11:57:28 Started by upstream project "Trigger" build number 54
11:57:28 originally caused by:
11:57:28 Started by user devspace
11:57:28 Restarted from build #53, stage OMERO Distribution
11:57:28 Running as SYSTEM
11:57:28 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
11:57:28 [OMERO-server] $ /bin/bash -xe /tmp/jenkins10685727187228832265.sh
11:57:28 + source /home/settings.env
11:57:28 ++ OMERO_DB_HOST=pg
11:57:28 ++ OMERO_DB_USER=postgres
11:57:28 ++ OMERO_DB_PASS=
11:57:28 ++ OMERO_ROOT_PASS=omero
11:57:28 ++ OMERO_DATA_DIR=/OMERO
11:57:28 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
11:57:28 + OMERO_DB_NAME=OMERO-server
11:57:28 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
11:57:28 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:57:28 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:57:28 + OMERO_DATA_DIR=/home/omero/omero-server-data
11:57:28 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
11:57:28 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
11:57:28 ++ deactivate nondestructive
11:57:28 ++ '[' -n '' ']'
11:57:28 ++ '[' -n '' ']'
11:57:28 ++ hash -r
11:57:28 ++ '[' -n '' ']'
11:57:28 ++ unset VIRTUAL_ENV
11:57:28 ++ unset VIRTUAL_ENV_PROMPT
11:57:28 ++ '[' '!' nondestructive = nondestructive ']'
11:57:28 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
11:57:28 ++ export VIRTUAL_ENV
11:57:28 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:57:28 ++ 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
11:57:28 ++ export PATH
11:57:28 ++ '[' -n '' ']'
11:57:28 ++ '[' -z '' ']'
11:57:28 ++ _OLD_VIRTUAL_PS1=
11:57:28 ++ PS1='(.venv3) '
11:57:28 ++ export PS1
11:57:28 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
11:57:28 ++ export VIRTUAL_ENV_PROMPT
11:57:28 ++ hash -r
11:57:28 + omero admin stop
11:57:29 Waiting on shutdown. Use CTRL-C to exit
11:57:29 .+ sleep 5
11:57:44 + deactivate
11:57:44 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
11:57:44 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:57:44 + export PATH
11:57:44 + unset _OLD_VIRTUAL_PATH
11:57:44 + '[' -n '' ']'
11:57:44 + hash -r
11:57:44 + '[' -n '' ']'
11:57:44 + unset VIRTUAL_ENV
11:57:44 + unset VIRTUAL_ENV_PROMPT
11:57:44 + '[' '!' '' = nondestructive ']'
11:57:44 + unset -f deactivate
11:57:44 + rm -rf /home/omero/workspace/OMERO-server/.venv3
11:57:44 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
11:57:48 + '[' false = true ']'
11:57:48 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
11:57:48 Skipping PURGE_DATA:CleanDbAndRepo
11:57:48 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.4-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-5.22.0.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.30.2.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
11:57:50 Copied 1 artifact from "OMERO-build" build number 31
11:57:50 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 27
11:57:50 Copied 2 artifacts from "OMERO-build-build" build number 31
11:57:50 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 24
11:57:50 [OMERO-server] $ /bin/bash -xe /tmp/jenkins9001918151290809068.sh
11:57:50 + source /home/settings.env
11:57:50 ++ OMERO_DB_HOST=pg
11:57:50 ++ OMERO_DB_USER=postgres
11:57:50 ++ OMERO_DB_PASS=
11:57:50 ++ OMERO_ROOT_PASS=omero
11:57:50 ++ OMERO_DATA_DIR=/OMERO
11:57:50 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
11:57:50 + OMERO_DB_NAME=OMERO-server
11:57:50 + OMERO_DATA_DIR=/home/omero/omero-server-data
11:57:50 + mkdir -p /home/omero/omero-server-data
11:57:50 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
11:57:50 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:57:50 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:57:50 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
11:57:50 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
11:57:50 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
11:57:50 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
11:57:50 ++ ls OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31.zip
11:57:50 + ZIP=OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31.zip
11:57:50 + '[' '!' -z '' ']'
11:57:50 + DIST=OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31
11:57:50 + unzip OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31.zip
11:57:50 Archive: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31.zip
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/blitz/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/grid/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/profiles/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/error/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/grid/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/luts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/luts/janelia/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/luts/matplotlib/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/luts/ncsa_paledit/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/luts/seaborn/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/luts/wcif/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/analysis_scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/annotation_scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/export_scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/figure_scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/import_scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/scripts/omero/util_scripts/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/server/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/share/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/share/licenses/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/misc/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__1/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__10/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__11/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__2/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__3/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__4/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__5/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__6/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__7/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__8/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__9/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__4/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__5/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__6/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__7/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.1__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.2__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.2__0/t/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.3__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.4__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.0__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.1__1/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.2__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4DEV__1/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4DEV__2/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4DEV__3/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/var/
11:57:50 creating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/var/tmp/
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/LICENSE.txt
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/backup.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/blitz/mail-senders.example
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/blitz/mail-server.example
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/build.properties
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/env.bat
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/env.sh
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/hibernate.properties
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/ice.config
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/logback-cli.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/logback-indexing-cli.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/logback-indexing.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/logback.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/mime.types
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/node1.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/node2.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/omero.properties
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/profiles/psql
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/rollover.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/Windows.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/error/maintainance.html
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/grid/README
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/grid/default.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/grid/templates.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/grid/windefault.xml
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/ice.config
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/internal.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/master.cfg
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/templates/robot.template
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/etc/testdropbox.config
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/history.rst
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/OMEZarrReader.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/accessors-smart.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/activation.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/aggdesigner-algorithm.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/aircompressor.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/annotations.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/antlr.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/aopalliance.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/apiguardian-api.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/asm.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/avatica-core.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/avatica-metrics.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/aws-java-sdk-core.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/aws-java-sdk-kms.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/aws-java-sdk-s3.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/base.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-anim.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-awt-util.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-bridge.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-codec.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-constants.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-css.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-dom.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-ext.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-gvt.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-i18n.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-parser.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-script.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-shared-resources.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-svg-dom.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-svggen.jar
11:57:50 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/lib/client/batik-transcoder.jar
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11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__5/OMERO3A__4.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__6/OMERO3A__5.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__7/OMERO3A__6.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__8/OMERO3A__6.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3A__9/OMERO3A__8.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__4/OMERO3__1.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__5/OMERO3__4.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__6/OMERO3__5.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO3__7/OMERO3__6.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.1__0/OMERO4__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.2__0/OMERO4.1__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO4__0/OMERO3A__11.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/psql-footer.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/psql-header.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/schema.sql
11:57:52 inflating: OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31/sql/psql/OMERO5.4__0/views.sql
11:57:52 + rm -f OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31.zip
11:57:52 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-586-ad2ef7b5d8-ice36-b31 /home/omero/workspace/OMERO-server/OMERO.server
11:57:52 + wget -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo.maven.apache.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
11:57:52 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:57:52 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:57:52 --2026-01-23 11:57:52-- https://repo.maven.apache.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
11:57:53 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:130c, ...
11:57:53 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
11:57:53 HTTP request sent, awaiting response... 200 OK
11:57:53 Length: 889211 (868K) [application/java-archive]
11:57:53 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
11:57:53
11:57:53 0K .......... .......... .......... .......... .......... 5% 3.28M 0s
11:57:53 50K .......... .......... .......... .......... .......... 11% 8.45M 0s
11:57:53 100K .......... .......... .......... .......... .......... 17% 4.49M 0s
11:57:53 150K .......... .......... .......... .......... .......... 23% 10.9M 0s
11:57:53 200K .......... .......... .......... .......... .......... 28% 10.8M 0s
11:57:53 250K .......... .......... .......... .......... .......... 34% 10.7M 0s
11:57:53 300K .......... .......... .......... .......... .......... 40% 25.3M 0s
11:57:53 350K .......... .......... .......... .......... .......... 46% 17.0M 0s
11:57:53 400K .......... .......... .......... .......... .......... 51% 17.1M 0s
11:57:53 450K .......... .......... .......... .......... .......... 57% 19.7M 0s
11:57:53 500K .......... .......... .......... .......... .......... 63% 18.1M 0s
11:57:53 550K .......... .......... .......... .......... .......... 69% 13.2M 0s
11:57:53 600K .......... .......... .......... .......... .......... 74% 23.4M 0s
11:57:53 650K .......... .......... .......... .......... .......... 80% 13.2M 0s
11:57:53 700K .......... .......... .......... .......... .......... 86% 19.8M 0s
11:57:53 750K .......... .......... .......... .......... .......... 92% 26.9M 0s
11:57:53 800K .......... .......... .......... .......... .......... 97% 13.1M 0s
11:57:53 850K .......... ........ 100% 199M=0.08s
11:57:53
11:57:53 2026-01-23 11:57:53 (11.2 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
11:57:53
11:57:53 + wget -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
11:57:53 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:57:53 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:57:53 --2026-01-23 11:57:53-- https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
11:57:53 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
11:57:53 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
11:57:53 HTTP request sent, awaiting response... 200 OK
11:57:53 Length: 73309 (72K) [application/java-archive]
11:57:53 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
11:57:53
11:57:53 0K .......... .......... .......... .......... .......... 69% 29.3M 0s
11:57:53 50K .......... .......... . 100% 1.68M=0.01s
11:57:53
11:57:53 2026-01-23 11:57:53 (4.92 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
11:57:53
11:57:53 + wget -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
11:57:53 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:57:53 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:57:53 --2026-01-23 11:57:53-- https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
11:57:53 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
11:57:53 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
11:57:53 HTTP request sent, awaiting response... 200 OK
11:57:53 Length: 63303 (62K) [application/java-archive]
11:57:53 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
11:57:53
11:57:53 0K .......... .......... .......... .......... .......... 80% 3.37M 0s
11:57:53 50K .......... . 100% 76.4M=0.01s
11:57:53
11:57:53 2026-01-23 11:57:53 (4.13 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
11:57:53
11:57:53 + wget -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
11:57:53 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:57:53 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:57:53 --2026-01-23 11:57:53-- https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
11:57:54 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
11:57:54 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
11:57:54 HTTP request sent, awaiting response... 200 OK
11:57:54 Length: 1271272 (1.2M) [application/java-archive]
11:57:54 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
11:57:54
11:57:54 0K .......... .......... .......... .......... .......... 4% 3.55M 0s
11:57:54 50K .......... .......... .......... .......... .......... 8% 9.75M 0s
11:57:54 100K .......... .......... .......... .......... .......... 12% 4.87M 0s
11:57:54 150K .......... .......... .......... .......... .......... 16% 10.7M 0s
11:57:54 200K .......... .......... .......... .......... .......... 20% 12.6M 0s
11:57:54 250K .......... .......... .......... .......... .......... 24% 11.1M 0s
11:57:54 300K .......... .......... .......... .......... .......... 28% 17.2M 0s
11:57:54 350K .......... .......... .......... .......... .......... 32% 19.0M 0s
11:57:54 400K .......... .......... .......... .......... .......... 36% 24.7M 0s
11:57:54 450K .......... .......... .......... .......... .......... 40% 17.6M 0s
11:57:54 500K .......... .......... .......... .......... .......... 44% 13.7M 0s
11:57:54 550K .......... .......... .......... .......... .......... 48% 24.7M 0s
11:57:54 600K .......... .......... .......... .......... .......... 52% 14.2M 0s
11:57:54 650K .......... .......... .......... .......... .......... 56% 16.6M 0s
11:57:54 700K .......... .......... .......... .......... .......... 60% 25.6M 0s
11:57:54 750K .......... .......... .......... .......... .......... 64% 15.0M 0s
11:57:54 800K .......... .......... .......... .......... .......... 68% 21.9M 0s
11:57:54 850K .......... .......... .......... .......... .......... 72% 13.2M 0s
11:57:54 900K .......... .......... .......... .......... .......... 76% 32.2M 0s
11:57:54 950K .......... .......... .......... .......... .......... 80% 16.2M 0s
11:57:54 1000K .......... .......... .......... .......... .......... 84% 25.3M 0s
11:57:54 1050K .......... .......... .......... .......... .......... 88% 13.4M 0s
11:57:54 1100K .......... .......... .......... .......... .......... 92% 13.2M 0s
11:57:54 1150K .......... .......... .......... .......... .......... 96% 30.3M 0s
11:57:54 1200K .......... .......... .......... .......... . 100% 35.4M=0.09s
11:57:54
11:57:54 2026-01-23 11:57:54 (13.3 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
11:57:54
11:57:54 + wget -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-core/1.12.659/aws-java-sdk-core-1.12.659.jar
11:57:54 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:57:54 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:57:54 --2026-01-23 11:57:54-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-core/1.12.659/aws-java-sdk-core-1.12.659.jar
11:57:54 Resolving repo1.maven.org (repo1.maven.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
11:57:54 Connecting to repo1.maven.org (repo1.maven.org)|104.18.18.12|:443... connected.
11:57:54 HTTP request sent, awaiting response... 200 OK
11:57:54 Length: 1036468 (1012K) [application/java-archive]
11:57:54 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-core-1.12.659.jar’
11:57:54
11:57:54 0K .......... .......... .......... .......... .......... 4% 35.3M 0s
11:57:54 50K .......... .......... .......... .......... .......... 9% 3.55M 0s
11:57:54 100K .......... .......... .......... .......... .......... 14% 162M 0s
11:57:54 150K .......... .......... .......... .......... .......... 19% 3.74M 0s
11:57:54 200K .......... .......... .......... .......... .......... 24% 79.5M 0s
11:57:54 250K .......... .......... .......... .......... .......... 29% 93.2M 0s
11:57:54 300K .......... .......... .......... .......... .......... 34% 61.5M 0s
11:57:54 350K .......... .......... .......... .......... .......... 39% 56.6M 0s
11:57:54 400K .......... .......... .......... .......... .......... 44% 4.28M 0s
11:57:54 450K .......... .......... .......... .......... .......... 49% 239M 0s
11:57:54 500K .......... .......... .......... .......... .......... 54% 82.5M 0s
11:57:54 550K .......... .......... .......... .......... .......... 59% 51.0M 0s
11:57:54 600K .......... .......... .......... .......... .......... 64% 254M 0s
11:57:54 650K .......... .......... .......... .......... .......... 69% 4.09M 0s
11:57:54 700K .......... .......... .......... .......... .......... 74% 98.3M 0s
11:57:54 750K .......... .......... .......... .......... .......... 79% 62.1M 0s
11:57:54 800K .......... .......... .......... .......... .......... 83% 263M 0s
11:57:54 850K .......... .......... .......... .......... .......... 88% 56.0M 0s
11:57:54 900K .......... .......... .......... .......... .......... 93% 4.12M 0s
11:57:54 950K .......... .......... .......... .......... .......... 98% 67.5M 0s
11:57:54 1000K .......... .. 100% 202M=0.07s
11:57:54
11:57:54 2026-01-23 11:57:54 (13.8 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-core-1.12.659.jar’ saved [1036468/1036468]
11:57:54
11:57:54 + for x in *.jar
11:57:54 + mv omero-zarr-pixel-buffer-0.6.2-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server
11:57:54 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
11:57:54 ++ deactivate nondestructive
11:57:54 ++ '[' -n '' ']'
11:57:54 ++ '[' -n '' ']'
11:57:54 ++ hash -r
11:57:54 ++ '[' -n '' ']'
11:57:54 ++ unset VIRTUAL_ENV
11:57:54 ++ unset VIRTUAL_ENV_PROMPT
11:57:54 ++ '[' '!' nondestructive = nondestructive ']'
11:57:54 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
11:57:54 ++ export VIRTUAL_ENV
11:57:54 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:57:54 ++ 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
11:57:54 ++ export PATH
11:57:54 ++ '[' -n '' ']'
11:57:54 ++ '[' -z '' ']'
11:57:54 ++ _OLD_VIRTUAL_PS1=
11:57:54 ++ PS1='(.venv3) '
11:57:54 ++ export PS1
11:57:54 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
11:57:54 ++ export VIRTUAL_ENV_PROMPT
11:57:54 ++ hash -r
11:57:54 + pip install -U pip
11:57:54 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
11:57:55 Collecting pip
11:57:55 Using cached pip-25.3-py3-none-any.whl (1.8 MB)
11:57:55 Installing collected packages: pip
11:57:55 Attempting uninstall: pip
11:57:55 Found existing installation: pip 22.3.1
11:57:55 Uninstalling pip-22.3.1:
11:57:55 Successfully uninstalled pip-22.3.1
11:57:56 Successfully installed pip-25.3
11:57:56 + 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
11:57:56 Collecting zeroc-ice==3.6.5
11:57:56 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)
11:57:58 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 21.3 MB/s 0:00:01
11:57:58 Installing collected packages: zeroc-ice
11:57:59 Successfully installed zeroc-ice-3.6.5
11:57:59 + pip install markdown
11:58:00 Collecting markdown
11:58:00 Using cached markdown-3.10.1-py3-none-any.whl.metadata (5.1 kB)
11:58:00 Using cached markdown-3.10.1-py3-none-any.whl (107 kB)
11:58:00 Installing collected packages: markdown
11:58:00 Successfully installed markdown-3.10.1
11:58:00 + pip install reportlab
11:58:00 Collecting reportlab
11:58:00 Using cached reportlab-4.4.9-py3-none-any.whl.metadata (1.7 kB)
11:58:00 Collecting pillow>=9.0.0 (from reportlab)
11:58:00 Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
11:58:00 Collecting charset-normalizer (from reportlab)
11:58:00 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)
11:58:00 Using cached reportlab-4.4.9-py3-none-any.whl (2.0 MB)
11:58:00 Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB)
11:58:00 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)
11:58:01 Installing collected packages: pillow, charset-normalizer, reportlab
11:58:01
11:58:01 Successfully installed charset-normalizer-3.4.4 pillow-12.1.0 reportlab-4.4.9
11:58:02 + pip install omego
11:58:02 Collecting omego
11:58:02 Using cached omego-0.7.0-py3-none-any.whl
11:58:02 Collecting future (from omego)
11:58:02 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
11:58:02 Collecting yaclifw>=0.1.1 (from omego)
11:58:02 Using cached yaclifw-0.2.0-py3-none-any.whl
11:58:02 Collecting six (from yaclifw>=0.1.1->omego)
11:58:02 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
11:58:02 Using cached future-1.0.0-py3-none-any.whl (491 kB)
11:58:02 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
11:58:02 Installing collected packages: six, future, yaclifw, omego
11:58:02
11:58:02 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
11:58:02 + pip install tables
11:58:03 Collecting tables
11:58:03 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
11:58:03 Collecting numpy>=1.20.0 (from tables)
11:58:03 Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
11:58:03 Collecting numexpr>=2.6.2 (from tables)
11:58:03 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
11:58:03 Collecting packaging (from tables)
11:58:03 Using cached packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
11:58:03 Collecting py-cpuinfo (from tables)
11:58:03 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
11:58:03 Collecting blosc2>=2.3.0 (from tables)
11:58:03 Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
11:58:03 Collecting typing-extensions>=4.4.0 (from tables)
11:58:03 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
11:58:03 Collecting ndindex (from blosc2>=2.3.0->tables)
11:58:03 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
11:58:03 Collecting msgpack (from blosc2>=2.3.0->tables)
11:58:03 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)
11:58:04 Collecting platformdirs (from blosc2>=2.3.0->tables)
11:58:04 Using cached platformdirs-4.5.1-py3-none-any.whl.metadata (12 kB)
11:58:04 Collecting requests (from blosc2>=2.3.0->tables)
11:58:04 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
11:58:04 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.4)
11:58:04 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
11:58:04 Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB)
11:58:04 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
11:58:04 Using cached urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB)
11:58:04 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
11:58:04 Using cached certifi-2026.1.4-py3-none-any.whl.metadata (2.5 kB)
11:58:04 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
11:58:04 Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
11:58:04 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
11:58:04 Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.7 MB)
11:58:04 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
11:58:04 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB)
11:58:04 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
11:58:04 Using cached packaging-26.0-py3-none-any.whl (74 kB)
11:58:04 Using cached platformdirs-4.5.1-py3-none-any.whl (18 kB)
11:58:04 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
11:58:04 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
11:58:04 Using cached idna-3.11-py3-none-any.whl (71 kB)
11:58:04 Using cached urllib3-2.6.3-py3-none-any.whl (131 kB)
11:58:04 Using cached certifi-2026.1.4-py3-none-any.whl (152 kB)
11:58:04 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
11:58:07
11:58:07 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-26.0 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
11:58:07 + pip install jinja2
11:58:07 Collecting jinja2
11:58:07 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
11:58:08 Collecting MarkupSafe>=2.0 (from jinja2)
11:58:08 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)
11:58:08 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
11:58:08 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
11:58:08 Installing collected packages: MarkupSafe, jinja2
11:58:08
11:58:08 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
11:58:08 + pip install omero-py
11:58:08 Collecting omero-py
11:58:08 Using cached omero_py-5.21.3-py3-none-any.whl.metadata (6.5 kB)
11:58:08 Collecting appdirs (from omero-py)
11:58:08 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
11:58:08 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
11:58:08 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.1)
11:58:08 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.1.0)
11:58:08 Collecting PyYAML (from omero-py)
11:58:08 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)
11:58:08 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
11:58:08 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
11:58:08 Collecting portalocker (from omero-py)
11:58:08 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
11:58:08 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.4)
11:58:08 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.11)
11:58:08 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.6.3)
11:58:08 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.1.4)
11:58:08 Using cached omero_py-5.21.3-py3-none-any.whl (2.8 MB)
11:58:08 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
11:58:08 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
11:58:08 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
11:58:08 Installing collected packages: appdirs, PyYAML, portalocker, omero-py
11:58:10
11:58:10 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.21.3 portalocker-3.2.0
11:58:10 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
11:58:10 Collecting omero-metadata
11:58:10 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-z35fbd8y/omero-metadata_921db6f3a02048fb85d97526eb6f2f4e
11:58:10 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-z35fbd8y/omero-metadata_921db6f3a02048fb85d97526eb6f2f4e
11:58:12 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit fcf137836b5576de59463a1392f743cb3a20e665
11:58:12 Installing build dependencies: started
11:58:13 Installing build dependencies: finished with status 'done'
11:58:13 Getting requirements to build wheel: started
11:58:13 Getting requirements to build wheel: finished with status 'done'
11:58:13 Preparing metadata (pyproject.toml): started
11:58:13 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:13 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.3)
11:58:13 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
11:58:13 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
11:58:13 Collecting pandas (from omero-metadata)
11:58:13 Using cached pandas-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
11:58:13 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
11:58:13 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
11:58:13 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.1)
11:58:13 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)
11:58:13 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)
11:58:13 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
11:58:13 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
11:58:13 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
11:58:13 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
11:58:13 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
11:58:13 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)
11:58:13 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)
11:58:13 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)
11:58:13 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)
11:58:13 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)
11:58:13 Using cached pandas-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.2 MB)
11:58:13 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
11:58:13 Building wheels for collected packages: omero-metadata
11:58:13 Building wheel for omero-metadata (pyproject.toml): started
11:58:14 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
11:58:14 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=a50d291db62d9c9da1a36e025e824dd783afc967bc3fd481aaf19bf7d1b34e89
11:58:14 Stored in directory: /tmp/pip-ephem-wheel-cache-51ozxvht/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
11:58:14 Successfully built omero-metadata
11:58:14 Installing collected packages: python-dateutil, pandas, omero-metadata
11:58:18
11:58:18 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.0 python-dateutil-2.9.0.post0
11:58:18 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
11:58:18 Collecting omero-cli-render
11:58:18 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-j9dhdzqu/omero-cli-render_fc28622b072c402d814e43901ac01b46
11:58:18 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-j9dhdzqu/omero-cli-render_fc28622b072c402d814e43901ac01b46
11:58:19 Running command git checkout -b merge_ci --track origin/merge_ci
11:58:20 Switched to a new branch 'merge_ci'
11:58:20 branch 'merge_ci' set up to track 'origin/merge_ci'.
11:58:20 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit d7b565b4c2e412d739d1ddc4923c02495a1220c4
11:58:20 Installing build dependencies: started
11:58:20 Installing build dependencies: finished with status 'done'
11:58:20 Getting requirements to build wheel: started
11:58:21 Getting requirements to build wheel: finished with status 'done'
11:58:21 Preparing metadata (pyproject.toml): started
11:58:21 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:21 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
11:58:21 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.3)
11:58:21 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
11:58:21 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
11:58:21 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.1)
11:58:21 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)
11:58:21 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)
11:58:21 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
11:58:21 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
11:58:21 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)
11:58:21 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)
11:58:21 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)
11:58:21 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)
11:58:21 Building wheels for collected packages: omero-cli-render
11:58:21 Building wheel for omero-cli-render (pyproject.toml): started
11:58:21 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
11:58:21 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19841 sha256=2c721bff6674f5baec1b7829121d2e20295d9be145b7453f42cc38ace89c9945
11:58:21 Stored in directory: /tmp/pip-ephem-wheel-cache-c1sfk0lz/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
11:58:21 Successfully built omero-cli-render
11:58:21 Installing collected packages: omero-cli-render
11:58:21 Successfully installed omero-cli-render-0.8.2.dev0
11:58:21 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
11:58:21 Collecting omero-cli-duplicate
11:58:21 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-murvacnj/omero-cli-duplicate_376c5014364d46f889bcf8b0400aee38
11:58:21 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-murvacnj/omero-cli-duplicate_376c5014364d46f889bcf8b0400aee38
11:58:25 Running command git checkout -b merge_ci --track origin/merge_ci
11:58:26 Switched to a new branch 'merge_ci'
11:58:26 branch 'merge_ci' set up to track 'origin/merge_ci'.
11:58:26 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 8ed30554af473b8b66daecc546237d807dffec71
11:58:26 Installing build dependencies: started
11:58:26 Installing build dependencies: finished with status 'done'
11:58:26 Getting requirements to build wheel: started
11:58:27 Getting requirements to build wheel: finished with status 'done'
11:58:27 Preparing metadata (pyproject.toml): started
11:58:27 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:27 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.3)
11:58:27 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
11:58:27 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
11:58:27 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.1)
11:58:27 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)
11:58:27 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
11:58:27 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)
11:58:27 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
11:58:27 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
11:58:27 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)
11:58:27 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)
11:58:27 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)
11:58:27 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)
11:58:27 Building wheels for collected packages: omero-cli-duplicate
11:58:27 Building wheel for omero-cli-duplicate (pyproject.toml): started
11:58:27 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
11:58:27 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=cf8231de48fca8df883ed5c2f4635b503312a7aab83cdc83828c81f8ccfa2967
11:58:27 Stored in directory: /tmp/pip-ephem-wheel-cache-4y2mkr87/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
11:58:27 Successfully built omero-cli-duplicate
11:58:27 Installing collected packages: omero-cli-duplicate
11:58:27 Successfully installed omero-cli-duplicate-0.4.1.dev0
11:58:27 + pip install omero-certificates
11:58:28 Collecting omero-certificates
11:58:28 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
11:58:28 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.3)
11:58:28 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
11:58:28 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
11:58:28 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.1)
11:58:28 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)
11:58:28 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
11:58:28 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)
11:58:28 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
11:58:28 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
11:58:28 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)
11:58:28 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)
11:58:28 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)
11:58:28 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)
11:58:28 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
11:58:28 Installing collected packages: omero-certificates
11:58:28 Successfully installed omero-certificates-0.4.0
11:58:28 + for x in *.tar.gz
11:58:28 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
11:58:28 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
11:58:28 Installing build dependencies: started
11:58:29 Installing build dependencies: finished with status 'done'
11:58:29 Getting requirements to build wheel: started
11:58:29 Getting requirements to build wheel: finished with status 'done'
11:58:29 Preparing metadata (pyproject.toml): started
11:58:29 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:29 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.3)
11:58:29 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
11:58:29 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
11:58:29 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.1)
11:58:29 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)
11:58:29 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
11:58:29 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)
11:58:29 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
11:58:29 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
11:58:29 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)
11:58:29 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)
11:58:29 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)
11:58:29 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)
11:58:29 Building wheels for collected packages: omero-dropbox
11:58:29 Building wheel for omero-dropbox (pyproject.toml): started
11:58:30 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
11:58:30 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=81311379ef0fcd24cefd8c8ffa81cdf39a7d548e4690f18afe197db3fdd08ade
11:58:30 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
11:58:30 Successfully built omero-dropbox
11:58:30 Installing collected packages: omero-dropbox
11:58:30 Successfully installed omero-dropbox-5.7.1.dev0
11:58:30 + for x in *.tar.gz
11:58:30 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
11:58:30 Processing ./omero_marshal-0.9.2.dev0.tar.gz
11:58:30 Installing build dependencies: started
11:58:31 Installing build dependencies: finished with status 'done'
11:58:31 Getting requirements to build wheel: started
11:58:31 Getting requirements to build wheel: finished with status 'done'
11:58:31 Preparing metadata (pyproject.toml): started
11:58:31 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:31 Building wheels for collected packages: omero_marshal
11:58:31 Building wheel for omero_marshal (pyproject.toml): started
11:58:32 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
11:58:32 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88128 sha256=340e6ad51f60b535247a78e15e390a32f6d3563d9c674657eb0e759d72e607ec
11:58:32 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
11:58:32 Successfully built omero_marshal
11:58:32 Installing collected packages: omero_marshal
11:58:32 Successfully installed omero_marshal-0.9.2.dev0
11:58:32 + for x in *.tar.gz
11:58:32 + pip install -U omero_py-5.22.0.dev0.tar.gz
11:58:32 Processing ./omero_py-5.22.0.dev0.tar.gz
11:58:33 Installing build dependencies: started
11:58:33 Installing build dependencies: finished with status 'done'
11:58:33 Getting requirements to build wheel: started
11:58:34 Getting requirements to build wheel: finished with status 'done'
11:58:34 Preparing metadata (pyproject.toml): started
11:58:34 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:34 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.4.4)
11:58:34 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.0.0)
11:58:34 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.4.1)
11:58:34 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (12.1.0)
11:58:34 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (6.0.3)
11:58:34 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)
11:58:34 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.32.5)
11:58:34 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.2.0)
11:58:34 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)
11:58:34 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.11)
11:58:34 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)
11:58:34 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)
11:58:34 Building wheels for collected packages: omero-py
11:58:34 Building wheel for omero-py (pyproject.toml): started
11:58:35 Building wheel for omero-py (pyproject.toml): finished with status 'done'
11:58:35 Created wheel for omero-py: filename=omero_py-5.22.0.dev0-py3-none-any.whl size=2786450 sha256=f5eed07d6878ce3fbc37ffe664ee141f1edd1689d3571b7ff357b34f080f689b
11:58:35 Stored in directory: /home/omero/.cache/pip/wheels/b2/dd/fb/0f3c8a08eddbfe6a2bff7fe7d61ee876973c474d282bc441e3
11:58:35 Successfully built omero-py
11:58:35 Installing collected packages: omero-py
11:58:35 Attempting uninstall: omero-py
11:58:35 Found existing installation: omero-py 5.21.3
11:58:35 Uninstalling omero-py-5.21.3:
11:58:35 Successfully uninstalled omero-py-5.21.3
11:58:37 Successfully installed omero-py-5.22.0.dev0
11:58:37 + for x in *.tar.gz
11:58:37 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
11:58:37 Processing ./omero_scripts-5.9.2.dev0.tar.gz
11:58:37 Installing build dependencies: started
11:58:38 Installing build dependencies: finished with status 'done'
11:58:38 Getting requirements to build wheel: started
11:58:39 Getting requirements to build wheel: finished with status 'done'
11:58:39 Preparing metadata (pyproject.toml): started
11:58:39 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:39 Building wheels for collected packages: omero-scripts
11:58:39 Building wheel for omero-scripts (pyproject.toml): started
11:58:39 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
11:58:39 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136991 sha256=efe1b863e0538a0323d17f7d026ff537fc04e9ac5e19864db893fc35bafe68ca
11:58:39 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
11:58:39 Successfully built omero-scripts
11:58:39 Installing collected packages: omero-scripts
11:58:39 Successfully installed omero-scripts-5.9.2.dev0
11:58:39 + for x in *.tar.gz
11:58:39 + pip install -U omero_web-5.30.2.dev0.tar.gz
11:58:40 Processing ./omero_web-5.30.2.dev0.tar.gz
11:58:40 Installing build dependencies: started
11:58:41 Installing build dependencies: finished with status 'done'
11:58:41 Getting requirements to build wheel: started
11:58:41 Getting requirements to build wheel: finished with status 'done'
11:58:41 Preparing metadata (pyproject.toml): started
11:58:41 Preparing metadata (pyproject.toml): finished with status 'done'
11:58:41 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)
11:58:41 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.30.2.dev0)
11:58:41 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
11:58:41 Collecting Django<5.3,>=5.2.9 (from omero-web==5.30.2.dev0)
11:58:41 Using cached django-5.2.10-py3-none-any.whl.metadata (4.1 kB)
11:58:41 Collecting django-pipeline (from omero-web==5.30.2.dev0)
11:58:41 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
11:58:41 Collecting django-cors-headers==3.7.0 (from omero-web==5.30.2.dev0)
11:58:41 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
11:58:42 Collecting whitenoise>=5.3.0 (from omero-web==5.30.2.dev0)
11:58:42 Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
11:58:42 Collecting gunicorn>=19.3 (from omero-web==5.30.2.dev0)
11:58:42 Using cached gunicorn-24.0.0-py3-none-any.whl.metadata (4.5 kB)
11:58:42 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)
11:58:42 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (12.1.0)
11:58:42 Collecting pytz (from omero-web==5.30.2.dev0)
11:58:42 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
11:58:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (3.2.0)
11:58:42 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (26.0)
11:58:42 Collecting importlib-resources (from omero-web==5.30.2.dev0)
11:58:42 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
11:58:42 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
11:58:42 Using cached asgiref-3.11.0-py3-none-any.whl.metadata (9.3 kB)
11:58:42 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
11:58:42 Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
11:58:42 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)
11:58:42 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)
11:58:42 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)
11:58:42 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)
11:58:42 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)
11:58:42 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)
11:58:42 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.30.2.dev0) (65.5.1)
11:58:42 Collecting wheel (from django-pipeline->omero-web==5.30.2.dev0)
11:58:42 Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
11:58:42 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)
11:58:42 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)
11:58:42 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)
11:58:42 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)
11:58:42 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
11:58:42 Using cached django-5.2.10-py3-none-any.whl (8.3 MB)
11:58:42 Using cached asgiref-3.11.0-py3-none-any.whl (24 kB)
11:58:42 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
11:58:42 Using cached gunicorn-24.0.0-py3-none-any.whl (110 kB)
11:58:42 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
11:58:42 Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
11:58:42 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
11:58:42 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
11:58:42 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
11:58:42 Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
11:58:42 Building wheels for collected packages: omero-web
11:58:42 Building wheel for omero-web (pyproject.toml): started
11:58:43 Building wheel for omero-web (pyproject.toml): finished with status 'done'
11:58:43 Created wheel for omero-web: filename=omero_web-5.30.2.dev0-py3-none-any.whl size=2818599 sha256=0f5e1e11667b9071bd0c1b001bd0e51f717eef4becc0f828e5e289b68a4b379e
11:58:43 Stored in directory: /home/omero/.cache/pip/wheels/22/8a/f9/2aa2b64b8351936989ad8693ee70db658c8360167f1ee574e7
11:58:43 Successfully built omero-web
11:58:43 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
11:58:46
11:58:46 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-24.0.0 importlib-resources-6.5.2 omero-web-5.30.2.dev0 pytz-2025.2 sqlparse-0.5.5 wheel-0.46.3 whitenoise-6.11.0
11:58:46 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
11:58:46 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:58:46 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:58:46 --2026-01-23 11:58:46-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
11:58:46 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ...
11:58:46 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
11:58:46 HTTP request sent, awaiting response... 200 OK
11:58:46 Length: 129238 (126K) [text/plain]
11:58:46 Saving to: ‘Figure_To_Pdf.py’
11:58:46
11:58:46 0K .......... .......... .......... .......... .......... 39% 3.89M 0s
11:58:46 50K .......... .......... .......... .......... .......... 79% 12.5M 0s
11:58:46 100K .......... .......... ...... 100% 5.43M=0.02s
11:58:46
11:58:46 2026-01-23 11:58:46 (5.82 MB/s) - ‘Figure_To_Pdf.py’ saved [129238/129238]
11:58:46
11:58:46 + chmod 755 Figure_To_Pdf.py
11:58:46 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
11:58:46 + omero config set omero.db.name OMERO-server
11:58:47 + omero config set omero.db.host pg
11:58:48 + omero config set omero.db.user postgres
11:58:49 + omero config set omero.data.dir /home/omero/omero-server-data
11:58:51 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
11:58:52 + omero config set omero.db.poolsize 25
11:58:53 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
11:58:54 + omero config set omero.security.trustStorePassword changeit
11:58:55 + omero config set omero.mail.config true
11:58:56 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
11:58:57 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
11:58:58 + omero certificates
11:58:59 OpenSSL 3.5.1 1 Jul 2025 (Library: OpenSSL 3.5.1 1 Jul 2025)
11:58:59 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
11:59:00 + '[' false = true ']'
11:59:00 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
11:59:00 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
11:59:00 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG dbcommand => upgrade
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG dbhost => localhost
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG dbname => OMERO-server
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG dbpass => omero
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG dbuser => omero
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG rootpass => omero
11:59:00 2026-01-23 11:59:00,222 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
11:59:00 2026-01-23 11:59:00,223 [omego.extern] INFO Executing : omero version
11:59:01 OMERO.py version:
11:59:01 OMERO.server version:
11:59:01 5.6.3-586-ad2ef7b5d8-ice36-b31
11:59:01 5.22.0.dev0
11:59:01 2026-01-23 11:59:01,380 [omego.extern] INFO Completed [1.157 s]
11:59:01 2026-01-23 11:59:01,380 [omego.extern] DEBUG Using omero CLI from omero
11:59:01 2026-01-23 11:59:01,380 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
11:59:01 2026-01-23 11:59:01,380 [omego.extern] INFO Running [current environment]: omero config get --show-password
11:59:01 2026-01-23 11:59:01,380 [omego.extern] INFO Executing : omero config get --show-password
11:59:02 2026-01-23 11:59:02,486 [omego.extern] INFO Completed [1.106 s]
11:59:02 2026-01-23 11:59:02,486 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
11:59:02 2026-01-23 11:59:02,486 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
11:59:02 2026-01-23 11:59:02,492 [omego.extern] INFO Completed [0.006 s]
11:59:02 2026-01-23 11:59:02,492 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.11\n'
11:59:02 2026-01-23 11:59:02,492 [ omego.db] INFO psql version: psql (PostgreSQL) 16.11
11:59:02
11:59:02 2026-01-23 11:59:02,492 [omego.extern] INFO Running [current environment]: omero config get --show-password
11:59:02 2026-01-23 11:59:02,492 [omego.extern] INFO Executing : omero config get --show-password
11:59:03 2026-01-23 11:59:03,604 [omego.extern] INFO Completed [1.112 s]
11:59:03 2026-01-23 11:59:03,604 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
11:59:03 2026-01-23 11:59:03,604 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
11:59:03 2026-01-23 11:59:03,613 [omego.extern] INFO Completed [0.009 s]
11:59:03 2026-01-23 11:59:03,613 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.7") at port "5432".\n'
11:59:03 2026-01-23 11:59:03,613 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
11:59:03 2026-01-23 11:59:03,613 [omego.extern] INFO Running [current environment]: omero config get --show-password
11:59:03 2026-01-23 11:59:03,613 [omego.extern] INFO Executing : omero config get --show-password
11:59:04 2026-01-23 11:59:04,756 [omego.extern] INFO Completed [1.143 s]
11:59:04 2026-01-23 11:59:04,756 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
11:59:04 2026-01-23 11:59:04,756 [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
11:59:04 2026-01-23 11:59:04,767 [omego.extern] INFO Completed [0.011 s]
11:59:04 2026-01-23 11:59:04,767 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
11:59:04 2026-01-23 11:59:04,767 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
11:59:04 2026-01-23 11:59:04,768 [ omego.db] INFO Database is already at OMERO5.4__0
11:59:04 + export LANG=en_US.UTF-8
11:59:04 + LANG=en_US.UTF-8
11:59:04 + export LANGUAGE=en_US:en
11:59:04 + LANGUAGE=en_US:en
11:59:04 + export LC_ALL=en_US.UTF-8
11:59:04 + LC_ALL=en_US.UTF-8
11:59:04 + BUILD_ID=DONT_KILL_ME
11:59:04 + omero admin start
11:59:09 No descriptor given. Using etc/grid/default.xml
11:59:15 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
11:59:15 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
11:59:15 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
11:59:15 Waiting on startup. Use CTRL-C to exit
11:59:15 + omero admin waitup
11:59:17 Waiting on startup. Use CTRL-C to exit
11:59:17 + omero admin diagnostics
11:59:19
11:59:19 ================================================================================
11:59:19 OMERO Diagnostics (admin)
11:59:19 ================================================================================
11:59:19
11:59:19 Commands: java -version 17.0.17 (/usr/bin/java)
11:59:19 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
11:59:19 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
11:59:19 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
11:59:19 Commands: psql --version 16.11 (/usr/bin/psql)
11:59:19 Commands: openssl version 3.5.11 (/usr/bin/openssl)
11:59:19
11:59:19 Component: OMERO.py 5.22.0.dev0
11:59:19 Component: OMERO.server 5.6.3-586-ad2ef7b5d8-ice36-b31
11:59:19
11:59:19 Server: icegridnode running
11:59:19 Server: Blitz-0 active (pid = 42945, enabled)
11:59:19 Server: Indexer-0 activating (enabled)
11:59:19 Server: OMERO.Glacier2 active (pid = 42980, enabled)
11:59:19 Server: OMERO.IceStorm active (pid = 43008, enabled)
11:59:19 Server: Processor-0 activating (enabled)
11:59:19 Server: Tables-0 activating (enabled)
11:59:19
11:59:19 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
11:59:19 Log files: Blitz-0.log 22.7 KB errors=0 warnings=1
11:59:19 Log files: DropBox.log n/a
11:59:19 Log files: FileServer.log n/a
11:59:19 Log files: Indexer-0.log 114 B
11:59:19 Log files: MonitorServer.log n/a
11:59:19 Log files: Processor-0.log 281 B
11:59:19 Log files: Tables-0.log 281 B
11:59:19 Log files: TestDropBox.log n/a
11:59:19 Log files: master.err empty
11:59:19 Log files: master.out 30.5 KB
11:59:19 Log files: Total size 0.05 MB
11:59:19
11:59:19
11:59:19 Environment:OMERO_HOME=(unset)
11:59:19 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:59:19 Environment:OMERO_NODE=(unset)
11:59:19 Environment:OMERO_MASTER=(unset)
11:59:19 Environment:OMERO_USERDIR=(unset)
11:59:19 Environment:OMERO_TMPDIR=(unset)
11:59:19 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
11:59:19 Environment:PYTHONPATH=(unset)
11:59:19 Environment:ICE_HOME=/opt/ice-3.6.5
11:59:19 Environment:LD_LIBRARY_PATH=(unset)
11:59:19 Environment:DYLD_LIBRARY_PATH=(unset)
11:59:20
11:59:20 OMERO SSL port:4064
11:59:20 OMERO TCP port:4063
11:59:20 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
11:59:20 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
11:59:20
11:59:20 JVM settings: Blitz-${index} -Xmx7200m
11:59:20 JVM settings: Indexer-${index} -Xmx4800m
11:59:20 JVM settings: PixelData-${index} -Xmx7200m
11:59:20 JVM settings: Repository-${index} -Xmx4800m
11:59:20
11:59:20 Jar: lib/server/formats-api.jar Bio-Formats API 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
11:59:20 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
11:59:20 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
11:59:20 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
11:59:20 Jar: lib/server/ome-common.jar OME Common Java 6.1.3-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
11:59:20 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
11:59:20 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
11:59:20 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
11:59:20 Jar: lib/server/ome-xml.jar OME XML library 6.5.4-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
11:59:20 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
11:59:20 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
11:59:20 Jar: lib/server/omero-gateway.jar jar 5.10.5-SNAPSHOT
11:59:20 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
11:59:20 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
11:59:20 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
11:59:20 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
11:59:20 Jar: lib/server/omero-zarr-pixel-buffer-0.6.2-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.6.2-SNAPSHOT e4fb0ec525b34157eab8ff984fcbb89bbea5287a
11:59:20 + deactivate
11:59:20 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
11:59:20 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:59:20 + export PATH
11:59:20 + unset _OLD_VIRTUAL_PATH
11:59:20 + '[' -n '' ']'
11:59:20 + hash -r
11:59:20 + '[' -n '' ']'
11:59:20 + unset VIRTUAL_ENV
11:59:20 + unset VIRTUAL_ENV_PROMPT
11:59:20 + '[' '!' '' = nondestructive ']'
11:59:20 + unset -f deactivate
11:59:20 Finished: SUCCESS
