00:46:42 Started by upstream project "Trigger" build number 50
00:46:42 originally caused by:
00:46:42 Started by timer
00:46:42 Running as SYSTEM
00:46:42 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:46:42 [OMERO-server] $ /bin/bash -xe /tmp/jenkins4836200685643995280.sh
00:46:42 + source /home/settings.env
00:46:42 ++ OMERO_DB_HOST=pg
00:46:42 ++ OMERO_DB_USER=postgres
00:46:42 ++ OMERO_DB_PASS=
00:46:42 ++ OMERO_ROOT_PASS=omero
00:46:42 ++ OMERO_DATA_DIR=/OMERO
00:46:42 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:46:42 + OMERO_DB_NAME=OMERO-server
00:46:42 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:46:42 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:46:42 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:46:42 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:46:42 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:46:42 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:46:42 ++ deactivate nondestructive
00:46:42 ++ '[' -n '' ']'
00:46:42 ++ '[' -n '' ']'
00:46:42 ++ hash -r
00:46:42 ++ '[' -n '' ']'
00:46:42 ++ unset VIRTUAL_ENV
00:46:42 ++ unset VIRTUAL_ENV_PROMPT
00:46:42 ++ '[' '!' nondestructive = nondestructive ']'
00:46:42 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:46:42 ++ export VIRTUAL_ENV
00:46:42 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:46:42 ++ 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
00:46:42 ++ export PATH
00:46:42 ++ '[' -n '' ']'
00:46:42 ++ '[' -z '' ']'
00:46:42 ++ _OLD_VIRTUAL_PS1=
00:46:42 ++ PS1='(.venv3) '
00:46:42 ++ export PS1
00:46:42 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:46:42 ++ export VIRTUAL_ENV_PROMPT
00:46:42 ++ hash -r
00:46:42 + omero admin stop
00:46:43 Waiting on shutdown. Use CTRL-C to exit
00:46:43 .+ sleep 5
00:46:58 + deactivate
00:46:58 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:46:58 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:46:58 + export PATH
00:46:58 + unset _OLD_VIRTUAL_PATH
00:46:58 + '[' -n '' ']'
00:46:58 + hash -r
00:46:58 + '[' -n '' ']'
00:46:58 + unset VIRTUAL_ENV
00:46:58 + unset VIRTUAL_ENV_PROMPT
00:46:58 + '[' '!' '' = nondestructive ']'
00:46:58 + unset -f deactivate
00:46:58 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:46:58 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:47:02 + '[' false = true ']'
00:47:02 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:47:02 Skipping PURGE_DATA:CleanDbAndRepo
00:47:02 + 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
00:47:04 Copied 1 artifact from "OMERO-build" build number 27
00:47:05 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 27
00:47:05 Copied 2 artifacts from "OMERO-build-build" build number 31
00:47:06 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 24
00:47:06 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11600576027653073567.sh
00:47:06 + source /home/settings.env
00:47:06 ++ OMERO_DB_HOST=pg
00:47:06 ++ OMERO_DB_USER=postgres
00:47:06 ++ OMERO_DB_PASS=
00:47:06 ++ OMERO_ROOT_PASS=omero
00:47:06 ++ OMERO_DATA_DIR=/OMERO
00:47:06 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:47:06 + OMERO_DB_NAME=OMERO-server
00:47:06 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:47:06 + mkdir -p /home/omero/omero-server-data
00:47:06 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:47:06 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:06 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:06 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:47:06 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:47:06 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:47:06 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:47:06 ++ ls OMERO.server-5.6.3-583-43bd9813d6-ice36-b27.zip
00:47:06 + ZIP=OMERO.server-5.6.3-583-43bd9813d6-ice36-b27.zip
00:47:06 + '[' '!' -z '' ']'
00:47:06 + DIST=OMERO.server-5.6.3-583-43bd9813d6-ice36-b27
00:47:06 + unzip OMERO.server-5.6.3-583-43bd9813d6-ice36-b27.zip
00:47:06 Archive: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27.zip
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/blitz/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/grid/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/profiles/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/error/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/grid/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/luts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/luts/janelia/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/luts/matplotlib/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/luts/ncsa_paledit/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/luts/seaborn/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/luts/wcif/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/analysis_scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/annotation_scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/export_scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/figure_scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/import_scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/scripts/omero/util_scripts/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/server/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/share/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/share/licenses/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/misc/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__1/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__10/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__11/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__2/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__3/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__4/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__5/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__6/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__7/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__8/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3A__9/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3__4/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3__5/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3__6/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO3__7/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.1__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.2__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.2__0/t/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.3__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.4__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.0__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.1__1/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.2__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4DEV__1/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4DEV__2/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4DEV__3/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/var/
00:47:06 creating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/var/tmp/
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/LICENSE.txt
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/backup.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/blitz/mail-senders.example
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/blitz/mail-server.example
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/build.properties
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/env.bat
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/env.sh
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/hibernate.properties
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/ice.config
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/logback-cli.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/logback-indexing-cli.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/logback-indexing.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/logback.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/mime.types
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/node1.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/node2.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/omero.properties
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/profiles/psql
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/rollover.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/Windows.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/error/maintainance.html
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/grid/README
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/grid/default.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/grid/templates.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/grid/windefault.xml
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/ice.config
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/internal.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/master.cfg
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/templates/robot.template
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/etc/testdropbox.config
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/history.rst
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/OMEZarrReader.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/accessors-smart.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/activation.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/aggdesigner-algorithm.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/aircompressor.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/annotations.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/antlr.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/aopalliance.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/apiguardian-api.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/asm.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/avatica-core.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/avatica-metrics.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/aws-java-sdk-core.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/aws-java-sdk-kms.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/aws-java-sdk-s3.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/base.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-anim.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-awt-util.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-bridge.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-codec.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-constants.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-css.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-dom.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-ext.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-gvt.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-i18n.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-parser.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-script.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-shared-resources.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-svg-dom.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-svggen.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-transcoder.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-util.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/batik-xml.jar
00:47:06 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/lib/client/btm.jar
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00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO4__0/OMERO3A__11.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/psql-footer.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/psql-header.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/schema.sql
00:47:08 inflating: OMERO.server-5.6.3-583-43bd9813d6-ice36-b27/sql/psql/OMERO5.4__0/views.sql
00:47:08 + rm -f OMERO.server-5.6.3-583-43bd9813d6-ice36-b27.zip
00:47:08 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-583-43bd9813d6-ice36-b27 /home/omero/workspace/OMERO-server/OMERO.server
00:47:08 + 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
00:47:08 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:47:08 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:47:08 --2026-01-23 00:47:08-- https://repo.maven.apache.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:47:08 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
00:47:08 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.18.12|:443... connected.
00:47:08 HTTP request sent, awaiting response... 200 OK
00:47:08 Length: 889211 (868K) [application/java-archive]
00:47:08 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:47:08
00:47:08 0K .......... .......... .......... .......... .......... 5% 3.55M 0s
00:47:08 50K .......... .......... .......... .......... .......... 11% 7.67M 0s
00:47:08 100K .......... .......... .......... .......... .......... 17% 5.01M 0s
00:47:08 150K .......... .......... .......... .......... .......... 23% 11.2M 0s
00:47:08 200K .......... .......... .......... .......... .......... 28% 10.5M 0s
00:47:08 250K .......... .......... .......... .......... .......... 34% 11.0M 0s
00:47:08 300K .......... .......... .......... .......... .......... 40% 17.8M 0s
00:47:08 350K .......... .......... .......... .......... .......... 46% 28.8M 0s
00:47:08 400K .......... .......... .......... .......... .......... 51% 17.2M 0s
00:47:08 450K .......... .......... .......... .......... .......... 57% 24.4M 0s
00:47:08 500K .......... .......... .......... .......... .......... 63% 11.5M 0s
00:47:08 550K .......... .......... .......... .......... .......... 69% 25.2M 0s
00:47:08 600K .......... .......... .......... .......... .......... 74% 13.6M 0s
00:47:08 650K .......... .......... .......... .......... .......... 80% 13.3M 0s
00:47:08 700K .......... .......... .......... .......... .......... 86% 92.0M 0s
00:47:08 750K .......... .......... .......... .......... .......... 92% 12.4M 0s
00:47:09 800K .......... .......... .......... .......... .......... 97% 25.4M 0s
00:47:09 850K .......... ........ 100% 11.4M=0.07s
00:47:09
00:47:09 2026-01-23 00:47:09 (11.5 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:47:09
00:47:09 + 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
00:47:09 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:47:09 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:47:09 --2026-01-23 00:47:09-- https://repo.maven.apache.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:47:09 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
00:47:09 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.18.12|:443... connected.
00:47:09 HTTP request sent, awaiting response... 200 OK
00:47:09 Length: 73309 (72K) [application/java-archive]
00:47:09 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:47:09
00:47:09 0K .......... .......... .......... .......... .......... 69% 25.3M 0s
00:47:09 50K .......... .......... . 100% 1.79M=0.01s
00:47:09
00:47:09 2026-01-23 00:47:09 (5.09 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:47:09
00:47:09 + 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
00:47:09 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:47:09 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:47:09 --2026-01-23 00:47:09-- https://repo.maven.apache.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:47:09 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
00:47:09 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.18.12|:443... connected.
00:47:09 HTTP request sent, awaiting response... 200 OK
00:47:09 Length: 63303 (62K) [application/java-archive]
00:47:09 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:47:09
00:47:09 0K .......... .......... .......... .......... .......... 80% 36.9M 0s
00:47:09 50K .......... . 100% 143M=0.001s
00:47:09
00:47:09 2026-01-23 00:47:09 (43.0 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:47:09
00:47:09 + 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
00:47:09 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:47:09 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:47:09 --2026-01-23 00:47:09-- https://repo.maven.apache.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:47:09 Resolving repo.maven.apache.org (repo.maven.apache.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
00:47:09 Connecting to repo.maven.apache.org (repo.maven.apache.org)|104.18.19.12|:443... connected.
00:47:09 HTTP request sent, awaiting response... 200 OK
00:47:09 Length: 1271272 (1.2M) [application/java-archive]
00:47:09 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:47:09
00:47:09 0K .......... .......... .......... .......... .......... 4% 33.4M 0s
00:47:09 50K .......... .......... .......... .......... .......... 8% 3.59M 0s
00:47:09 100K .......... .......... .......... .......... .......... 12% 3.94M 0s
00:47:09 150K .......... .......... .......... .......... .......... 16% 42.0M 0s
00:47:09 200K .......... .......... .......... .......... .......... 20% 116M 0s
00:47:09 250K .......... .......... .......... .......... .......... 24% 50.9M 0s
00:47:09 300K .......... .......... .......... .......... .......... 28% 64.1M 0s
00:47:09 350K .......... .......... .......... .......... .......... 32% 4.77M 0s
00:47:09 400K .......... .......... .......... .......... .......... 36% 37.4M 0s
00:47:09 450K .......... .......... .......... .......... .......... 40% 129M 0s
00:47:09 500K .......... .......... .......... .......... .......... 44% 30.8M 0s
00:47:09 550K .......... .......... .......... .......... .......... 48% 52.8M 0s
00:47:09 600K .......... .......... .......... .......... .......... 52% 139M 0s
00:47:09 650K .......... .......... .......... .......... .......... 56% 4.58M 0s
00:47:09 700K .......... .......... .......... .......... .......... 60% 67.5M 0s
00:47:09 750K .......... .......... .......... .......... .......... 64% 27.9M 0s
00:47:09 800K .......... .......... .......... .......... .......... 68% 116M 0s
00:47:09 850K .......... .......... .......... .......... .......... 72% 52.8M 0s
00:47:09 900K .......... .......... .......... .......... .......... 76% 4.91M 0s
00:47:09 950K .......... .......... .......... .......... .......... 80% 75.1M 0s
00:47:09 1000K .......... .......... .......... .......... .......... 84% 29.1M 0s
00:47:09 1050K .......... .......... .......... .......... .......... 88% 92.2M 0s
00:47:09 1100K .......... .......... .......... .......... .......... 92% 5.56M 0s
00:47:09 1150K .......... .......... .......... .......... .......... 96% 21.9M 0s
00:47:09 1200K .......... .......... .......... .......... . 100% 87.8M=0.08s
00:47:09
00:47:09 2026-01-23 00:47:09 (14.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:47:09
00:47:09 + 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
00:47:09 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:47:09 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:47:09 --2026-01-23 00:47:09-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-core/1.12.659/aws-java-sdk-core-1.12.659.jar
00:47:10 Resolving repo1.maven.org (repo1.maven.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:120c, ...
00:47:10 Connecting to repo1.maven.org (repo1.maven.org)|104.18.18.12|:443... connected.
00:47:10 HTTP request sent, awaiting response... 200 OK
00:47:10 Length: 1036468 (1012K) [application/java-archive]
00:47:10 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-core-1.12.659.jar’
00:47:10
00:47:10 0K .......... .......... .......... .......... .......... 4% 3.55M 0s
00:47:10 50K .......... .......... .......... .......... .......... 9% 8.48M 0s
00:47:10 100K .......... .......... .......... .......... .......... 14% 4.67M 0s
00:47:10 150K .......... .......... .......... .......... .......... 19% 10.6M 0s
00:47:10 200K .......... .......... .......... .......... .......... 24% 10.5M 0s
00:47:10 250K .......... .......... .......... .......... .......... 29% 11.3M 0s
00:47:10 300K .......... .......... .......... .......... .......... 34% 19.5M 0s
00:47:10 350K .......... .......... .......... .......... .......... 39% 17.5M 0s
00:47:10 400K .......... .......... .......... .......... .......... 44% 19.9M 0s
00:47:10 450K .......... .......... .......... .......... .......... 49% 24.9M 0s
00:47:10 500K .......... .......... .......... .......... .......... 54% 12.8M 0s
00:47:10 550K .......... .......... .......... .......... .......... 59% 25.9M 0s
00:47:10 600K .......... .......... .......... .......... .......... 64% 13.9M 0s
00:47:10 650K .......... .......... .......... .......... .......... 69% 14.7M 0s
00:47:10 700K .......... .......... .......... .......... .......... 74% 46.0M 0s
00:47:10 750K .......... .......... .......... .......... .......... 79% 12.9M 0s
00:47:10 800K .......... .......... .......... .......... .......... 83% 25.7M 0s
00:47:10 850K .......... .......... .......... .......... .......... 88% 14.1M 0s
00:47:10 900K .......... .......... .......... .......... .......... 93% 10.6M 0s
00:47:10 950K .......... .......... .......... .......... .......... 98% 137M 0s
00:47:10 1000K .......... .. 100% 262M=0.08s
00:47:10
00:47:10 2026-01-23 00:47:10 (12.2 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-core-1.12.659.jar’ saved [1036468/1036468]
00:47:10
00:47:10 + for x in *.jar
00:47:10 + mv omero-zarr-pixel-buffer-0.6.2-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server
00:47:10 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:47:10 ++ deactivate nondestructive
00:47:10 ++ '[' -n '' ']'
00:47:10 ++ '[' -n '' ']'
00:47:10 ++ hash -r
00:47:10 ++ '[' -n '' ']'
00:47:10 ++ unset VIRTUAL_ENV
00:47:10 ++ unset VIRTUAL_ENV_PROMPT
00:47:10 ++ '[' '!' nondestructive = nondestructive ']'
00:47:10 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:47:10 ++ export VIRTUAL_ENV
00:47:10 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:47:10 ++ 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
00:47:10 ++ export PATH
00:47:10 ++ '[' -n '' ']'
00:47:10 ++ '[' -z '' ']'
00:47:10 ++ _OLD_VIRTUAL_PS1=
00:47:10 ++ PS1='(.venv3) '
00:47:10 ++ export PS1
00:47:10 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:47:10 ++ export VIRTUAL_ENV_PROMPT
00:47:10 ++ hash -r
00:47:10 + pip install -U pip
00:47:10 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:47:10 Collecting pip
00:47:10 Using cached pip-25.3-py3-none-any.whl (1.8 MB)
00:47:10 Installing collected packages: pip
00:47:10 Attempting uninstall: pip
00:47:10 Found existing installation: pip 22.3.1
00:47:11 Uninstalling pip-22.3.1:
00:47:11 Successfully uninstalled pip-22.3.1
00:47:11 Successfully installed pip-25.3
00:47:11 + 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
00:47:12 Collecting zeroc-ice==3.6.5
00:47:12 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)
00:47:14 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 19.9 MB/s 0:00:01
00:47:14 Installing collected packages: zeroc-ice
00:47:15 Successfully installed zeroc-ice-3.6.5
00:47:15 + pip install markdown
00:47:15 Collecting markdown
00:47:15 Using cached markdown-3.10.1-py3-none-any.whl.metadata (5.1 kB)
00:47:15 Using cached markdown-3.10.1-py3-none-any.whl (107 kB)
00:47:15 Installing collected packages: markdown
00:47:15 Successfully installed markdown-3.10.1
00:47:15 + pip install reportlab
00:47:16 Collecting reportlab
00:47:16 Using cached reportlab-4.4.9-py3-none-any.whl.metadata (1.7 kB)
00:47:16 Collecting pillow>=9.0.0 (from reportlab)
00:47:16 Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
00:47:16 Collecting charset-normalizer (from reportlab)
00:47:16 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)
00:47:16 Using cached reportlab-4.4.9-py3-none-any.whl (2.0 MB)
00:47:16 Using cached pillow-12.1.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.0 MB)
00:47:16 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)
00:47:16 Installing collected packages: pillow, charset-normalizer, reportlab
00:47:17
00:47:17 Successfully installed charset-normalizer-3.4.4 pillow-12.1.0 reportlab-4.4.9
00:47:17 + pip install omego
00:47:18 Collecting omego
00:47:18 Using cached omego-0.7.0-py3-none-any.whl
00:47:18 Collecting future (from omego)
00:47:18 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:47:18 Collecting yaclifw>=0.1.1 (from omego)
00:47:18 Using cached yaclifw-0.2.0-py3-none-any.whl
00:47:18 Collecting six (from yaclifw>=0.1.1->omego)
00:47:18 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:47:18 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:47:18 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:47:18 Installing collected packages: six, future, yaclifw, omego
00:47:18
00:47:18 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:47:18 + pip install tables
00:47:19 Collecting tables
00:47:19 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:47:19 Collecting numpy>=1.20.0 (from tables)
00:47:19 Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
00:47:19 Collecting numexpr>=2.6.2 (from tables)
00:47:19 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:47:19 Collecting packaging (from tables)
00:47:19 Using cached packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
00:47:19 Collecting py-cpuinfo (from tables)
00:47:19 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:47:19 Collecting blosc2>=2.3.0 (from tables)
00:47:19 Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
00:47:19 Collecting typing-extensions>=4.4.0 (from tables)
00:47:19 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
00:47:19 Collecting ndindex (from blosc2>=2.3.0->tables)
00:47:19 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
00:47:19 Collecting msgpack (from blosc2>=2.3.0->tables)
00:47:19 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)
00:47:19 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:47:19 Using cached platformdirs-4.5.1-py3-none-any.whl.metadata (12 kB)
00:47:19 Collecting requests (from blosc2>=2.3.0->tables)
00:47:19 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
00:47:19 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.4)
00:47:19 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:47:19 Using cached idna-3.11-py3-none-any.whl.metadata (8.4 kB)
00:47:20 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:47:20 Using cached urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB)
00:47:20 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:47:20 Using cached certifi-2026.1.4-py3-none-any.whl.metadata (2.5 kB)
00:47:20 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:47:20 Using cached blosc2-3.12.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
00:47:20 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
00:47:20 Using cached numpy-2.4.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.7 MB)
00:47:20 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
00:47:20 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB)
00:47:20 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
00:47:20 Using cached packaging-26.0-py3-none-any.whl (74 kB)
00:47:20 Using cached platformdirs-4.5.1-py3-none-any.whl (18 kB)
00:47:20 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:47:20 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
00:47:20 Using cached idna-3.11-py3-none-any.whl (71 kB)
00:47:20 Using cached urllib3-2.6.3-py3-none-any.whl (131 kB)
00:47:20 Using cached certifi-2026.1.4-py3-none-any.whl (152 kB)
00:47:20 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:47:23
00:47:23 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
00:47:23 + pip install jinja2
00:47:23 Collecting jinja2
00:47:23 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:47:24 Collecting MarkupSafe>=2.0 (from jinja2)
00:47:24 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)
00:47:24 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:47:24 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
00:47:24 Installing collected packages: MarkupSafe, jinja2
00:47:24
00:47:24 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
00:47:24 + pip install omero-py
00:47:24 Collecting omero-py
00:47:24 Using cached omero_py-5.21.3-py3-none-any.whl.metadata (6.5 kB)
00:47:24 Collecting appdirs (from omero-py)
00:47:24 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:47:24 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:47:24 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.1)
00:47:24 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.1.0)
00:47:24 Collecting PyYAML (from omero-py)
00:47:24 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)
00:47:24 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:47:24 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
00:47:24 Collecting portalocker (from omero-py)
00:47:24 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:47:24 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.4)
00:47:24 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.11)
00:47:24 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.6.3)
00:47:24 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.1.4)
00:47:24 Using cached omero_py-5.21.3-py3-none-any.whl (2.8 MB)
00:47:24 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:47:24 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:47:24 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
00:47:24 Installing collected packages: appdirs, PyYAML, portalocker, omero-py
00:47:26
00:47:26 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.21.3 portalocker-3.2.0
00:47:26 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:47:27 Collecting omero-metadata
00:47:27 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-lptwxeea/omero-metadata_c07cf3f5555e4b2d8582cebf2542fc55
00:47:27 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-lptwxeea/omero-metadata_c07cf3f5555e4b2d8582cebf2542fc55
00:47:27 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 7c7af4f19467b64fe2e11fe9422c2b2e5f1d4422
00:47:27 Installing build dependencies: started
00:47:28 Installing build dependencies: finished with status 'done'
00:47:28 Getting requirements to build wheel: started
00:47:28 Getting requirements to build wheel: finished with status 'done'
00:47:28 Preparing metadata (pyproject.toml): started
00:47:29 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:29 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.3)
00:47:29 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
00:47:29 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:47:29 Collecting pandas (from omero-metadata)
00:47:29 Using cached pandas-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
00:47:29 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:47:29 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:47:29 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.1)
00:47:29 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)
00:47:29 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)
00:47:29 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
00:47:29 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:47:29 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
00:47:29 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
00:47:29 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:47:29 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)
00:47:29 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)
00:47:29 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)
00:47:29 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)
00:47:29 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)
00:47:29 Using cached pandas-3.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.2 MB)
00:47:29 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:47:29 Building wheels for collected packages: omero-metadata
00:47:29 Building wheel for omero-metadata (pyproject.toml): started
00:47:29 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:47:29 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=77c5561580887360a767edbdd02ed8f5a9138463b4f0ba273ec1067328a5a7dc
00:47:29 Stored in directory: /tmp/pip-ephem-wheel-cache-nx9eb99k/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:47:29 Successfully built omero-metadata
00:47:29 Installing collected packages: python-dateutil, pandas, omero-metadata
00:47:34
00:47:34 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.0 python-dateutil-2.9.0.post0
00:47:34 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:47:34 Collecting omero-cli-render
00:47:34 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-ys90ypak/omero-cli-render_5e695a6a1e19468796db66823e7b510c
00:47:34 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-ys90ypak/omero-cli-render_5e695a6a1e19468796db66823e7b510c
00:47:35 Running command git checkout -b merge_ci --track origin/merge_ci
00:47:35 Switched to a new branch 'merge_ci'
00:47:35 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:47:35 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 9696c38b026b5247efb3a41ef5a5335841158c43
00:47:35 Installing build dependencies: started
00:47:36 Installing build dependencies: finished with status 'done'
00:47:36 Getting requirements to build wheel: started
00:47:36 Getting requirements to build wheel: finished with status 'done'
00:47:36 Preparing metadata (pyproject.toml): started
00:47:36 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:36 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
00:47:36 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.3)
00:47:36 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:47:36 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:47:36 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.1)
00:47:36 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)
00:47:36 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
00:47:36 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
00:47:36 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:47:36 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)
00:47:36 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)
00:47:36 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)
00:47:36 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)
00:47:36 Building wheels for collected packages: omero-cli-render
00:47:36 Building wheel for omero-cli-render (pyproject.toml): started
00:47:37 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:47:37 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19841 sha256=ce983166e1fe40382cc39af9a5a3c25ef27845783811dfcd5303317a2c3e7f2a
00:47:37 Stored in directory: /tmp/pip-ephem-wheel-cache-1xwfhnac/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:47:37 Successfully built omero-cli-render
00:47:37 Installing collected packages: omero-cli-render
00:47:37 Successfully installed omero-cli-render-0.8.2.dev0
00:47:37 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:47:37 Collecting omero-cli-duplicate
00:47:37 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-prkvmurg/omero-cli-duplicate_9e60445302964b04a34361043f702a41
00:47:37 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-prkvmurg/omero-cli-duplicate_9e60445302964b04a34361043f702a41
00:47:38 Running command git checkout -b merge_ci --track origin/merge_ci
00:47:38 Switched to a new branch 'merge_ci'
00:47:38 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:47:38 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 54862d08abd4d50495a5244673fa7aae23d5e15d
00:47:38 Installing build dependencies: started
00:47:39 Installing build dependencies: finished with status 'done'
00:47:39 Getting requirements to build wheel: started
00:47:39 Getting requirements to build wheel: finished with status 'done'
00:47:39 Preparing metadata (pyproject.toml): started
00:47:39 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:39 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.3)
00:47:39 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:47:39 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:47:39 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.1)
00:47:39 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)
00:47:39 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
00:47:39 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)
00:47:39 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
00:47:39 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:47:39 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)
00:47:39 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)
00:47:39 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)
00:47:39 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)
00:47:39 Building wheels for collected packages: omero-cli-duplicate
00:47:39 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:47:40 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:47:40 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=2c47b268260cf75def7e9d44c7553d14009386d199fd0fb212dea7be1b8189df
00:47:40 Stored in directory: /tmp/pip-ephem-wheel-cache-9jyug25i/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:47:40 Successfully built omero-cli-duplicate
00:47:40 Installing collected packages: omero-cli-duplicate
00:47:40 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:47:40 + pip install omero-certificates
00:47:41 Collecting omero-certificates
00:47:41 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:47:41 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.3)
00:47:41 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:47:41 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:47:41 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.1)
00:47:41 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)
00:47:41 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
00:47:41 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)
00:47:41 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
00:47:41 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:47:41 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)
00:47:41 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)
00:47:41 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)
00:47:41 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)
00:47:41 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:47:41 Installing collected packages: omero-certificates
00:47:41 Successfully installed omero-certificates-0.4.0
00:47:41 + for x in *.tar.gz
00:47:41 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:47:41 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:47:41 Installing build dependencies: started
00:47:42 Installing build dependencies: finished with status 'done'
00:47:42 Getting requirements to build wheel: started
00:47:42 Getting requirements to build wheel: finished with status 'done'
00:47:42 Preparing metadata (pyproject.toml): started
00:47:42 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:42 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.3)
00:47:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:47:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:47:42 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.1)
00:47:42 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)
00:47:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
00:47:42 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)
00:47:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
00:47:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:47:42 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)
00:47:42 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)
00:47:42 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)
00:47:42 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)
00:47:42 Building wheels for collected packages: omero-dropbox
00:47:42 Building wheel for omero-dropbox (pyproject.toml): started
00:47:43 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:47:43 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=6ffff12ee826bd033edd4f169f54de5e032f27ea3ccd1eb6242a7c9881e22a2d
00:47:43 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:47:43 Successfully built omero-dropbox
00:47:43 Installing collected packages: omero-dropbox
00:47:43 Successfully installed omero-dropbox-5.7.1.dev0
00:47:43 + for x in *.tar.gz
00:47:43 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
00:47:43 Processing ./omero_marshal-0.9.2.dev0.tar.gz
00:47:43 Installing build dependencies: started
00:47:44 Installing build dependencies: finished with status 'done'
00:47:44 Getting requirements to build wheel: started
00:47:44 Getting requirements to build wheel: finished with status 'done'
00:47:44 Preparing metadata (pyproject.toml): started
00:47:44 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:44 Building wheels for collected packages: omero_marshal
00:47:44 Building wheel for omero_marshal (pyproject.toml): started
00:47:45 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:47:45 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88128 sha256=fbf3ee6f6f02e52b4c2d69847ec6fc9d147963f00d3b09b7a2c851a1c03141a8
00:47:45 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
00:47:45 Successfully built omero_marshal
00:47:45 Installing collected packages: omero_marshal
00:47:45 Successfully installed omero_marshal-0.9.2.dev0
00:47:45 + for x in *.tar.gz
00:47:45 + pip install -U omero_py-5.22.0.dev0.tar.gz
00:47:45 Processing ./omero_py-5.22.0.dev0.tar.gz
00:47:46 Installing build dependencies: started
00:47:46 Installing build dependencies: finished with status 'done'
00:47:46 Getting requirements to build wheel: started
00:47:47 Getting requirements to build wheel: finished with status 'done'
00:47:47 Preparing metadata (pyproject.toml): started
00:47:47 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:47 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.4.4)
00:47:47 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (1.0.0)
00:47:47 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.4.1)
00:47:47 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (12.1.0)
00:47:47 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (6.0.3)
00:47:47 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)
00:47:47 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (2.32.5)
00:47:47 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.0.dev0) (3.2.0)
00:47:47 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)
00:47:47 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.0.dev0) (3.11)
00:47:47 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)
00:47:47 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)
00:47:47 Building wheels for collected packages: omero-py
00:47:47 Building wheel for omero-py (pyproject.toml): started
00:47:48 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:47:48 Created wheel for omero-py: filename=omero_py-5.22.0.dev0-py3-none-any.whl size=2786450 sha256=b001cba16c8da40a2c6cb34019635b89c56b4dab9bc070b39415024de656fa85
00:47:48 Stored in directory: /home/omero/.cache/pip/wheels/b2/dd/fb/0f3c8a08eddbfe6a2bff7fe7d61ee876973c474d282bc441e3
00:47:48 Successfully built omero-py
00:47:48 Installing collected packages: omero-py
00:47:48 Attempting uninstall: omero-py
00:47:48 Found existing installation: omero-py 5.21.3
00:47:48 Uninstalling omero-py-5.21.3:
00:47:48 Successfully uninstalled omero-py-5.21.3
00:47:50 Successfully installed omero-py-5.22.0.dev0
00:47:50 + for x in *.tar.gz
00:47:50 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:47:51 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:47:51 Installing build dependencies: started
00:47:51 Installing build dependencies: finished with status 'done'
00:47:51 Getting requirements to build wheel: started
00:47:52 Getting requirements to build wheel: finished with status 'done'
00:47:52 Preparing metadata (pyproject.toml): started
00:47:52 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:52 Building wheels for collected packages: omero-scripts
00:47:52 Building wheel for omero-scripts (pyproject.toml): started
00:47:52 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:47:52 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136991 sha256=ceac80c5f2d5ad3923fc9406a7ce4082863f52558cf8413f30450a860387f07d
00:47:52 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:47:52 Successfully built omero-scripts
00:47:52 Installing collected packages: omero-scripts
00:47:52 Successfully installed omero-scripts-5.9.2.dev0
00:47:52 + for x in *.tar.gz
00:47:52 + pip install -U omero_web-5.30.2.dev0.tar.gz
00:47:53 Processing ./omero_web-5.30.2.dev0.tar.gz
00:47:53 Installing build dependencies: started
00:47:54 Installing build dependencies: finished with status 'done'
00:47:54 Getting requirements to build wheel: started
00:47:54 Getting requirements to build wheel: finished with status 'done'
00:47:54 Preparing metadata (pyproject.toml): started
00:47:54 Preparing metadata (pyproject.toml): finished with status 'done'
00:47:54 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)
00:47:54 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.30.2.dev0)
00:47:54 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:47:54 Collecting Django<5.3,>=5.2.9 (from omero-web==5.30.2.dev0)
00:47:54 Using cached django-5.2.10-py3-none-any.whl.metadata (4.1 kB)
00:47:55 Collecting django-pipeline (from omero-web==5.30.2.dev0)
00:47:55 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
00:47:55 Collecting django-cors-headers==3.7.0 (from omero-web==5.30.2.dev0)
00:47:55 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:47:55 Collecting whitenoise>=5.3.0 (from omero-web==5.30.2.dev0)
00:47:55 Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
00:47:55 Collecting gunicorn>=19.3 (from omero-web==5.30.2.dev0)
00:47:55 Downloading gunicorn-24.0.0-py3-none-any.whl.metadata (4.5 kB)
00:47:55 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)
00:47:55 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (12.1.0)
00:47:55 Collecting pytz (from omero-web==5.30.2.dev0)
00:47:55 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:47:55 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (3.2.0)
00:47:55 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.30.2.dev0) (26.0)
00:47:55 Collecting importlib-resources (from omero-web==5.30.2.dev0)
00:47:55 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:47:55 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
00:47:55 Using cached asgiref-3.11.0-py3-none-any.whl.metadata (9.3 kB)
00:47:55 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.30.2.dev0)
00:47:55 Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
00:47:55 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)
00:47:55 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)
00:47:55 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)
00:47:55 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)
00:47:55 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)
00:47:55 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)
00:47:55 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.30.2.dev0) (65.5.1)
00:47:55 Collecting wheel (from django-pipeline->omero-web==5.30.2.dev0)
00:47:55 Downloading wheel-0.46.3-py3-none-any.whl.metadata (2.4 kB)
00:47:55 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)
00:47:55 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)
00:47:55 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)
00:47:55 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)
00:47:55 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:47:55 Using cached django-5.2.10-py3-none-any.whl (8.3 MB)
00:47:55 Using cached asgiref-3.11.0-py3-none-any.whl (24 kB)
00:47:55 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:47:55 Downloading gunicorn-24.0.0-py3-none-any.whl (110 kB)
00:47:55 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
00:47:55 Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
00:47:55 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
00:47:55 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:47:55 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:47:55 Downloading wheel-0.46.3-py3-none-any.whl (30 kB)
00:47:55 Building wheels for collected packages: omero-web
00:47:55 Building wheel for omero-web (pyproject.toml): started
00:47:56 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:47:56 Created wheel for omero-web: filename=omero_web-5.30.2.dev0-py3-none-any.whl size=2818599 sha256=5f6a9da8eb29c82a0097b4ce0f89d93c6f0ee25da42126a010896a008ba17b2e
00:47:56 Stored in directory: /home/omero/.cache/pip/wheels/22/8a/f9/2aa2b64b8351936989ad8693ee70db658c8360167f1ee574e7
00:47:56 Successfully built omero-web
00:47:56 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
00:47:59
00:47:59 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
00:47:59 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:47:59 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:47:59 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:47:59 --2026-01-23 00:47:59-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:47:59 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.110.133, ...
00:47:59 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
00:47:59 HTTP request sent, awaiting response... 200 OK
00:47:59 Length: 129238 (126K) [text/plain]
00:47:59 Saving to: ‘Figure_To_Pdf.py’
00:47:59
00:47:59 0K .......... .......... .......... .......... .......... 39% 3.89M 0s
00:47:59 50K .......... .......... .......... .......... .......... 79% 13.6M 0s
00:47:59 100K .......... .......... ...... 100% 4.88M=0.02s
00:47:59
00:47:59 2026-01-23 00:47:59 (5.76 MB/s) - ‘Figure_To_Pdf.py’ saved [129238/129238]
00:47:59
00:47:59 + chmod 755 Figure_To_Pdf.py
00:47:59 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:47:59 + omero config set omero.db.name OMERO-server
00:48:01 + omero config set omero.db.host pg
00:48:02 + omero config set omero.db.user postgres
00:48:03 + omero config set omero.data.dir /home/omero/omero-server-data
00:48:04 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:48:05 + omero config set omero.db.poolsize 25
00:48:06 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:48:07 + omero config set omero.security.trustStorePassword changeit
00:48:08 + omero config set omero.mail.config true
00:48:09 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:48:11 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:48:12 + omero certificates
00:48:13 OpenSSL 3.5.1 1 Jul 2025 (Library: OpenSSL 3.5.1 1 Jul 2025)
00:48:13 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:48:13 + '[' false = true ']'
00:48:13 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:48:13 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:48:13 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG dbcommand => upgrade
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG dbhost => localhost
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG dbname => OMERO-server
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG dbpass => omero
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG dbuser => omero
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG rootpass => omero
00:48:13 2026-01-23 00:48:13,429 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:48:13 2026-01-23 00:48:13,430 [omego.extern] INFO Executing : omero version
00:48:14 OMERO.py version:
00:48:14 OMERO.server version:
00:48:14 5.6.3-583-43bd9813d6-ice36-b27
00:48:14 5.22.0.dev0
00:48:14 2026-01-23 00:48:14,627 [omego.extern] INFO Completed [1.197 s]
00:48:14 2026-01-23 00:48:14,627 [omego.extern] DEBUG Using omero CLI from omero
00:48:14 2026-01-23 00:48:14,627 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:48:14 2026-01-23 00:48:14,627 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:48:14 2026-01-23 00:48:14,627 [omego.extern] INFO Executing : omero config get --show-password
00:48:15 2026-01-23 00:48:15,733 [omego.extern] INFO Completed [1.106 s]
00:48:15 2026-01-23 00:48:15,733 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:48:15 2026-01-23 00:48:15,733 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:48:15 2026-01-23 00:48:15,739 [omego.extern] INFO Completed [0.005 s]
00:48:15 2026-01-23 00:48:15,739 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.11\n'
00:48:15 2026-01-23 00:48:15,739 [ omego.db] INFO psql version: psql (PostgreSQL) 16.11
00:48:15
00:48:15 2026-01-23 00:48:15,739 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:48:15 2026-01-23 00:48:15,739 [omego.extern] INFO Executing : omero config get --show-password
00:48:16 2026-01-23 00:48:16,837 [omego.extern] INFO Completed [1.098 s]
00:48:16 2026-01-23 00:48:16,837 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:48:16 2026-01-23 00:48:16,837 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:48:16 2026-01-23 00:48:16,849 [omego.extern] INFO Completed [0.012 s]
00:48:16 2026-01-23 00:48:16,849 [ 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'
00:48:16 2026-01-23 00:48:16,849 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:48:16 2026-01-23 00:48:16,849 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:48:16 2026-01-23 00:48:16,849 [omego.extern] INFO Executing : omero config get --show-password
00:48:17 2026-01-23 00:48:17,953 [omego.extern] INFO Completed [1.104 s]
00:48:17 2026-01-23 00:48:17,953 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:48:17 2026-01-23 00:48:17,953 [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
00:48:17 2026-01-23 00:48:17,963 [omego.extern] INFO Completed [0.010 s]
00:48:17 2026-01-23 00:48:17,964 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:48:17 2026-01-23 00:48:17,964 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:48:17 2026-01-23 00:48:17,965 [ omego.db] INFO Database is already at OMERO5.4__0
00:48:17 + export LANG=en_US.UTF-8
00:48:17 + LANG=en_US.UTF-8
00:48:17 + export LANGUAGE=en_US:en
00:48:17 + LANGUAGE=en_US:en
00:48:17 + export LC_ALL=en_US.UTF-8
00:48:17 + LC_ALL=en_US.UTF-8
00:48:17 + BUILD_ID=DONT_KILL_ME
00:48:17 + omero admin start
00:48:22 No descriptor given. Using etc/grid/default.xml
00:48:30 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:48:30 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:48:30 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:48:30 Waiting on startup. Use CTRL-C to exit
00:48:30 + omero admin waitup
00:48:31 Waiting on startup. Use CTRL-C to exit
00:48:31 + omero admin diagnostics
00:48:32
00:48:32 ================================================================================
00:48:32 OMERO Diagnostics (admin)
00:48:32 ================================================================================
00:48:32
00:48:32 Commands: java -version 17.0.17 (/usr/bin/java)
00:48:32 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:48:32 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:48:32 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:48:32 Commands: psql --version 16.11 (/usr/bin/psql)
00:48:32 Commands: openssl version 3.5.11 (/usr/bin/openssl)
00:48:32
00:48:32 Component: OMERO.py 5.22.0.dev0
00:48:32 Component: OMERO.server 5.6.3-583-43bd9813d6-ice36-b27
00:48:32
00:48:32 Server: icegridnode running
00:48:32 Server: Blitz-0 active (pid = 22537, enabled)
00:48:32 Server: Indexer-0 activating (enabled)
00:48:32 Server: OMERO.Glacier2 active (pid = 22570, enabled)
00:48:32 Server: OMERO.IceStorm active (pid = 22598, enabled)
00:48:32 Server: Processor-0 activating (enabled)
00:48:32 Server: Tables-0 activating (enabled)
00:48:32
00:48:32 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:48:32 Log files: Blitz-0.log 23.7 KB errors=0 warnings=1
00:48:32 Log files: DropBox.log n/a
00:48:32 Log files: FileServer.log n/a
00:48:32 Log files: Indexer-0.log 114 B
00:48:32 Log files: MonitorServer.log n/a
00:48:32 Log files: Processor-0.log 281 B
00:48:32 Log files: Tables-0.log 281 B
00:48:32 Log files: TestDropBox.log n/a
00:48:32 Log files: master.err empty
00:48:32 Log files: master.out 30.5 KB
00:48:32 Log files: Total size 0.05 MB
00:48:32
00:48:32
00:48:32 Environment:OMERO_HOME=(unset)
00:48:32 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:32 Environment:OMERO_NODE=(unset)
00:48:32 Environment:OMERO_MASTER=(unset)
00:48:32 Environment:OMERO_USERDIR=(unset)
00:48:32 Environment:OMERO_TMPDIR=(unset)
00:48:32 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
00:48:32 Environment:PYTHONPATH=(unset)
00:48:32 Environment:ICE_HOME=/opt/ice-3.6.5
00:48:32 Environment:LD_LIBRARY_PATH=(unset)
00:48:32 Environment:DYLD_LIBRARY_PATH=(unset)
00:48:32
00:48:32 OMERO SSL port:4064
00:48:32 OMERO TCP port:4063
00:48:32 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:48:32 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:48:32
00:48:32 JVM settings: Blitz-${index} -Xmx7200m
00:48:32 JVM settings: Indexer-${index} -Xmx4800m
00:48:32 JVM settings: PixelData-${index} -Xmx7200m
00:48:32 JVM settings: Repository-${index} -Xmx4800m
00:48:32
00:48:32 Jar: lib/server/formats-api.jar Bio-Formats API 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
00:48:32 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
00:48:32 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.5.0-SNAPSHOT 23 January 2026 582a7639ab17a56cb26a2716fcdeb63205a9a301
00:48:32 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
00:48:32 Jar: lib/server/ome-common.jar OME Common Java 6.1.3-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
00:48:32 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
00:48:32 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
00:48:32 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
00:48:32 Jar: lib/server/ome-xml.jar OME XML library 6.5.4-SNAPSHOT 23 January 2026 8128676de0878375b47392f5ac30a57ff7437810
00:48:33 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:48:33 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:48:33 Jar: lib/server/omero-gateway.jar jar 5.10.5-SNAPSHOT
00:48:33 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:48:33 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:48:33 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:48:33 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:48:33 Jar: lib/server/omero-zarr-pixel-buffer-0.6.2-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.6.2-SNAPSHOT e4fb0ec525b34157eab8ff984fcbb89bbea5287a
00:48:33 + deactivate
00:48:33 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:48:33 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:33 + export PATH
00:48:33 + unset _OLD_VIRTUAL_PATH
00:48:33 + '[' -n '' ']'
00:48:33 + hash -r
00:48:33 + '[' -n '' ']'
00:48:33 + unset VIRTUAL_ENV
00:48:33 + unset VIRTUAL_ENV_PROMPT
00:48:33 + '[' '!' '' = nondestructive ']'
00:48:33 + unset -f deactivate
00:48:33 Finished: SUCCESS
