08:28:37 Started by upstream project "Trigger" build number 53
08:28:37 originally caused by:
08:28:37 Started by user devspace
08:28:37 Restarted from build #52, stage OMERO Distribution
08:28:37 Running as SYSTEM
08:28:37 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
08:28:37 [OMERO-server] $ /bin/bash -xe /tmp/jenkins16964341123940881151.sh
08:28:37 + source /home/settings.env
08:28:37 ++ OMERO_DB_HOST=pg
08:28:37 ++ OMERO_DB_USER=postgres
08:28:37 ++ OMERO_DB_PASS=
08:28:37 ++ OMERO_ROOT_PASS=omero
08:28:37 ++ OMERO_DATA_DIR=/OMERO
08:28:37 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
08:28:37 + OMERO_DB_NAME=OMERO-server
08:28:37 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
08:28:37 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:28:37 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:28:37 + OMERO_DATA_DIR=/home/omero/omero-server-data
08:28:37 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
08:28:37 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
08:28:37 ++ deactivate nondestructive
08:28:37 ++ '[' -n '' ']'
08:28:37 ++ '[' -n '' ']'
08:28:37 ++ hash -r
08:28:37 ++ '[' -n '' ']'
08:28:37 ++ unset VIRTUAL_ENV
08:28:37 ++ unset VIRTUAL_ENV_PROMPT
08:28:37 ++ '[' '!' nondestructive = nondestructive ']'
08:28:37 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
08:28:37 ++ export VIRTUAL_ENV
08:28:37 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:28:37 ++ 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
08:28:37 ++ export PATH
08:28:37 ++ '[' -n '' ']'
08:28:37 ++ '[' -z '' ']'
08:28:37 ++ _OLD_VIRTUAL_PS1=
08:28:37 ++ PS1='(.venv3) '
08:28:37 ++ export PS1
08:28:37 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
08:28:37 ++ export VIRTUAL_ENV_PROMPT
08:28:37 ++ hash -r
08:28:37 + omero admin stop
08:28:38 Waiting on shutdown. Use CTRL-C to exit
08:28:38 .+ sleep 5
08:28:54 + deactivate
08:28:54 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
08:28:54 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:28:54 + export PATH
08:28:54 + unset _OLD_VIRTUAL_PATH
08:28:54 + '[' -n '' ']'
08:28:54 + hash -r
08:28:54 + '[' -n '' ']'
08:28:54 + unset VIRTUAL_ENV
08:28:54 + unset VIRTUAL_ENV_PROMPT
08:28:54 + '[' '!' '' = nondestructive ']'
08:28:54 + unset -f deactivate
08:28:54 + rm -rf /home/omero/workspace/OMERO-server/.venv3
08:28:54 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
08:28:58 + '[' false = true ']'
08:28:58 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
08:28:58 Skipping PURGE_DATA:CleanDbAndRepo
08:28:58 + 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
08:28:59 Copied 1 artifact from "OMERO-build" build number 30
08:29:00 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 27
08:29:00 Copied 2 artifacts from "OMERO-build-build" build number 31
08:29:00 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 24
08:29:00 [OMERO-server] $ /bin/bash -xe /tmp/jenkins15366464512803881370.sh
08:29:00 + source /home/settings.env
08:29:00 ++ OMERO_DB_HOST=pg
08:29:00 ++ OMERO_DB_USER=postgres
08:29:00 ++ OMERO_DB_PASS=
08:29:00 ++ OMERO_ROOT_PASS=omero
08:29:00 ++ OMERO_DATA_DIR=/OMERO
08:29:00 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
08:29:00 + OMERO_DB_NAME=OMERO-server
08:29:00 + OMERO_DATA_DIR=/home/omero/omero-server-data
08:29:00 + mkdir -p /home/omero/omero-server-data
08:29:00 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
08:29:00 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:29:00 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:29:00 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
08:29:00 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
08:29:00 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
08:29:00 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
08:29:00 ++ ls OMERO.server-5.6.3-585-e85749924e-ice36-b30.zip
08:29:00 + ZIP=OMERO.server-5.6.3-585-e85749924e-ice36-b30.zip
08:29:00 + '[' '!' -z '' ']'
08:29:00 + DIST=OMERO.server-5.6.3-585-e85749924e-ice36-b30
08:29:00 + unzip OMERO.server-5.6.3-585-e85749924e-ice36-b30.zip
08:29:00 Archive: OMERO.server-5.6.3-585-e85749924e-ice36-b30.zip
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/blitz/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/grid/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/profiles/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/error/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/grid/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/luts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/luts/janelia/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/luts/matplotlib/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/luts/ncsa_paledit/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/luts/seaborn/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/luts/wcif/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/analysis_scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/annotation_scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/export_scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/figure_scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/import_scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/scripts/omero/util_scripts/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/server/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/share/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/share/licenses/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/misc/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__1/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__10/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__11/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__2/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__3/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__4/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__5/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__6/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__7/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__8/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3A__9/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3__4/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3__5/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3__6/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO3__7/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO4.1__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO4.2__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO4.2__0/t/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO4.3__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO4.4__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO4__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.0__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.1__1/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.2__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4DEV__1/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4DEV__2/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4DEV__3/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/var/
08:29:00 creating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/var/tmp/
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/LICENSE.txt
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/backup.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/blitz/mail-senders.example
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/blitz/mail-server.example
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/build.properties
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/env.bat
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/env.sh
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/hibernate.properties
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/ice.config
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/logback-cli.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/logback-indexing-cli.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/logback-indexing.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/logback.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/mime.types
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/node1.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/node2.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/omero.properties
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/profiles/psql
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/rollover.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/Windows.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/error/maintainance.html
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/grid/README
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/grid/default.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/grid/templates.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/grid/windefault.xml
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/ice.config
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/internal.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/master.cfg
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/templates/robot.template
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/etc/testdropbox.config
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/history.rst
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/OMEZarrReader.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/accessors-smart.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/activation.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/aggdesigner-algorithm.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/aircompressor.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/annotations.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/antlr.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/aopalliance.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/apiguardian-api.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/asm.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/avatica-core.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/avatica-metrics.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/aws-java-sdk-core.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/aws-java-sdk-kms.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/aws-java-sdk-s3.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/base.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-anim.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-awt-util.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-bridge.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-codec.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-constants.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-css.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-dom.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-ext.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-gvt.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-i18n.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-parser.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-script.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-shared-resources.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-svg-dom.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-svggen.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-transcoder.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-util.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/batik-xml.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/btm.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/calcite-core.jar
08:29:00 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/lib/client/calcite-linq4j.jar
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08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/psql-footer.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/psql-header.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/schema.sql
08:29:02 inflating: OMERO.server-5.6.3-585-e85749924e-ice36-b30/sql/psql/OMERO5.4__0/views.sql
08:29:02 + rm -f OMERO.server-5.6.3-585-e85749924e-ice36-b30.zip
08:29:02 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-585-e85749924e-ice36-b30 /home/omero/workspace/OMERO-server/OMERO.server
08:29:02 + 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
08:29:02 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:29:02 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:29:02 --2026-01-23 08:29:02-- https://repo.maven.apache.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
08:29:02 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
08:29:02 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
08:29:02 HTTP request sent, awaiting response... 200 OK
08:29:02 Length: 889211 (868K) [application/java-archive]
08:29:02 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
08:29:02
08:29:02 0K .......... .......... .......... .......... .......... 5% 3.53M 0s
08:29:02 50K .......... .......... .......... .......... .......... 11% 7.35M 0s
08:29:02 100K .......... .......... .......... .......... .......... 17% 5.15M 0s
08:29:02 150K .......... .......... .......... .......... .......... 23% 9.81M 0s
08:29:02 200K .......... .......... .......... .......... .......... 28% 12.8M 0s
08:29:02 250K .......... .......... .......... .......... .......... 34% 12.7M 0s
08:29:02 300K .......... .......... .......... .......... .......... 40% 17.5M 0s
08:29:02 350K .......... .......... .......... .......... .......... 46% 17.7M 0s
08:29:02 400K .......... .......... .......... .......... .......... 51% 20.8M 0s
08:29:02 450K .......... .......... .......... .......... .......... 57% 18.0M 0s
08:29:02 500K .......... .......... .......... .......... .......... 63% 16.6M 0s
08:29:02 550K .......... .......... .......... .......... .......... 69% 13.1M 0s
08:29:02 600K .......... .......... .......... .......... .......... 74% 53.5M 0s
08:29:02 650K .......... .......... .......... .......... .......... 80% 11.8M 0s
08:29:02 700K .......... .......... .......... .......... .......... 86% 17.6M 0s
08:29:02 750K .......... .......... .......... .......... .......... 92% 23.5M 0s
08:29:02 800K .......... .......... .......... .......... .......... 97% 10.8M 0s
08:29:02 850K .......... ........ 100% 260M=0.07s
08:29:02
08:29:02 2026-01-23 08:29:02 (11.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
08:29:02
08:29:02 + 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
08:29:02 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:29:02 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:29:02 --2026-01-23 08:29:02-- https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
08:29:02 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
08:29:02 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.18.12|:443... connected.
08:29:03 HTTP request sent, awaiting response... 200 OK
08:29:03 Length: 73309 (72K) [application/java-archive]
08:29:03 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
08:29:03
08:29:03 0K .......... .......... .......... .......... .......... 69% 3.45M 0s
08:29:03 50K .......... .......... . 100% 11.0M=0.02s
08:29:03
08:29:03 2026-01-23 08:29:03 (4.35 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
08:29:03
08:29:03 + 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
08:29:03 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:29:03 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:29:03 --2026-01-23 08:29:03-- https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
08:29:03 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
08:29:03 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
08:29:03 HTTP request sent, awaiting response... 200 OK
08:29:03 Length: 63303 (62K) [application/java-archive]
08:29:03 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
08:29:03
08:29:03 0K .......... .......... .......... .......... .......... 80% 31.8M 0s
08:29:03 50K .......... . 100% 173M=0.002s
08:29:03
08:29:03 2026-01-23 08:29:03 (37.7 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
08:29:03
08:29:03 + 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
08:29:03 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:29:03 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:29:03 --2026-01-23 08:29:03-- https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
08:29:03 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:120c, ...
08:29:03 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.18.12|:443... connected.
08:29:03 HTTP request sent, awaiting response... 200 OK
08:29:03 Length: 1271272 (1.2M) [application/java-archive]
08:29:03 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
08:29:03
08:29:03 0K .......... .......... .......... .......... .......... 4% 3.51M 0s
08:29:03 50K .......... .......... .......... .......... .......... 8% 22.9M 0s
08:29:03 100K .......... .......... .......... .......... .......... 12% 3.31M 0s
08:29:03 150K .......... .......... .......... .......... .......... 16% 10.7M 0s
08:29:03 200K .......... .......... .......... .......... .......... 20% 13.6M 0s
08:29:03 250K .......... .......... .......... .......... .......... 24% 22.2M 0s
08:29:03 300K .......... .......... .......... .......... .......... 28% 9.65M 0s
08:29:03 350K .......... .......... .......... .......... .......... 32% 17.9M 0s
08:29:03 400K .......... .......... .......... .......... .......... 36% 14.0M 0s
08:29:03 450K .......... .......... .......... .......... .......... 40% 20.3M 0s
08:29:03 500K .......... .......... .......... .......... .......... 44% 347M 0s
08:29:03 550K .......... .......... .......... .......... .......... 48% 9.99M 0s
08:29:03 600K .......... .......... .......... .......... .......... 52% 42.0M 0s
08:29:03 650K .......... .......... .......... .......... .......... 56% 9.39M 0s
08:29:03 700K .......... .......... .......... .......... .......... 60% 22.6M 0s
08:29:03 750K .......... .......... .......... .......... .......... 64% 278M 0s
08:29:03 800K .......... .......... .......... .......... .......... 68% 10.2M 0s
08:29:03 850K .......... .......... .......... .......... .......... 72% 36.2M 0s
08:29:03 900K .......... .......... .......... .......... .......... 76% 9.46M 0s
08:29:03 950K .......... .......... .......... .......... .......... 80% 20.5M 0s
08:29:03 1000K .......... .......... .......... .......... .......... 84% 330M 0s
08:29:03 1050K .......... .......... .......... .......... .......... 88% 10.9M 0s
08:29:03 1100K .......... .......... .......... .......... .......... 92% 20.5M 0s
08:29:03 1150K .......... .......... .......... .......... .......... 96% 11.6M 0s
08:29:03 1200K .......... .......... .......... .......... . 100% 20.0M=0.1s
08:29:03
08:29:03 2026-01-23 08:29:03 (12.7 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
08:29:03
08:29:03 + 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
08:29:03 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:29:03 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:29:03 --2026-01-23 08:29:03-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-core/1.12.659/aws-java-sdk-core-1.12.659.jar
08:29:03 Resolving repo1.maven.org (repo1.maven.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
08:29:03 Connecting to repo1.maven.org (repo1.maven.org)|104.18.19.12|:443... connected.
08:29:04 HTTP request sent, awaiting response... 200 OK
08:29:04 Length: 1036468 (1012K) [application/java-archive]
08:29:04 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-core-1.12.659.jar’
08:29:04
08:29:04 0K .......... .......... .......... .......... .......... 4% 3.54M 0s
08:29:04 50K .......... .......... .......... .......... .......... 9% 8.49M 0s
08:29:04 100K .......... .......... .......... .......... .......... 14% 4.59M 0s
08:29:04 150K .......... .......... .......... .......... .......... 19% 10.5M 0s
08:29:04 200K .......... .......... .......... .......... .......... 24% 12.8M 0s
08:29:04 250K .......... .......... .......... .......... .......... 29% 11.5M 0s
08:29:04 300K .......... .......... .......... .......... .......... 34% 14.5M 0s
08:29:04 350K .......... .......... .......... .......... .......... 39% 17.7M 0s
08:29:04 400K .......... .......... .......... .......... .......... 44% 25.4M 0s
08:29:04 450K .......... .......... .......... .......... .......... 49% 15.3M 0s
08:29:04 500K .......... .......... .......... .......... .......... 54% 20.2M 0s
08:29:04 550K .......... .......... .......... .......... .......... 59% 14.9M 0s
08:29:04 600K .......... .......... .......... .......... .......... 64% 23.5M 0s
08:29:04 650K .......... .......... .......... .......... .......... 69% 14.1M 0s
08:29:04 700K .......... .......... .......... .......... .......... 74% 20.1M 0s
08:29:04 750K .......... .......... .......... .......... .......... 79% 19.2M 0s
08:29:04 800K .......... .......... .......... .......... .......... 83% 15.1M 0s
08:29:04 850K .......... .......... .......... .......... .......... 88% 13.9M 0s
08:29:04 900K .......... .......... .......... .......... .......... 93% 26.9M 0s
08:29:04 950K .......... .......... .......... .......... .......... 98% 38.2M 0s
08:29:04 1000K .......... .. 100% 212M=0.08s
08:29:04
08:29:04 2026-01-23 08:29:04 (12.3 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-core-1.12.659.jar’ saved [1036468/1036468]
08:29:04
08:29:04 + for x in *.jar
08:29:04 + mv omero-zarr-pixel-buffer-0.6.2-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server
08:29:04 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
08:29:04 ++ deactivate nondestructive
08:29:04 ++ '[' -n '' ']'
08:29:04 ++ '[' -n '' ']'
08:29:04 ++ hash -r
08:29:04 ++ '[' -n '' ']'
08:29:04 ++ unset VIRTUAL_ENV
08:29:04 ++ unset VIRTUAL_ENV_PROMPT
08:29:04 ++ '[' '!' nondestructive = nondestructive ']'
08:29:04 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
08:29:04 ++ export VIRTUAL_ENV
08:29:04 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:29:04 ++ 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
08:29:04 ++ export PATH
08:29:04 ++ '[' -n '' ']'
08:29:04 ++ '[' -z '' ']'
08:29:04 ++ _OLD_VIRTUAL_PS1=
08:29:04 ++ PS1='(.venv3) '
08:29:04 ++ export PS1
08:29:04 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
08:29:04 ++ export VIRTUAL_ENV_PROMPT
08:29:04 ++ hash -r
08:29:04 + pip install -U pip
08:29:04 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
08:29:04 Collecting pip
08:29:04 Using cached pip-25.3-py3-none-any.whl (1.8 MB)
08:29:04 Installing collected packages: pip
08:29:04 Attempting uninstall: pip
08:29:04 Found existing installation: pip 22.3.1
08:29:04 Uninstalling pip-22.3.1:
08:29:04 Successfully uninstalled pip-22.3.1
08:29:05 Successfully installed pip-25.3
08:29:05 + 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
08:29:06 Collecting zeroc-ice==3.6.5
08:29:06 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)
08:29:09 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 12.8 MB/s 0:00:02
08:29:09 Installing collected packages: zeroc-ice
08:29:10 Successfully installed zeroc-ice-3.6.5
08:29:10 + pip install markdown
08:29:10 Collecting markdown
08:29:10 Using cached markdown-3.10.1-py3-none-any.whl.metadata (5.1 kB)
08:29:10 Using cached markdown-3.10.1-py3-none-any.whl (107 kB)
08:29:10 Installing collected packages: markdown
08:29:10 Successfully installed markdown-3.10.1
08:29:10 + pip install reportlab
08:29:11 Collecting reportlab
08:29:11 Using cached reportlab-4.4.9-py3-none-any.whl.metadata (1.7 kB)
08:29:11 Collecting pillow>=9.0.0 (from reportlab)
08:29:11 Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
08:29:11 Collecting charset-normalizer (from reportlab)
08:29:11 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)
08:29:11 Using cached reportlab-4.4.9-py3-none-any.whl (2.0 MB)
08:29:11 Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB)
08:29:11 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)
08:29:11 Installing collected packages: pillow, charset-normalizer, reportlab
08:29:12
08:29:12 Successfully installed charset-normalizer-3.4.4 pillow-12.1.0 reportlab-4.4.9
08:29:12 + pip install omego
08:29:13 Collecting omego
08:29:13 Using cached omego-0.7.0-py3-none-any.whl
08:29:13 Collecting future (from omego)
08:29:13 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
08:29:13 Collecting yaclifw>=0.1.1 (from omego)
08:29:13 Using cached yaclifw-0.2.0-py3-none-any.whl
08:29:13 Collecting six (from yaclifw>=0.1.1->omego)
08:29:13 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
08:29:13 Using cached future-1.0.0-py3-none-any.whl (491 kB)
08:29:13 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
08:29:13 Installing collected packages: six, future, yaclifw, omego
08:29:13
08:29:13 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
08:29:13 + pip install tables
08:29:13 Collecting tables
08:29:13 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
08:29:14 Collecting numpy>=1.20.0 (from tables)
08:29:14 Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
08:29:14 Collecting numexpr>=2.6.2 (from tables)
08:29:14 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
08:29:14 Collecting packaging (from tables)
08:29:14 Using cached packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
08:29:14 Collecting py-cpuinfo (from tables)
08:29:14 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
08:29:14 Collecting blosc2>=2.3.0 (from tables)
08:29:14 Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
08:29:14 Collecting typing-extensions>=4.4.0 (from tables)
08:29:14 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
08:29:14 Collecting ndindex (from blosc2>=2.3.0->tables)
08:29:14 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
08:29:14 Collecting msgpack (from blosc2>=2.3.0->tables)
08:29:14 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)
08:29:14 Collecting platformdirs (from blosc2>=2.3.0->tables)
08:29:14 Using cached platformdirs-4.5.1-py3-none-any.whl.metadata (12 kB)
08:29:14 Collecting requests (from blosc2>=2.3.0->tables)
08:29:14 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
08:29:14 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.4)
08:29:14 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
08:29:14 Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB)
08:29:14 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
08:29:14 Using cached urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB)
08:29:14 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
08:29:14 Using cached certifi-2026.1.4-py3-none-any.whl.metadata (2.5 kB)
08:29:14 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
08:29:14 Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
08:29:14 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
08:29:14 Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.7 MB)
08:29:14 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
08:29:14 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB)
08:29:14 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
08:29:14 Using cached packaging-26.0-py3-none-any.whl (74 kB)
08:29:14 Using cached platformdirs-4.5.1-py3-none-any.whl (18 kB)
08:29:14 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
08:29:14 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
08:29:14 Using cached idna-3.11-py3-none-any.whl (71 kB)
08:29:14 Using cached urllib3-2.6.3-py3-none-any.whl (131 kB)
08:29:14 Using cached certifi-2026.1.4-py3-none-any.whl (152 kB)
08:29:15 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
08:29:18
08:29:18 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
08:29:19 + pip install jinja2
08:29:19 Collecting jinja2
08:29:19 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
08:29:19 Collecting MarkupSafe>=2.0 (from jinja2)
08:29:19 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)
08:29:19 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
08:29:19 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
08:29:19 Installing collected packages: MarkupSafe, jinja2
08:29:19
08:29:19 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
08:29:19 + pip install omero-py
08:29:20 Collecting omero-py
08:29:20 Using cached omero_py-5.21.3-py3-none-any.whl.metadata (6.5 kB)
08:29:20 Collecting appdirs (from omero-py)
08:29:20 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
08:29:20 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
08:29:20 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.1)
08:29:20 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.1.0)
08:29:20 Collecting PyYAML (from omero-py)
08:29:20 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)
08:29:20 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
08:29:20 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
08:29:20 Collecting portalocker (from omero-py)
08:29:20 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
08:29:20 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.4)
08:29:20 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.11)
08:29:20 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.6.3)
08:29:20 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.1.4)
08:29:20 Using cached omero_py-5.21.3-py3-none-any.whl (2.8 MB)
08:29:20 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
08:29:20 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
08:29:20 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
08:29:20 Installing collected packages: appdirs, PyYAML, portalocker, omero-py
08:29:22
08:29:22 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.21.3 portalocker-3.2.0
08:29:22 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
08:29:22 Collecting omero-metadata
08:29:22 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-yaafrnnd/omero-metadata_36c34a5c79614d80954860cf1c217657
08:29:22 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-yaafrnnd/omero-metadata_36c34a5c79614d80954860cf1c217657
08:29:23 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 29cdf6af43480b2f1aa8ee54d124042345e5ef29
08:29:23 Installing build dependencies: started
08:29:23 Installing build dependencies: finished with status 'done'
08:29:23 Getting requirements to build wheel: started
08:29:24 Getting requirements to build wheel: finished with status 'done'
08:29:24 Preparing metadata (pyproject.toml): started
08:29:24 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:24 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.3)
08:29:24 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
08:29:24 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
08:29:24 Collecting pandas (from omero-metadata)
08:29:24 Using cached pandas-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
08:29:24 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
08:29:24 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
08:29:24 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.1)
08:29:24 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)
08:29:24 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)
08:29:24 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
08:29:24 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
08:29:24 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
08:29:24 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
08:29:24 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
08:29:24 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)
08:29:24 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)
08:29:24 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)
08:29:24 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)
08:29:24 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)
08:29:24 Using cached pandas-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.2 MB)
08:29:24 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
08:29:24 Building wheels for collected packages: omero-metadata
08:29:24 Building wheel for omero-metadata (pyproject.toml): started
08:29:25 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
08:29:25 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=30044bd3b4962d6e004a3e8ab38a8e8d113af311dfe56d662fc251046c6fa287
08:29:25 Stored in directory: /tmp/pip-ephem-wheel-cache-alq7540z/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
08:29:25 Successfully built omero-metadata
08:29:25 Installing collected packages: python-dateutil, pandas, omero-metadata
08:29:29
08:29:29 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.0 python-dateutil-2.9.0.post0
08:29:29 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
08:29:29 Collecting omero-cli-render
08:29:29 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-g913zelh/omero-cli-render_85d0838c5d414d6586784ee797e4d595
08:29:29 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-g913zelh/omero-cli-render_85d0838c5d414d6586784ee797e4d595
08:29:30 Running command git checkout -b merge_ci --track origin/merge_ci
08:29:30 Switched to a new branch 'merge_ci'
08:29:30 branch 'merge_ci' set up to track 'origin/merge_ci'.
08:29:30 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit ebdc8af96ee7ba55316b053389dcef6965452b3e
08:29:30 Installing build dependencies: started
08:29:31 Installing build dependencies: finished with status 'done'
08:29:31 Getting requirements to build wheel: started
08:29:32 Getting requirements to build wheel: finished with status 'done'
08:29:32 Preparing metadata (pyproject.toml): started
08:29:32 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:32 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
08:29:32 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.3)
08:29:32 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
08:29:32 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
08:29:32 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.1)
08:29:32 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)
08:29:32 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)
08:29:32 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
08:29:32 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
08:29:32 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)
08:29:32 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)
08:29:32 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)
08:29:32 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)
08:29:32 Building wheels for collected packages: omero-cli-render
08:29:32 Building wheel for omero-cli-render (pyproject.toml): started
08:29:32 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
08:29:32 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19841 sha256=58bac19fca1dc2369941ac3037caffa892a9b3d121ea1efbdf1e518a8954e27b
08:29:32 Stored in directory: /tmp/pip-ephem-wheel-cache-i962folq/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
08:29:32 Successfully built omero-cli-render
08:29:32 Installing collected packages: omero-cli-render
08:29:32 Successfully installed omero-cli-render-0.8.2.dev0
08:29:32 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
08:29:32 Collecting omero-cli-duplicate
08:29:32 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-vy5f4vys/omero-cli-duplicate_138b4d778e4a40b98f82f5be73bedbf8
08:29:32 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-vy5f4vys/omero-cli-duplicate_138b4d778e4a40b98f82f5be73bedbf8
08:29:33 Running command git checkout -b merge_ci --track origin/merge_ci
08:29:33 Switched to a new branch 'merge_ci'
08:29:33 branch 'merge_ci' set up to track 'origin/merge_ci'.
08:29:33 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 03e5b4b59507999e241ec82d93ff171bf017bb2f
08:29:33 Installing build dependencies: started
08:29:34 Installing build dependencies: finished with status 'done'
08:29:34 Getting requirements to build wheel: started
08:29:35 Getting requirements to build wheel: finished with status 'done'
08:29:35 Preparing metadata (pyproject.toml): started
08:29:35 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:35 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.3)
08:29:35 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
08:29:35 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
08:29:35 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.1)
08:29:35 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)
08:29:35 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
08:29:35 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)
08:29:35 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
08:29:35 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
08:29:35 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)
08:29:35 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)
08:29:35 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)
08:29:35 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)
08:29:35 Building wheels for collected packages: omero-cli-duplicate
08:29:35 Building wheel for omero-cli-duplicate (pyproject.toml): started
08:29:35 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
08:29:35 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=7f54f025daa837719368ae034c61a8dd908ab526d0d5b34c1aa9454f95d7eabe
08:29:35 Stored in directory: /tmp/pip-ephem-wheel-cache-o_1g1y9e/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
08:29:35 Successfully built omero-cli-duplicate
08:29:35 Installing collected packages: omero-cli-duplicate
08:29:36 Successfully installed omero-cli-duplicate-0.4.1.dev0
08:29:36 + pip install omero-certificates
08:29:36 Collecting omero-certificates
08:29:36 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
08:29:36 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.3)
08:29:36 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
08:29:36 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
08:29:36 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.1)
08:29:36 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)
08:29:36 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
08:29:36 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)
08:29:36 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
08:29:36 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
08:29:36 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)
08:29:36 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)
08:29:36 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)
08:29:36 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)
08:29:36 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
08:29:36 Installing collected packages: omero-certificates
08:29:36 Successfully installed omero-certificates-0.4.0
08:29:36 + for x in *.tar.gz
08:29:36 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
08:29:37 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
08:29:37 Installing build dependencies: started
08:29:37 Installing build dependencies: finished with status 'done'
08:29:37 Getting requirements to build wheel: started
08:29:38 Getting requirements to build wheel: finished with status 'done'
08:29:38 Preparing metadata (pyproject.toml): started
08:29:38 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:38 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.3)
08:29:38 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
08:29:38 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
08:29:38 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.1)
08:29:38 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)
08:29:38 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
08:29:38 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)
08:29:38 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
08:29:38 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
08:29:38 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)
08:29:38 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)
08:29:38 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)
08:29:38 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)
08:29:38 Building wheels for collected packages: omero-dropbox
08:29:38 Building wheel for omero-dropbox (pyproject.toml): started
08:29:38 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
08:29:38 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=99050e15d10ff67ad46427343ea48312ed965ec26a1638201217122dd7798c8c
08:29:38 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
08:29:38 Successfully built omero-dropbox
08:29:38 Installing collected packages: omero-dropbox
08:29:38 Successfully installed omero-dropbox-5.7.1.dev0
08:29:38 + for x in *.tar.gz
08:29:38 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
08:29:39 Processing ./omero_marshal-0.9.2.dev0.tar.gz
08:29:39 Installing build dependencies: started
08:29:39 Installing build dependencies: finished with status 'done'
08:29:39 Getting requirements to build wheel: started
08:29:40 Getting requirements to build wheel: finished with status 'done'
08:29:40 Preparing metadata (pyproject.toml): started
08:29:40 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:40 Building wheels for collected packages: omero_marshal
08:29:40 Building wheel for omero_marshal (pyproject.toml): started
08:29:40 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
08:29:40 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88128 sha256=520df0441808e414653873f210f414b657fd80d77c3c2094fa3138847d3e2990
08:29:40 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
08:29:40 Successfully built omero_marshal
08:29:40 Installing collected packages: omero_marshal
08:29:40 Successfully installed omero_marshal-0.9.2.dev0
08:29:40 + for x in *.tar.gz
08:29:40 + pip install -U omero_py-5.22.0.dev0.tar.gz
08:29:41 Processing ./omero_py-5.22.0.dev0.tar.gz
08:29:41 Installing build dependencies: started
08:29:42 Installing build dependencies: finished with status 'done'
08:29:42 Getting requirements to build wheel: started
08:29:42 Getting requirements to build wheel: finished with status 'done'
08:29:42 Preparing metadata (pyproject.toml): started
08:29:42 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.4.4)
08:29:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.0.0)
08:29:42 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.4.1)
08:29:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (12.1.0)
08:29:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (6.0.3)
08:29:42 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)
08:29:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.32.5)
08:29:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.2.0)
08:29:42 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)
08:29:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.11)
08:29:42 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)
08:29:42 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)
08:29:42 Building wheels for collected packages: omero-py
08:29:42 Building wheel for omero-py (pyproject.toml): started
08:29:43 Building wheel for omero-py (pyproject.toml): finished with status 'done'
08:29:43 Created wheel for omero-py: filename=omero_py-5.22.0.dev0-py3-none-any.whl size=2786450 sha256=6f82c8dc790ada8ef62c65602507d78159d0d9298b859fc216c2acd809d65c88
08:29:43 Stored in directory: /home/omero/.cache/pip/wheels/b2/dd/fb/0f3c8a08eddbfe6a2bff7fe7d61ee876973c474d282bc441e3
08:29:43 Successfully built omero-py
08:29:43 Installing collected packages: omero-py
08:29:43 Attempting uninstall: omero-py
08:29:43 Found existing installation: omero-py 5.21.3
08:29:44 Uninstalling omero-py-5.21.3:
08:29:44 Successfully uninstalled omero-py-5.21.3
08:29:46 Successfully installed omero-py-5.22.0.dev0
08:29:46 + for x in *.tar.gz
08:29:46 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
08:29:46 Processing ./omero_scripts-5.9.2.dev0.tar.gz
08:29:46 Installing build dependencies: started
08:29:47 Installing build dependencies: finished with status 'done'
08:29:47 Getting requirements to build wheel: started
08:29:47 Getting requirements to build wheel: finished with status 'done'
08:29:47 Preparing metadata (pyproject.toml): started
08:29:47 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:47 Building wheels for collected packages: omero-scripts
08:29:47 Building wheel for omero-scripts (pyproject.toml): started
08:29:48 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
08:29:48 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136991 sha256=c5c9b948e73daddfae60313c080ebe5846449b1570c13a49e1035818b343ba49
08:29:48 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
08:29:48 Successfully built omero-scripts
08:29:48 Installing collected packages: omero-scripts
08:29:48 Successfully installed omero-scripts-5.9.2.dev0
08:29:48 + for x in *.tar.gz
08:29:48 + pip install -U omero_web-5.30.2.dev0.tar.gz
08:29:48 Processing ./omero_web-5.30.2.dev0.tar.gz
08:29:48 Installing build dependencies: started
08:29:49 Installing build dependencies: finished with status 'done'
08:29:49 Getting requirements to build wheel: started
08:29:50 Getting requirements to build wheel: finished with status 'done'
08:29:50 Preparing metadata (pyproject.toml): started
08:29:50 Preparing metadata (pyproject.toml): finished with status 'done'
08:29:50 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)
08:29:50 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.30.2.dev0)
08:29:50 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
08:29:50 Collecting Django<5.3,>=5.2.9 (from omero-web==5.30.2.dev0)
08:29:50 Using cached django-5.2.10-py3-none-any.whl.metadata (4.1 kB)
08:29:50 Collecting django-pipeline (from omero-web==5.30.2.dev0)
08:29:50 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
08:29:50 Collecting django-cors-headers==3.7.0 (from omero-web==5.30.2.dev0)
08:29:50 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
08:29:50 Collecting whitenoise>=5.3.0 (from omero-web==5.30.2.dev0)
08:29:50 Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
08:29:50 Collecting gunicorn>=19.3 (from omero-web==5.30.2.dev0)
08:29:50 Using cached gunicorn-24.0.0-py3-none-any.whl.metadata (4.5 kB)
08:29:50 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)
08:29:50 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (12.1.0)
08:29:50 Collecting pytz (from omero-web==5.30.2.dev0)
08:29:50 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
08:29:50 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (3.2.0)
08:29:50 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (26.0)
08:29:50 Collecting importlib-resources (from omero-web==5.30.2.dev0)
08:29:50 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
08:29:50 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
08:29:50 Using cached asgiref-3.11.0-py3-none-any.whl.metadata (9.3 kB)
08:29:50 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
08:29:50 Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
08:29:50 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)
08:29:50 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)
08:29:50 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)
08:29:50 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)
08:29:50 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)
08:29:50 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)
08:29:50 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.30.2.dev0) (65.5.1)
08:29:50 Collecting wheel (from django-pipeline->omero-web==5.30.2.dev0)
08:29:50 Using cached wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
08:29:50 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)
08:29:50 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)
08:29:50 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)
08:29:50 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)
08:29:50 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
08:29:50 Using cached django-5.2.10-py3-none-any.whl (8.3 MB)
08:29:50 Using cached asgiref-3.11.0-py3-none-any.whl (24 kB)
08:29:50 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
08:29:50 Using cached gunicorn-24.0.0-py3-none-any.whl (110 kB)
08:29:50 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
08:29:50 Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
08:29:50 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
08:29:50 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
08:29:50 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
08:29:50 Using cached wheel-0.46.3-py3-none-any.whl (30 kB)
08:29:50 Building wheels for collected packages: omero-web
08:29:50 Building wheel for omero-web (pyproject.toml): started
08:29:52 Building wheel for omero-web (pyproject.toml): finished with status 'done'
08:29:52 Created wheel for omero-web: filename=omero_web-5.30.2.dev0-py3-none-any.whl size=2818599 sha256=e0b0c2b70dc665b9d404510049f385efb1a7bd7c578fe14095a18dd307e93f3d
08:29:52 Stored in directory: /home/omero/.cache/pip/wheels/22/8a/f9/2aa2b64b8351936989ad8693ee70db658c8360167f1ee574e7
08:29:52 Successfully built omero-web
08:29:52 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
08:29:54
08:29:54 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
08:29:54 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
08:29:54 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:29:54 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:29:54 --2026-01-23 08:29:54-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
08:29:54 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.110.133, ...
08:29:55 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
08:29:55 HTTP request sent, awaiting response... 200 OK
08:29:55 Length: 129238 (126K) [text/plain]
08:29:55 Saving to: ‘Figure_To_Pdf.py’
08:29:55
08:29:55 0K .......... .......... .......... .......... .......... 39% 3.89M 0s
08:29:55 50K .......... .......... .......... .......... .......... 79% 6.46M 0s
08:29:55 100K .......... .......... ...... 100% 3.51M=0.03s
08:29:55
08:29:55 2026-01-23 08:29:55 (4.50 MB/s) - ‘Figure_To_Pdf.py’ saved [129238/129238]
08:29:55
08:29:55 + chmod 755 Figure_To_Pdf.py
08:29:55 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
08:29:55 + omero config set omero.db.name OMERO-server
08:29:56 + omero config set omero.db.host pg
08:29:57 + omero config set omero.db.user postgres
08:29:58 + omero config set omero.data.dir /home/omero/omero-server-data
08:29:59 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
08:30:00 + omero config set omero.db.poolsize 25
08:30:01 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
08:30:03 + omero config set omero.security.trustStorePassword changeit
08:30:04 + omero config set omero.mail.config true
08:30:05 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
08:30:06 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
08:30:07 + omero certificates
08:30:08 OpenSSL 3.5.1 1 Jul 2025 (Library: OpenSSL 3.5.1 1 Jul 2025)
08:30:08 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
08:30:08 + '[' false = true ']'
08:30:08 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
08:30:08 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
08:30:08 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG dbcommand => upgrade
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG dbhost => localhost
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG dbname => OMERO-server
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG dbpass => omero
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG dbuser => omero
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG rootpass => omero
08:30:08 2026-01-23 08:30:08,922 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
08:30:08 2026-01-23 08:30:08,922 [omego.extern] INFO Executing : omero version
08:30:09 OMERO.py version:
08:30:09 OMERO.server version:
08:30:09 5.6.3-585-e85749924e-ice36-b30
08:30:09 5.22.0.dev0
08:30:10 2026-01-23 08:30:10,111 [omego.extern] INFO Completed [1.189 s]
08:30:10 2026-01-23 08:30:10,111 [omego.extern] DEBUG Using omero CLI from omero
08:30:10 2026-01-23 08:30:10,111 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
08:30:10 2026-01-23 08:30:10,111 [omego.extern] INFO Running [current environment]: omero config get --show-password
08:30:10 2026-01-23 08:30:10,111 [omego.extern] INFO Executing : omero config get --show-password
08:30:11 2026-01-23 08:30:11,225 [omego.extern] INFO Completed [1.114 s]
08:30:11 2026-01-23 08:30:11,225 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
08:30:11 2026-01-23 08:30:11,225 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
08:30:11 2026-01-23 08:30:11,231 [omego.extern] INFO Completed [0.005 s]
08:30:11 2026-01-23 08:30:11,231 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.11\n'
08:30:11 2026-01-23 08:30:11,231 [ omego.db] INFO psql version: psql (PostgreSQL) 16.11
08:30:11
08:30:11 2026-01-23 08:30:11,231 [omego.extern] INFO Running [current environment]: omero config get --show-password
08:30:11 2026-01-23 08:30:11,231 [omego.extern] INFO Executing : omero config get --show-password
08:30:12 2026-01-23 08:30:12,371 [omego.extern] INFO Completed [1.140 s]
08:30:12 2026-01-23 08:30:12,371 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
08:30:12 2026-01-23 08:30:12,371 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
08:30:12 2026-01-23 08:30:12,380 [omego.extern] INFO Completed [0.009 s]
08:30:12 2026-01-23 08:30:12,380 [ 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'
08:30:12 2026-01-23 08:30:12,380 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
08:30:12 2026-01-23 08:30:12,380 [omego.extern] INFO Running [current environment]: omero config get --show-password
08:30:12 2026-01-23 08:30:12,380 [omego.extern] INFO Executing : omero config get --show-password
08:30:13 2026-01-23 08:30:13,519 [omego.extern] INFO Completed [1.139 s]
08:30:13 2026-01-23 08:30:13,519 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
08:30:13 2026-01-23 08:30:13,519 [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
08:30:13 2026-01-23 08:30:13,529 [omego.extern] INFO Completed [0.010 s]
08:30:13 2026-01-23 08:30:13,530 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
08:30:13 2026-01-23 08:30:13,530 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
08:30:13 2026-01-23 08:30:13,531 [ omego.db] INFO Database is already at OMERO5.4__0
08:30:13 + export LANG=en_US.UTF-8
08:30:13 + LANG=en_US.UTF-8
08:30:13 + export LANGUAGE=en_US:en
08:30:13 + LANGUAGE=en_US:en
08:30:13 + export LC_ALL=en_US.UTF-8
08:30:13 + LC_ALL=en_US.UTF-8
08:30:13 + BUILD_ID=DONT_KILL_ME
08:30:13 + omero admin start
08:30:17 No descriptor given. Using etc/grid/default.xml
08:30:25 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
08:30:25 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
08:30:25 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
08:30:25 Waiting on startup. Use CTRL-C to exit
08:30:25 + omero admin waitup
08:30:26 Waiting on startup. Use CTRL-C to exit
08:30:26 + omero admin diagnostics
08:30:27
08:30:27 ================================================================================
08:30:27 OMERO Diagnostics (admin)
08:30:27 ================================================================================
08:30:27
08:30:27 Commands: java -version 17.0.17 (/usr/bin/java)
08:30:27 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
08:30:27 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
08:30:27 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
08:30:27 Commands: psql --version 16.11 (/usr/bin/psql)
08:30:27 Commands: openssl version 3.5.11 (/usr/bin/openssl)
08:30:27
08:30:27 Component: OMERO.py 5.22.0.dev0
08:30:27 Component: OMERO.server 5.6.3-585-e85749924e-ice36-b30
08:30:27
08:30:27 Server: icegridnode running
08:30:28 Server: Blitz-0 active (pid = 32893, enabled)
08:30:28 Server: Indexer-0 activating (enabled)
08:30:28 Server: OMERO.Glacier2 active (pid = 32928, enabled)
08:30:28 Server: OMERO.IceStorm active (pid = 32956, enabled)
08:30:28 Server: Processor-0 activating (enabled)
08:30:28 Server: Tables-0 activating (enabled)
08:30:28
08:30:28 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
08:30:28 Log files: Blitz-0.log 22.7 KB errors=0 warnings=1
08:30:28 Log files: DropBox.log n/a
08:30:28 Log files: FileServer.log n/a
08:30:28 Log files: Indexer-0.log 114 B
08:30:28 Log files: MonitorServer.log n/a
08:30:28 Log files: Processor-0.log 281 B
08:30:28 Log files: Tables-0.log 281 B
08:30:28 Log files: TestDropBox.log n/a
08:30:28 Log files: master.err empty
08:30:28 Log files: master.out 30.5 KB
08:30:28 Log files: Total size 0.05 MB
08:30:28
08:30:28
08:30:28 Environment:OMERO_HOME=(unset)
08:30:28 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:30:28 Environment:OMERO_NODE=(unset)
08:30:28 Environment:OMERO_MASTER=(unset)
08:30:28 Environment:OMERO_USERDIR=(unset)
08:30:28 Environment:OMERO_TMPDIR=(unset)
08:30:28 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
08:30:28 Environment:PYTHONPATH=(unset)
08:30:28 Environment:ICE_HOME=/opt/ice-3.6.5
08:30:28 Environment:LD_LIBRARY_PATH=(unset)
08:30:28 Environment:DYLD_LIBRARY_PATH=(unset)
08:30:28
08:30:28 OMERO SSL port:4064
08:30:28 OMERO TCP port:4063
08:30:28 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
08:30:28 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
08:30:28
08:30:28 JVM settings: Blitz-${index} -Xmx7200m
08:30:28 JVM settings: Indexer-${index} -Xmx4800m
08:30:28 JVM settings: PixelData-${index} -Xmx7200m
08:30:28 JVM settings: Repository-${index} -Xmx4800m
08:30:28
08:30:28 Jar: lib/server/formats-api.jar Bio-Formats API 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
08:30:28 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
08:30:28 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
08:30:28 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
08:30:28 Jar: lib/server/ome-common.jar OME Common Java 6.1.3-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
08:30:28 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
08:30:28 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
08:30:28 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
08:30:28 Jar: lib/server/ome-xml.jar OME XML library 6.5.4-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
08:30:28 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
08:30:28 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
08:30:28 Jar: lib/server/omero-gateway.jar jar 5.10.5-SNAPSHOT
08:30:28 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
08:30:28 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
08:30:28 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
08:30:28 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
08:30:28 Jar: lib/server/omero-zarr-pixel-buffer-0.6.2-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.6.2-SNAPSHOT e4fb0ec525b34157eab8ff984fcbb89bbea5287a
08:30:28 + deactivate
08:30:28 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
08:30:28 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:30:28 + export PATH
08:30:28 + unset _OLD_VIRTUAL_PATH
08:30:28 + '[' -n '' ']'
08:30:28 + hash -r
08:30:28 + '[' -n '' ']'
08:30:28 + unset VIRTUAL_ENV
08:30:28 + unset VIRTUAL_ENV_PROMPT
08:30:28 + '[' '!' '' = nondestructive ']'
08:30:28 + unset -f deactivate
08:30:28 Finished: SUCCESS
