev0-py3-none-any.whl size=2787060 sha256=9d5133211e57a4e9a6a10608e75017530b73640dc4d23d6904f4b3708c882bcc
01:52:56   Stored in directory: /home/omero/.cache/pip/wheels/ec/3f/72/4027ca0a7faf1f66d4577cc07619b0497ac8e99396d43dd8fa
01:52:56 Successfully built omero-py
01:52:56 Installing collected packages: omero-py
01:52:56   Attempting uninstall: omero-py
01:52:56     Found existing installation: omero-py 5.22.1
01:52:57     Uninstalling omero-py-5.22.1:
01:53:07       Successfully uninstalled omero-py-5.22.1
01:53:21 Successfully installed omero-py-5.22.2.dev0
01:53:21 + for x in *.tar.gz
01:53:21 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
01:53:22 Processing ./omero_scripts-5.10.1.dev0.tar.gz
01:53:22   Installing build dependencies: started
01:53:23   Installing build dependencies: finished with status 'done'
01:53:23   Getting requirements to build wheel: started
01:53:24   Getting requirements to build wheel: finished with status 'done'
01:53:24   Preparing metadata (pyproject.toml): started
01:53:24   Preparing metadata (pyproject.toml): finished with status 'done'
01:53:24 Building wheels for collected packages: omero-scripts
01:53:24   Building wheel for omero-scripts (pyproject.toml): started
01:53:24   Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
01:53:24   Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137216 sha256=98e6a8b329bd627a7a262e30d387f45ed914e4e7ba412af61682d789b7ec2c55
01:53:24   Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
01:53:24 Successfully built omero-scripts
01:53:24 Installing collected packages: omero-scripts
01:53:25 Successfully installed omero-scripts-5.10.1.dev0
01:53:25 + for x in *.tar.gz
01:53:25 + pip install -U omero_web-5.32.1.dev0.tar.gz
01:53:26 Processing ./omero_web-5.32.1.dev0.tar.gz
01:53:26   Installing build dependencies: started
01:53:28   Installing build dependencies: finished with status 'done'
01:53:28   Getting requirements to build wheel: started
01:53:28   Getting requirements to build wheel: finished with status 'done'
01:53:28   Preparing metadata (pyproject.toml): started
01:53:28   Preparing metadata (pyproject.toml): finished with status 'done'
01:53:28 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (5.22.2.dev0)
01:53:29 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.32.1.dev0)
01:53:29   Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
01:53:29 Collecting Django<5.3,>=5.2.9 (from omero-web==5.32.1.dev0)
01:53:29   Using cached django-5.2.16-py3-none-any.whl.metadata (4.1 kB)
01:53:29 Collecting django-pipeline>=4.1.0 (from omero-web==5.32.1.dev0)
01:53:29   Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
01:53:29 Collecting django-cors-headers==3.7.0 (from omero-web==5.32.1.dev0)
01:53:29   Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
01:53:29 Collecting whitenoise>=5.3.0 (from omero-web==5.32.1.dev0)
01:53:29   Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
01:53:29 Collecting gunicorn>=19.3 (from omero-web==5.32.1.dev0)
01:53:29   Using cached gunicorn-26.0.0-py3-none-any.whl.metadata (5.4 kB)
01:53:29 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (0.9.2.dev0)
01:53:29 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (12.3.0)
01:53:29 Collecting pytz (from omero-web==5.32.1.dev0)
01:53:29   Using cached pytz-2026.2-py2.py3-none-any.whl.metadata (22 kB)
01:53:29 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (3.2.0)
01:53:29 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (26.2)
01:53:29 Collecting importlib-resources (from omero-web==5.32.1.dev0)
01:53:29   Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
01:53:30 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
01:53:30   Using cached asgiref-3.12.1-py3-none-any.whl.metadata (9.4 kB)
01:53:30 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
01:53:30   Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
01:53:30 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0) (65.5.1)
01:53:30 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0)
01:53:30   Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
01:53:30 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (1.4.4)
01:53:30 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (1.0.0)
01:53:30 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (2.4.6)
01:53:30 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (6.0.3)
01:53:30 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==5.32.1.dev0) (3.6.5)
01:53:30 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (2.34.2)
01:53:30 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (3.4.9)
01:53:30 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (3.18)
01:53:30 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (2.7.0)
01:53:30 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (2026.6.17)
01:53:30 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
01:53:30 Using cached django-5.2.16-py3-none-any.whl (8.3 MB)
01:53:30 Using cached asgiref-3.12.1-py3-none-any.whl (25 kB)
01:53:30 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
01:53:30 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
01:53:30 Using cached gunicorn-26.0.0-py3-none-any.whl (212 kB)
01:53:30 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
01:53:30 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
01:53:30 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
01:53:30 Using cached pytz-2026.2-py2.py3-none-any.whl (510 kB)
01:53:30 Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
01:53:30 Building wheels for collected packages: omero-web
01:53:30   Building wheel for omero-web (pyproject.toml): started
01:53:32   Building wheel for omero-web (pyproject.toml): finished with status 'done'
01:53:32   Created wheel for omero-web: filename=omero_web-5.32.1.dev0-py3-none-any.whl size=2820645 sha256=25db9991da691256b45f1c1f402bdd21bfe6a4ae399dc27ec8dddfaee18542b7
01:53:32   Stored in directory: /home/omero/.cache/pip/wheels/e6/f6/6f/ec36dda9edad720aabd7330edafa8a6a62d6ebfa4c7467248f
01:53:32 Successfully built omero-web
01:53:32 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
01:54:34 
01:54:34 Successfully installed Django-5.2.16 asgiref-3.12.1 concurrent-log-handler-0.9.29 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-26.0.0 importlib-resources-7.1.0 omero-web-5.32.1.dev0 pytz-2026.2 sqlparse-0.5.5 wheel-0.47.0 whitenoise-6.12.0
01:54:34 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
01:54:34 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
01:54:34 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
01:54:34 --2026-07-19 01:54:34--  https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
01:54:35 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ...
01:54:35 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
01:54:35 HTTP request sent, awaiting response... 200 OK
01:54:35 Length: 139337 (136K) [text/plain]
01:54:35 Saving to: ‘Figure_To_Pdf.py’
01:54:35 
01:54:35      0K .......... .......... .......... .......... .......... 36% 2.91M 0s
01:54:35     50K .......... .......... .......... .......... .......... 73% 5.23M 0s
01:54:35    100K .......... .......... .......... ......               100% 6.75M=0.03s
01:54:35 
01:54:35 2026-07-19 01:54:35 (4.24 MB/s) - ‘Figure_To_Pdf.py’ saved [139337/139337]
01:54:35 
01:54:35 + chmod 755 Figure_To_Pdf.py
01:54:35 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
01:54:35 + omero config set omero.db.name OMERO-server
01:54:41 + omero config set omero.db.host pg
01:54:45 + omero config set omero.db.user postgres
01:54:50 + omero config set omero.data.dir /home/omero/omero-server-data
01:54:54 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
01:54:59 + omero config set omero.db.poolsize 25
01:55:03 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
01:55:08 + omero config set omero.security.trustStorePassword changeit
01:55:13 + omero config set omero.mail.config true
01:55:17 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
01:55:22 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
01:55:26 + omero certificates
01:55:30 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
01:55:30 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
01:55:31 + '[' false = true ']'
01:55:31 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
01:55:31 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
01:55:31 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
01:55:31 2026-07-19 01:55:31,298 [    omego.db] DEBUG            dbcommand => upgrade
01:55:31 2026-07-19 01:55:31,298 [    omego.db] DEBUG               dbhost => localhost
01:55:31 2026-07-19 01:55:31,298 [    omego.db] DEBUG               dbname => OMERO-server
01:55:31 2026-07-19 01:55:31,298 [    omego.db] DEBUG               dbpass => omero
01:55:31 2026-07-19 01:55:31,298 [    omego.db] DEBUG               dbuser => omero
01:55:31 2026-07-19 01:55:31,298 [    omego.db] DEBUG             rootpass => omero
01:55:31 2026-07-19 01:55:31,299 [    omego.db] DEBUG            serverdir => /home/omero/workspace/OMERO-server/OMERO.server
01:55:31 2026-07-19 01:55:31,299 [omego.extern] INFO  Executing : omero version
01:55:35 OMERO.py version:
01:55:35 OMERO.server version:
01:55:35 5.6.3-627-05c9d1bf8e-ice36-b13
01:55:35 5.22.2.dev0
01:55:35 2026-07-19 01:55:35,884 [omego.extern] INFO  Completed [4.585 s]
01:55:35 2026-07-19 01:55:35,884 [omego.extern] DEBUG Using omero CLI from omero
01:55:35 2026-07-19 01:55:35,884 [    omego.db] INFO  DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
01:55:35 2026-07-19 01:55:35,884 [omego.extern] INFO  Running [current environment]: omero config get --show-password
01:55:35 2026-07-19 01:55:35,884 [omego.extern] INFO  Executing : omero config get --show-password
01:55:40 2026-07-19 01:55:40,446 [omego.extern] INFO  Completed [4.562 s]
01:55:40 2026-07-19 01:55:40,447 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
01:55:40 2026-07-19 01:55:40,447 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
01:55:40 2026-07-19 01:55:40,453 [omego.extern] INFO  Completed [0.006 s]
01:55:40 2026-07-19 01:55:40,453 [    omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.14\n'
01:55:40 2026-07-19 01:55:40,453 [    omego.db] INFO  psql version: psql (PostgreSQL) 16.14
01:55:40 
01:55:40 2026-07-19 01:55:40,453 [omego.extern] INFO  Running [current environment]: omero config get --show-password
01:55:40 2026-07-19 01:55:40,453 [omego.extern] INFO  Executing : omero config get --show-password
01:55:45 2026-07-19 01:55:45,186 [omego.extern] INFO  Completed [4.733 s]
01:55:45 2026-07-19 01:55:45,187 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
01:55:45 2026-07-19 01:55:45,187 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
01:55:45 2026-07-19 01:55:45,202 [omego.extern] INFO  Completed [0.015 s]
01:55:45 2026-07-19 01:55:45,202 [    omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.5") at port "5432".\n'
01:55:45 2026-07-19 01:55:45,202 [    omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
01:55:45 2026-07-19 01:55:45,202 [omego.extern] INFO  Running [current environment]: omero config get --show-password
01:55:45 2026-07-19 01:55:45,202 [omego.extern] INFO  Executing : omero config get --show-password
01:55:49 2026-07-19 01:55:49,779 [omego.extern] INFO  Completed [4.577 s]
01:55:49 2026-07-19 01:55:49,779 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
01:55:49 2026-07-19 01:55:49,780 [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
01:55:49 2026-07-19 01:55:49,807 [omego.extern] INFO  Completed [0.027 s]
01:55:49 2026-07-19 01:55:49,807 [    omego.db] DEBUG stdout: b'OMERO5.4|0\n'
01:55:49 2026-07-19 01:55:49,807 [    omego.db] INFO  Current omero db version: ('OMERO5.4', '0')
01:55:49 2026-07-19 01:55:49,850 [    omego.db] INFO  Database is already at OMERO5.4__0
01:55:49 + export LANG=en_US.UTF-8
01:55:49 + LANG=en_US.UTF-8
01:55:49 + export LANGUAGE=en_US:en
01:55:49 + LANGUAGE=en_US:en
01:55:49 + export LC_ALL=en_US.UTF-8
01:55:49 + LC_ALL=en_US.UTF-8
01:55:49 + BUILD_ID=DONT_KILL_ME
01:55:49 + omero admin start
01:55:59 No descriptor given. Using etc/grid/default.xml
01:56:10 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
01:56:10 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
01:56:10 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
01:56:10 Waiting on startup. Use CTRL-C to exit
01:56:10 + omero admin waitup
01:56:15 Waiting on startup. Use CTRL-C to exit
01:56:16 + omero admin diagnostics
01:56:20 
01:56:20 ================================================================================
01:56:20 OMERO Diagnostics (admin)
01:56:20 ================================================================================
01:56:20         
01:56:20 Commands:   java -version                  21.0.11   (/usr/bin/java)
01:56:20 Commands:   python -V                      3.11.13   (/home/omero/workspace/OMERO-server/.venv3/bin/python)
01:56:20 Commands:   icegridnode --version          3.6.5     (/opt/ice-3.6.5/bin/icegridnode)
01:56:20 Commands:   icegridadmin --version         3.6.5     (/opt/ice-3.6.5/bin/icegridadmin)
01:56:20 Commands:   psql --version                 16.14     (/usr/bin/psql)
01:56:20 Commands:   openssl version                3.5.527   (/usr/bin/openssl)
01:56:20 
01:56:20 Component:  OMERO.py                       5.22.2.dev0
01:56:20 Component:  OMERO.server                   5.6.3-627-05c9d1bf8e-ice36-b13
01:56:20 
01:56:20 Server:     icegridnode                    running
01:56:20 Server:     Blitz-0                        active (pid = 34470, enabled)
01:56:20 Server:     Indexer-0                      active (pid = 34492, enabled)
01:56:20 Server:     OMERO.Glacier2                 active (pid = 34532, enabled)
01:56:20 Server:     OMERO.IceStorm                 active (pid = 34497, enabled)
01:56:20 Server:     Processor-0                    active (pid = 34513, enabled)
01:56:20 Server:     Tables-0                       active (pid = 34529, enabled)
01:56:20 
01:56:20 Log dir:    /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
01:56:20 Log files:  Blitz-0.log                    32.1 KB       errors=0    warnings=1   
01:56:20 Log files:  DropBox.log                    n/a
01:56:20 Log files:  FileServer.log                 n/a
01:56:20 Log files:  Indexer-0.log                  2.6 KB       
01:56:20 Log files:  MonitorServer.log              n/a
01:56:20 Log files:  Processor-0.log                735 B        
01:56:20 Log files:  Tables-0.log                   961 B        
01:56:20 Log files:  TestDropBox.log                n/a
01:56:20 Log files:  master.err                     empty
01:56:20 Log files:  master.out                     30.5 KB      
01:56:20 Log files:  Total size                     0.07 MB
01:56:20 
01:56:20 
01:56:20 Environment:OMERO_HOME=(unset)             
01:56:20 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 
01:56:20 Environment:OMERO_NODE=(unset)             
01:56:20 Environment:OMERO_MASTER=(unset)           
01:56:20 Environment:OMERO_USERDIR=(unset)          
01:56:20 Environment:OMERO_TMPDIR=(unset)           
01:56:20 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 
01:56:20 Environment:PYTHONPATH=(unset)             
01:56:20 Environment:ICE_HOME=/opt/ice-3.6.5        
01:56:20 Environment:LD_LIBRARY_PATH=(unset)        
01:56:20 Environment:DYLD_LIBRARY_PATH=(unset)      
01:56:20 
01:56:20 OMERO SSL port:4064                           
01:56:20 OMERO TCP port:4063                           
01:56:20 OMERO data dir:'/home/omero/omero-server-data' Exists? True	Is writable? True
01:56:20 OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)
01:56:20 
01:56:20 JVM settings: Blitz-${index}                -Xmx7200m
01:56:20 JVM settings: Indexer-${index}              -Xmx4800m
01:56:20 JVM settings: PixelData-${index}            -Xmx7200m
01:56:20 JVM settings: Repository-${index}           -Xmx4800m
01:56:21 
01:56:21 Jar:        lib/server/formats-api.jar     Bio-Formats API	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
01:56:21 Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
01:56:21 Jar:        lib/server/formats-gpl.jar     Bio-Formats library	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
01:56:21 Jar:        lib/server/ome-codecs.jar      OME Codecs	1.1.3	26 February 2026	70fd9b72a9834f1af4852c1e5b5676c57a2c360e
01:56:21 Jar:        lib/server/ome-common.jar      OME Common Java	6.2.1	27 February 2026	a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
01:56:21 Jar:        lib/server/ome-jai.jar         OME JAI	0.1.5	30 June 2025	257a1c1410c0103485248d05752a5174262a38b6
01:56:21 Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)	5.3.4	25 June 2025	57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
01:56:21 Jar:        lib/server/ome-poi.jar         OME POI	5.3.11	11 November 2025	a2f3944ac71db9e7e51a6f64ec46beeb60613afb
01:56:21 Jar:        lib/server/ome-xml.jar         OME XML library	6.5.3	22 January 2026	21d1362abd9ce26e13888d2b2d028753d21ac96e
01:56:21 Jar:        lib/server/omero-blitz.jar     jar	5.8.6-SNAPSHOT		
01:56:21 Jar:        lib/server/omero-common.jar    jar	5.7.6-SNAPSHOT		
01:56:21 Jar:        lib/server/omero-gateway.jar   jar	5.11.1-SNAPSHOT		
01:56:21 Jar:        lib/server/omero-model.jar     jar	5.7.6-SNAPSHOT		
01:56:21 Jar:        lib/server/omero-renderer.jar  jar	5.6.6-SNAPSHOT		
01:56:21 Jar:        lib/server/omero-romio.jar     jar	5.8.6-SNAPSHOT		
01:56:21 Jar:        lib/server/omero-server.jar    jar	5.7.6-SNAPSHOT		
01:56:21 + deactivate
01:56:21 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
01:56:21 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:56:21 + export PATH
01:56:21 + unset _OLD_VIRTUAL_PATH
01:56:21 + '[' -n '' ']'
01:56:21 + hash -r
01:56:21 + '[' -n '' ']'
01:56:21 + unset VIRTUAL_ENV
01:56:21 + unset VIRTUAL_ENV_PROMPT
01:56:21 + '[' '!' '' = nondestructive ']'
01:56:21 + unset -f deactivate
01:56:21 Finished: SUCCESS