12:41:23 Started by user devspace
12:41:23 Running as SYSTEM
12:41:23 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
12:41:23 [OMERO-server] $ /bin/bash -xe /tmp/jenkins16308146010172484403.sh
12:41:23 + source /home/settings.env
12:41:23 ++ OMERO_DB_HOST=pg
12:41:23 ++ OMERO_DB_USER=postgres
12:41:23 ++ OMERO_DB_PASS=
12:41:23 ++ OMERO_ROOT_PASS=omero
12:41:23 ++ OMERO_DATA_DIR=/OMERO
12:41:23 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
12:41:23 + OMERO_DB_NAME=OMERO-server
12:41:23 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
12:41:23 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:41:23 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:41:23 + OMERO_DATA_DIR=/home/omero/omero-server-data
12:41:23 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
12:41:23 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
12:41:23 ++ deactivate nondestructive
12:41:23 ++ '[' -n '' ']'
12:41:23 ++ '[' -n '' ']'
12:41:23 ++ hash -r
12:41:23 ++ '[' -n '' ']'
12:41:23 ++ unset VIRTUAL_ENV
12:41:23 ++ unset VIRTUAL_ENV_PROMPT
12:41:23 ++ '[' '!' nondestructive = nondestructive ']'
12:41:23 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
12:41:23 ++ export VIRTUAL_ENV
12:41:23 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:41:23 ++ 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
12:41:23 ++ export PATH
12:41:23 ++ '[' -n '' ']'
12:41:23 ++ '[' -z '' ']'
12:41:23 ++ _OLD_VIRTUAL_PS1=
12:41:23 ++ PS1='(.venv3) '
12:41:23 ++ export PS1
12:41:23 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
12:41:23 ++ export VIRTUAL_ENV_PROMPT
12:41:23 ++ hash -r
12:41:23 + omero admin stop
12:41:24 Waiting on shutdown. Use CTRL-C to exit
12:41:24 .+ sleep 5
12:41:39 + deactivate
12:41:39 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
12:41:39 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:41:39 + export PATH
12:41:39 + unset _OLD_VIRTUAL_PATH
12:41:39 + '[' -n '' ']'
12:41:39 + hash -r
12:41:39 + '[' -n '' ']'
12:41:39 + unset VIRTUAL_ENV
12:41:39 + unset VIRTUAL_ENV_PROMPT
12:41:39 + '[' '!' '' = nondestructive ']'
12:41:39 + unset -f deactivate
12:41:39 + rm -rf /home/omero/workspace/OMERO-server/.venv3
12:41:40 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
12:41:44 + '[' false = true ']'
12:41:44 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
12:41:44 Skipping PURGE_DATA:CleanDbAndRepo
12:41:44 + 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-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.21.1.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-5.29.2.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
12:41:45 Copied 1 artifact from "OMERO-build" build number 471
12:41:46 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 464
12:41:46 Copied 2 artifacts from "OMERO-build-build" build number 494
12:41:46 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 4
12:41:46 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11789973685108881225.sh
12:41:46 + source /home/settings.env
12:41:46 ++ OMERO_DB_HOST=pg
12:41:46 ++ OMERO_DB_USER=postgres
12:41:46 ++ OMERO_DB_PASS=
12:41:46 ++ OMERO_ROOT_PASS=omero
12:41:46 ++ OMERO_DATA_DIR=/OMERO
12:41:46 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
12:41:46 + OMERO_DB_NAME=OMERO-server
12:41:46 + OMERO_DATA_DIR=/home/omero/omero-server-data
12:41:46 + mkdir -p /home/omero/omero-server-data
12:41:46 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
12:41:46 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:41:46 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:41:46 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
12:41:46 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
12:41:46 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
12:41:46 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
12:41:46 ++ ls OMERO.server-5.6.3-571-fbdab3a624-ice36-b471.zip
12:41:46 + ZIP=OMERO.server-5.6.3-571-fbdab3a624-ice36-b471.zip
12:41:46 + '[' '!' -z '' ']'
12:41:46 + DIST=OMERO.server-5.6.3-571-fbdab3a624-ice36-b471
12:41:46 + unzip OMERO.server-5.6.3-571-fbdab3a624-ice36-b471.zip
12:41:46 Archive: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471.zip
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/blitz/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/grid/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/profiles/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/error/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/grid/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/luts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/luts/janelia/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/luts/matplotlib/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/luts/ncsa_paledit/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/luts/seaborn/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/luts/wcif/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/analysis_scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/annotation_scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/export_scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/figure_scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/import_scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/scripts/omero/util_scripts/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/server/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/share/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/share/licenses/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/misc/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__1/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__10/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__11/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__2/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__3/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__4/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__5/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__6/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__7/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__8/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3A__9/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3__4/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3__5/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3__6/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO3__7/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO4.1__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO4.2__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO4.2__0/t/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO4.3__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO4.4__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO4__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.0__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.1__1/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.2__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.3__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4DEV__1/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4DEV__2/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4DEV__3/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/
12:41:46 creating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/var/
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/LICENSE.txt
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/backup.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/blitz/mail-senders.example
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/blitz/mail-server.example
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/build.properties
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/env.bat
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/env.sh
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/hibernate.properties
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/ice.config
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/logback-cli.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/logback-indexing-cli.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/logback-indexing.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/logback.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/mime.types
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/node1.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/node2.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/omero.properties
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/profiles/psql
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/rollover.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/Windows.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/error/maintainance.html
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/grid/README
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/grid/default.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/grid/templates.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/grid/windefault.xml
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/ice.config
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/internal.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/master.cfg
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/templates/robot.template
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/etc/testdropbox.config
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/history.rst
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/OMEZarrReader.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/accessors-smart.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/activation.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/aggdesigner-algorithm.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/aircompressor.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/antlr.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/aopalliance.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/apiguardian-api.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/asm.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/avatica-core.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/avatica-metrics.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/aws-java-sdk-core.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/aws-java-sdk-kms.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/aws-java-sdk-s3.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/base.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-anim.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-awt-util.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-bridge.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-codec.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-constants.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-css.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-dom.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-ext.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-gvt.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-i18n.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-parser.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-script.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-shared-resources.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-svg-dom.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-svggen.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-transcoder.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-util.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/batik-xml.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/btm.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/calcite-core.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/calcite-linq4j.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/cdm-core.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/checker-qual.jar
12:41:46 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/lib/client/commons-beanutils.jar
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12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/psql-footer.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/psql-header.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/schema.sql
12:41:48 inflating: OMERO.server-5.6.3-571-fbdab3a624-ice36-b471/sql/psql/OMERO5.4__0/views.sql
12:41:48 + rm -f OMERO.server-5.6.3-571-fbdab3a624-ice36-b471.zip
12:41:48 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-571-fbdab3a624-ice36-b471 /home/omero/workspace/OMERO-server/OMERO.server
12:41:48 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
12:41:48 + JAR=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
12:41:48 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
12:41:48 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
12:41:48 + mv /home/omero/workspace/OMERO-server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
12:41:48 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
12:41:48 --2025-07-18 12:41:48-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
12:41:48 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
12:41:48 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
12:41:48 HTTP request sent, awaiting response... 200 OK
12:41:48 Length: 889211 (868K) [application/java-archive]
12:41:48 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
12:41:48
12:41:48 0K .......... .......... .......... .......... .......... 5% 3.93M 0s
12:41:48 50K .......... .......... .......... .......... .......... 11% 10.8M 0s
12:41:48 100K .......... .......... .......... .......... .......... 17% 6.13M 0s
12:41:48 150K .......... .......... .......... .......... .......... 23% 12.0M 0s
12:41:48 200K .......... .......... .......... .......... .......... 28% 24.9M 0s
12:41:48 250K .......... .......... .......... .......... .......... 34% 8.65M 0s
12:41:48 300K .......... .......... .......... .......... .......... 40% 40.7M 0s
12:41:48 350K .......... .......... .......... .......... .......... 46% 47.8M 0s
12:41:48 400K .......... .......... .......... .......... .......... 51% 13.5M 0s
12:41:48 450K .......... .......... .......... .......... .......... 57% 11.4M 0s
12:41:48 500K .......... .......... .......... .......... .......... 63% 76.6M 0s
12:41:48 550K .......... .......... .......... .......... .......... 69% 37.4M 0s
12:41:48 600K .......... .......... .......... .......... .......... 74% 31.5M 0s
12:41:48 650K .......... .......... .......... .......... .......... 80% 8.29M 0s
12:41:48 700K .......... .......... .......... .......... .......... 86% 43.7M 0s
12:41:48 750K .......... .......... .......... .......... .......... 92% 62.3M 0s
12:41:48 800K .......... .......... .......... .......... .......... 97% 39.5M 0s
12:41:48 850K .......... ........ 100% 190M=0.06s
12:41:48
12:41:48 2025-07-18 12:41:48 (14.3 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
12:41:48
12:41:48 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
12:41:48 --2025-07-18 12:41:48-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
12:41:48 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
12:41:48 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
12:41:48 HTTP request sent, awaiting response... 200 OK
12:41:48 Length: 73309 (72K) [application/java-archive]
12:41:48 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
12:41:48
12:41:48 0K .......... .......... .......... .......... .......... 69% 4.03M 0s
12:41:48 50K .......... .......... . 100% 11.1M=0.01s
12:41:48
12:41:48 2025-07-18 12:41:48 (4.98 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
12:41:48
12:41:48 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
12:41:48 --2025-07-18 12:41:48-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
12:41:48 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
12:41:48 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
12:41:49 HTTP request sent, awaiting response... 200 OK
12:41:49 Length: 63303 (62K) [application/java-archive]
12:41:49 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
12:41:49
12:41:49 0K .......... .......... .......... .......... .......... 80% 4.12M 0s
12:41:49 50K .......... . 100% 14.3M=0.01s
12:41:49
12:41:49 2025-07-18 12:41:49 (4.77 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
12:41:49
12:41:49 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
12:41:49 --2025-07-18 12:41:49-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
12:41:49 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
12:41:49 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
12:41:49 HTTP request sent, awaiting response... 200 OK
12:41:49 Length: 1271272 (1.2M) [application/java-archive]
12:41:49 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
12:41:49
12:41:49 0K .......... .......... .......... .......... .......... 4% 4.15M 0s
12:41:49 50K .......... .......... .......... .......... .......... 8% 5.16M 0s
12:41:49 100K .......... .......... .......... .......... .......... 12% 24.9M 0s
12:41:49 150K .......... .......... .......... .......... .......... 16% 23.1M 0s
12:41:49 200K .......... .......... .......... .......... .......... 20% 7.77M 0s
12:41:49 250K .......... .......... .......... .......... .......... 24% 38.6M 0s
12:41:49 300K .......... .......... .......... .......... .......... 28% 44.7M 0s
12:41:49 350K .......... .......... .......... .......... .......... 32% 31.6M 0s
12:41:49 400K .......... .......... .......... .......... .......... 36% 32.5M 0s
12:41:49 450K .......... .......... .......... .......... .......... 40% 9.29M 0s
12:41:49 500K .......... .......... .......... .......... .......... 44% 22.1M 0s
12:41:49 550K .......... .......... .......... .......... .......... 48% 30.5M 0s
12:41:49 600K .......... .......... .......... .......... .......... 52% 134M 0s
12:41:49 650K .......... .......... .......... .......... .......... 56% 32.9M 0s
12:41:49 700K .......... .......... .......... .......... .......... 60% 8.78M 0s
12:41:49 750K .......... .......... .......... .......... .......... 64% 29.9M 0s
12:41:49 800K .......... .......... .......... .......... .......... 68% 29.5M 0s
12:41:49 850K .......... .......... .......... .......... .......... 72% 73.6M 0s
12:41:49 900K .......... .......... .......... .......... .......... 76% 39.5M 0s
12:41:49 950K .......... .......... .......... .......... .......... 80% 8.91M 0s
12:41:49 1000K .......... .......... .......... .......... .......... 84% 30.9M 0s
12:41:49 1050K .......... .......... .......... .......... .......... 88% 148M 0s
12:41:49 1100K .......... .......... .......... .......... .......... 92% 22.7M 0s
12:41:49 1150K .......... .......... .......... .......... .......... 96% 44.1M 0s
12:41:49 1200K .......... .......... .......... .......... . 100% 9.95M=0.07s
12:41:49
12:41:49 2025-07-18 12:41:49 (16.5 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
12:41:49
12:41:49 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
12:41:49 ++ deactivate nondestructive
12:41:49 ++ '[' -n '' ']'
12:41:49 ++ '[' -n '' ']'
12:41:49 ++ hash -r
12:41:49 ++ '[' -n '' ']'
12:41:49 ++ unset VIRTUAL_ENV
12:41:49 ++ unset VIRTUAL_ENV_PROMPT
12:41:49 ++ '[' '!' nondestructive = nondestructive ']'
12:41:49 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
12:41:49 ++ export VIRTUAL_ENV
12:41:49 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:41:49 ++ 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
12:41:49 ++ export PATH
12:41:49 ++ '[' -n '' ']'
12:41:49 ++ '[' -z '' ']'
12:41:49 ++ _OLD_VIRTUAL_PS1=
12:41:49 ++ PS1='(.venv3) '
12:41:49 ++ export PS1
12:41:49 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
12:41:49 ++ export VIRTUAL_ENV_PROMPT
12:41:49 ++ hash -r
12:41:49 + pip install -U pip
12:41:49 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
12:41:49 Collecting pip
12:41:49 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
12:41:49 Installing collected packages: pip
12:41:49 Attempting uninstall: pip
12:41:49 Found existing installation: pip 22.3.1
12:41:50 Uninstalling pip-22.3.1:
12:41:50 Successfully uninstalled pip-22.3.1
12:41:50 Successfully installed pip-25.1.1
12:41:50 WARNING: There was an error checking the latest version of pip.
12:41:51 + 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
12:41:51 Collecting zeroc-ice==3.6.5
12:41:51 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)
12:41:53 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 19.6 MB/s eta 0:00:00
12:41:54 Installing collected packages: zeroc-ice
12:41:54 Successfully installed zeroc-ice-3.6.5
12:41:54 + pip install markdown
12:41:55 Collecting markdown
12:41:55 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB)
12:41:55 Using cached markdown-3.8.2-py3-none-any.whl (106 kB)
12:41:55 Installing collected packages: markdown
12:41:55 Successfully installed markdown-3.8.2
12:41:55 + pip install reportlab
12:41:55 Collecting reportlab
12:41:55 Using cached reportlab-4.4.2-py3-none-any.whl.metadata (1.8 kB)
12:41:56 Collecting pillow>=9.0.0 (from reportlab)
12:41:56 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
12:41:56 Collecting charset-normalizer (from reportlab)
12:41:56 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
12:41:56 Using cached reportlab-4.4.2-py3-none-any.whl (2.0 MB)
12:41:56 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
12:41:56 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
12:41:56 Installing collected packages: pillow, charset-normalizer, reportlab
12:41:57
12:41:57 Successfully installed charset-normalizer-3.4.2 pillow-11.3.0 reportlab-4.4.2
12:41:57 + pip install pyarrow
12:41:57 Collecting pyarrow
12:41:58 Downloading pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
12:41:58 Downloading pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
12:42:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.8/42.8 MB 18.6 MB/s eta 0:00:00
12:42:00 Installing collected packages: pyarrow
12:42:02 Successfully installed pyarrow-21.0.0
12:42:02 + pip install omego
12:42:02 Collecting omego
12:42:02 Using cached omego-0.7.0-py3-none-any.whl
12:42:02 Collecting future (from omego)
12:42:02 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
12:42:02 Collecting yaclifw>=0.1.1 (from omego)
12:42:02 Using cached yaclifw-0.2.0-py3-none-any.whl
12:42:02 Collecting six (from yaclifw>=0.1.1->omego)
12:42:02 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
12:42:02 Using cached future-1.0.0-py3-none-any.whl (491 kB)
12:42:02 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
12:42:02 Installing collected packages: six, future, yaclifw, omego
12:42:03
12:42:03 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
12:42:03 + pip install tables
12:42:03 Collecting tables
12:42:03 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
12:42:03 Collecting numpy>=1.20.0 (from tables)
12:42:03 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (62 kB)
12:42:03 Collecting numexpr>=2.6.2 (from tables)
12:42:03 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
12:42:03 Collecting packaging (from tables)
12:42:03 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
12:42:03 Collecting py-cpuinfo (from tables)
12:42:03 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
12:42:04 Collecting blosc2>=2.3.0 (from tables)
12:42:04 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.0 kB)
12:42:04 Collecting typing-extensions>=4.4.0 (from tables)
12:42:04 Using cached typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB)
12:42:04 Collecting ndindex (from blosc2>=2.3.0->tables)
12:42:04 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
12:42:04 Collecting msgpack (from blosc2>=2.3.0->tables)
12:42:04 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
12:42:04 Collecting platformdirs (from blosc2>=2.3.0->tables)
12:42:04 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
12:42:04 Collecting requests (from blosc2>=2.3.0->tables)
12:42:04 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)
12:42:04 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2)
12:42:04 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
12:42:04 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
12:42:04 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
12:42:04 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
12:42:04 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
12:42:04 Using cached certifi-2025.7.14-py3-none-any.whl.metadata (2.4 kB)
12:42:04 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
12:42:04 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB)
12:42:04 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB)
12:42:04 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl (16.9 MB)
12:42:04 Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB)
12:42:04 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
12:42:04 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
12:42:04 Using cached packaging-25.0-py3-none-any.whl (66 kB)
12:42:04 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
12:42:04 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
12:42:04 Using cached requests-2.32.4-py3-none-any.whl (64 kB)
12:42:04 Using cached idna-3.10-py3-none-any.whl (70 kB)
12:42:04 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
12:42:04 Using cached certifi-2025.7.14-py3-none-any.whl (162 kB)
12:42:04 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
12:42:08
12:42:08 Successfully installed blosc2-3.6.1 certifi-2025.7.14 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.11.0 numpy-2.3.1 packaging-25.0 platformdirs-4.3.8 py-cpuinfo-9.0.0 requests-2.32.4 tables-3.10.2 typing-extensions-4.14.1 urllib3-2.5.0
12:42:08 + pip install jinja2
12:42:08 Collecting jinja2
12:42:08 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
12:42:08 Collecting MarkupSafe>=2.0 (from jinja2)
12:42:08 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
12:42:08 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
12:42:08 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
12:42:08 Installing collected packages: MarkupSafe, jinja2
12:42:08
12:42:08 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
12:42:08 + pip install boto3
12:42:09 Collecting boto3
12:42:09 Using cached boto3-1.39.8-py3-none-any.whl.metadata (6.6 kB)
12:42:10 Collecting botocore<1.40.0,>=1.39.8 (from boto3)
12:42:10 Using cached botocore-1.39.8-py3-none-any.whl.metadata (5.7 kB)
12:42:10 Collecting jmespath<2.0.0,>=0.7.1 (from boto3)
12:42:10 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
12:42:10 Collecting s3transfer<0.14.0,>=0.13.0 (from boto3)
12:42:10 Using cached s3transfer-0.13.0-py3-none-any.whl.metadata (1.7 kB)
12:42:10 Collecting python-dateutil<3.0.0,>=2.1 (from botocore<1.40.0,>=1.39.8->boto3)
12:42:10 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
12:42:10 Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.40.0,>=1.39.8->boto3) (2.5.0)
12:42:10 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.40.0,>=1.39.8->boto3) (1.17.0)
12:42:10 Using cached boto3-1.39.8-py3-none-any.whl (139 kB)
12:42:10 Using cached botocore-1.39.8-py3-none-any.whl (13.9 MB)
12:42:10 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
12:42:10 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
12:42:10 Using cached s3transfer-0.13.0-py3-none-any.whl (85 kB)
12:42:10 Installing collected packages: python-dateutil, jmespath, botocore, s3transfer, boto3
12:42:11
12:42:11 Successfully installed boto3-1.39.8 botocore-1.39.8 jmespath-1.0.1 python-dateutil-2.9.0.post0 s3transfer-0.13.0
12:42:11 + pip install smart-open
12:42:11 Collecting smart-open
12:42:11 Using cached smart_open-7.3.0.post1-py3-none-any.whl.metadata (24 kB)
12:42:12 Collecting wrapt (from smart-open)
12:42:12 Using cached wrapt-1.17.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)
12:42:12 Using cached smart_open-7.3.0.post1-py3-none-any.whl (61 kB)
12:42:12 Using cached wrapt-1.17.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (83 kB)
12:42:12 Installing collected packages: wrapt, smart-open
12:42:12
12:42:12 Successfully installed smart-open-7.3.0.post1 wrapt-1.17.2
12:42:12 + pip install omero-py
12:42:12 Collecting omero-py
12:42:12 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB)
12:42:12 Collecting urllib3<2 (from omero-py)
12:42:12 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
12:42:12 Collecting appdirs (from omero-py)
12:42:12 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
12:42:12 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
12:42:12 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.1)
12:42:12 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
12:42:12 Collecting PyYAML (from omero-py)
12:42:12 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
12:42:12 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
12:42:12 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4)
12:42:12 Collecting portalocker (from omero-py)
12:42:12 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
12:42:12 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
12:42:12 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
12:42:12 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.7.14)
12:42:12 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB)
12:42:12 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
12:42:12 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
12:42:12 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
12:42:12 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
12:42:12 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, omero-py
12:42:12 Attempting uninstall: urllib3
12:42:12 Found existing installation: urllib3 2.5.0
12:42:12 Uninstalling urllib3-2.5.0:
12:42:12 Successfully uninstalled urllib3-2.5.0
12:42:14
12:42:14 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20
12:42:14 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
12:42:15 Collecting omero-metadata
12:42:15 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-lhlgszex/omero-metadata_adef5a2385c145afa2df2e4f504d0e6c
12:42:15 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-lhlgszex/omero-metadata_adef5a2385c145afa2df2e4f504d0e6c
12:42:16 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit fc9e036fa89d690ce99dd62a6f14d07df63882c8
12:42:16 Installing build dependencies: started
12:42:16 Installing build dependencies: finished with status 'done'
12:42:16 Getting requirements to build wheel: started
12:42:17 Getting requirements to build wheel: finished with status 'done'
12:42:17 Preparing metadata (pyproject.toml): started
12:42:17 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:17 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0)
12:42:17 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
12:42:17 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
12:42:17 Collecting pandas (from omero-metadata)
12:42:17 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
12:42:17 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
12:42:17 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
12:42:17 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
12:42:17 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.1)
12:42:17 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (11.3.0)
12:42:17 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)
12:42:17 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4)
12:42:17 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
12:42:17 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
12:42:17 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
12:42:17 Collecting pytz>=2020.1 (from pandas->omero-metadata)
12:42:17 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
12:42:17 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
12:42:17 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
12:42:17 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)
12:42:17 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.2)
12:42:17 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.10)
12:42:17 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.7.14)
12:42:17 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
12:42:17 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
12:42:17 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
12:42:17 Building wheels for collected packages: omero-metadata
12:42:17 Building wheel for omero-metadata (pyproject.toml): started
12:42:18 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
12:42:18 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=0dc4d5000f2ecd8de766e923c00b4d208ae40cf0d7d4de2ad98b97f2570861cc
12:42:18 Stored in directory: /tmp/pip-ephem-wheel-cache-o8r2o8ro/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
12:42:18 Successfully built omero-metadata
12:42:18 Installing collected packages: pytz, tzdata, pandas, omero-metadata
12:42:23
12:42:23 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.1 pytz-2025.2 tzdata-2025.2
12:42:23 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
12:42:23 Collecting omero-cli-render
12:42:23 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-evt_7g2h/omero-cli-render_441b2c465cc640df8254ca086eed432f
12:42:23 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-evt_7g2h/omero-cli-render_441b2c465cc640df8254ca086eed432f
12:42:24 Running command git checkout -b merge_ci --track origin/merge_ci
12:42:24 Switched to a new branch 'merge_ci'
12:42:24 branch 'merge_ci' set up to track 'origin/merge_ci'.
12:42:24 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit f0aa652d7231279ce4e07c6ce2d3c1fa921ebb59
12:42:24 Installing build dependencies: started
12:42:25 Installing build dependencies: finished with status 'done'
12:42:25 Getting requirements to build wheel: started
12:42:26 Getting requirements to build wheel: finished with status 'done'
12:42:26 Preparing metadata (pyproject.toml): started
12:42:26 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:26 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
12:42:26 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0)
12:42:26 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
12:42:26 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
12:42:26 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
12:42:26 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.1)
12:42:26 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.3.0)
12:42:26 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)
12:42:26 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4)
12:42:26 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
12:42:26 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.2)
12:42:26 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.10)
12:42:26 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.7.14)
12:42:26 Building wheels for collected packages: omero-cli-render
12:42:26 Building wheel for omero-cli-render (pyproject.toml): started
12:42:26 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
12:42:26 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=9e174a029654362516c86fbde5ceb2bb7d837a709aab7ee54bb2c5232393654c
12:42:26 Stored in directory: /tmp/pip-ephem-wheel-cache-wbibsgvu/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
12:42:26 Successfully built omero-cli-render
12:42:26 Installing collected packages: omero-cli-render
12:42:26 Successfully installed omero-cli-render-0.8.2.dev0
12:42:26 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
12:42:26 Collecting omero-cli-duplicate
12:42:26 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-h4o721gy/omero-cli-duplicate_4b240352c2d84748b9d0938d17d8db67
12:42:27 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-h4o721gy/omero-cli-duplicate_4b240352c2d84748b9d0938d17d8db67
12:42:27 Running command git checkout -b merge_ci --track origin/merge_ci
12:42:29 Switched to a new branch 'merge_ci'
12:42:29 branch 'merge_ci' set up to track 'origin/merge_ci'.
12:42:29 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit ffa122e1387972b54ff9e41aa3a44fbcfc667ed9
12:42:29 Installing build dependencies: started
12:42:30 Installing build dependencies: finished with status 'done'
12:42:30 Getting requirements to build wheel: started
12:42:30 Getting requirements to build wheel: finished with status 'done'
12:42:30 Preparing metadata (pyproject.toml): started
12:42:30 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:30 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0)
12:42:30 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
12:42:30 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
12:42:30 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
12:42:30 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.1)
12:42:30 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.3.0)
12:42:30 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
12:42:30 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)
12:42:30 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4)
12:42:30 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
12:42:30 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.2)
12:42:30 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.10)
12:42:30 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.7.14)
12:42:30 Building wheels for collected packages: omero-cli-duplicate
12:42:30 Building wheel for omero-cli-duplicate (pyproject.toml): started
12:42:30 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
12:42:30 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=2efcb45cc3d3f909cd50f69874f9179d0c76d3d11a07e7b6dd1de5c0418f153a
12:42:30 Stored in directory: /tmp/pip-ephem-wheel-cache-276nna98/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
12:42:30 Successfully built omero-cli-duplicate
12:42:30 Installing collected packages: omero-cli-duplicate
12:42:30 Successfully installed omero-cli-duplicate-0.4.1.dev0
12:42:31 + pip install omero-certificates
12:42:31 Collecting omero-certificates
12:42:31 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
12:42:31 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0)
12:42:31 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
12:42:31 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
12:42:31 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
12:42:31 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.1)
12:42:31 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (11.3.0)
12:42:31 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
12:42:31 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)
12:42:31 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4)
12:42:31 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
12:42:31 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.2)
12:42:31 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
12:42:31 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.7.14)
12:42:31 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
12:42:31 Installing collected packages: omero-certificates
12:42:31 Successfully installed omero-certificates-0.4.0
12:42:31 + for x in *.tar.gz
12:42:31 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
12:42:32 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
12:42:32 Installing build dependencies: started
12:42:32 Installing build dependencies: finished with status 'done'
12:42:32 Getting requirements to build wheel: started
12:42:33 Getting requirements to build wheel: finished with status 'done'
12:42:33 Preparing metadata (pyproject.toml): started
12:42:33 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:33 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0)
12:42:33 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
12:42:33 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
12:42:33 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
12:42:33 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.1)
12:42:33 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.3.0)
12:42:33 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
12:42:33 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)
12:42:33 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4)
12:42:33 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
12:42:33 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.2)
12:42:33 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10)
12:42:33 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.7.14)
12:42:33 Building wheels for collected packages: omero-dropbox
12:42:33 Building wheel for omero-dropbox (pyproject.toml): started
12:42:33 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
12:42:33 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=0b0fc39e0cb38f97862ea49b4598fb1ed0cca356bf7b8cd047777cc7ce14b9fa
12:42:33 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
12:42:33 Successfully built omero-dropbox
12:42:33 Installing collected packages: omero-dropbox
12:42:33 Successfully installed omero-dropbox-5.7.1.dev0
12:42:33 + for x in *.tar.gz
12:42:33 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
12:42:34 Processing ./omero_marshal-0.9.1.dev0.tar.gz
12:42:34 Installing build dependencies: started
12:42:35 Installing build dependencies: finished with status 'done'
12:42:35 Getting requirements to build wheel: started
12:42:35 Getting requirements to build wheel: finished with status 'done'
12:42:35 Preparing metadata (pyproject.toml): started
12:42:35 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:35 Building wheels for collected packages: omero_marshal
12:42:35 Building wheel for omero_marshal (pyproject.toml): started
12:42:36 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
12:42:36 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=969e4dadad9c13b63963628a5218bc2bf54b54f4759f030e076cecca66c9a800
12:42:36 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
12:42:36 Successfully built omero_marshal
12:42:36 Installing collected packages: omero_marshal
12:42:36 Successfully installed omero_marshal-0.9.1.dev0
12:42:36 + for x in *.tar.gz
12:42:36 + pip install -U omero_py-5.21.1.dev0.tar.gz
12:42:37 Processing ./omero_py-5.21.1.dev0.tar.gz
12:42:37 Installing build dependencies: started
12:42:38 Installing build dependencies: finished with status 'done'
12:42:38 Getting requirements to build wheel: started
12:42:38 Getting requirements to build wheel: finished with status 'done'
12:42:38 Preparing metadata (pyproject.toml): started
12:42:38 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:38 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20)
12:42:38 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4)
12:42:38 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0)
12:42:38 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.1)
12:42:38 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0)
12:42:38 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2)
12:42:38 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.6.5)
12:42:38 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4)
12:42:38 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0)
12:42:38 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.4.2)
12:42:38 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10)
12:42:38 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.7.14)
12:42:38 Building wheels for collected packages: omero-py
12:42:38 Building wheel for omero-py (pyproject.toml): started
12:42:40 Building wheel for omero-py (pyproject.toml): finished with status 'done'
12:42:40 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783499 sha256=50b02863d3afa6418343abadb8ef5df8d32697e62741bc315555ccad4872b4e8
12:42:40 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d
12:42:40 Successfully built omero-py
12:42:40 Installing collected packages: omero-py
12:42:40 Attempting uninstall: omero-py
12:42:40 Found existing installation: omero-py 5.21.0
12:42:40 Uninstalling omero-py-5.21.0:
12:42:40 Successfully uninstalled omero-py-5.21.0
12:42:42 Successfully installed omero-py-5.21.1.dev0
12:42:42 + for x in *.tar.gz
12:42:42 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
12:42:43 Processing ./omero_scripts-5.9.2.dev0.tar.gz
12:42:43 Installing build dependencies: started
12:42:43 Installing build dependencies: finished with status 'done'
12:42:43 Getting requirements to build wheel: started
12:42:44 Getting requirements to build wheel: finished with status 'done'
12:42:44 Preparing metadata (pyproject.toml): started
12:42:44 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:44 Building wheels for collected packages: omero-scripts
12:42:44 Building wheel for omero-scripts (pyproject.toml): started
12:42:44 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
12:42:44 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=b6ec9c5a8b947b9309ab7451e2053eda29dea3cc445ff83cf0d73b52fe1602c9
12:42:44 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
12:42:44 Successfully built omero-scripts
12:42:44 Installing collected packages: omero-scripts
12:42:44 Successfully installed omero-scripts-5.9.2.dev0
12:42:45 + for x in *.tar.gz
12:42:45 + pip install -U omero_web-5.29.2.dev0.tar.gz
12:42:45 Processing ./omero_web-5.29.2.dev0.tar.gz
12:42:45 Installing build dependencies: started
12:42:46 Installing build dependencies: finished with status 'done'
12:42:46 Getting requirements to build wheel: started
12:42:46 Getting requirements to build wheel: finished with status 'done'
12:42:46 Preparing metadata (pyproject.toml): started
12:42:47 Preparing metadata (pyproject.toml): finished with status 'done'
12:42:47 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (5.21.1.dev0)
12:42:47 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0)
12:42:47 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
12:42:48 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0)
12:42:48 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB)
12:42:48 Collecting django-pipeline (from omero-web==5.29.2.dev0)
12:42:48 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
12:42:48 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0)
12:42:48 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
12:42:48 Collecting django-csp (from omero-web==5.29.2.dev0)
12:42:48 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
12:42:48 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0)
12:42:48 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
12:42:48 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0)
12:42:48 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
12:42:48 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (0.9.1.dev0)
12:42:48 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.3.0)
12:42:48 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2)
12:42:48 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0)
12:42:48 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0)
12:42:48 Collecting importlib-resources (from omero-web==5.29.2.dev0)
12:42:48 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
12:42:48 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
12:42:48 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB)
12:42:48 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
12:42:48 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
12:42:49 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.26.20)
12:42:49 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.4.4)
12:42:49 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.0.0)
12:42:49 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.3.1)
12:42:49 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (6.0.2)
12:42:49 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==5.29.2.dev0) (3.6.5)
12:42:49 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.32.4)
12:42:49 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1)
12:42:49 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0)
12:42:49 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
12:42:49 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.4.2)
12:42:49 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.10)
12:42:49 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (2025.7.14)
12:42:49 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
12:42:49 Using cached django-4.2.23-py3-none-any.whl (8.0 MB)
12:42:49 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB)
12:42:49 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
12:42:49 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
12:42:49 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
12:42:49 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
12:42:49 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
12:42:49 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
12:42:49 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
12:42:49 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
12:42:49 Building wheels for collected packages: omero-web
12:42:49 Building wheel for omero-web (pyproject.toml): started
12:42:50 Building wheel for omero-web (pyproject.toml): finished with status 'done'
12:42:50 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=fa6772b5d49692cec2e2924897d95db3e6e5103b60da88ef9de013569af2556d
12:42:50 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c
12:42:50 Successfully built omero-web
12:42:50 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
12:42:53
12:42:53 Successfully installed Django-4.2.23 asgiref-3.9.1 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.0.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.2.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.9.0
12:42:53 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
12:42:53 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
12:42:53 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
12:42:53 --2025-07-18 12:42:53-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
12:42:53 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.108.133, 185.199.111.133, ...
12:42:53 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
12:42:53 HTTP request sent, awaiting response... 200 OK
12:42:53 Length: 125072 (122K) [text/plain]
12:42:53 Saving to: ‘Figure_To_Pdf.py’
12:42:53
12:42:53 0K .......... .......... .......... .......... .......... 40% 4.27M 0s
12:42:53 50K .......... .......... .......... .......... .......... 81% 5.27M 0s
12:42:53 100K .......... .......... .. 100% 47.6M=0.02s
12:42:53
12:42:53 2025-07-18 12:42:53 (5.63 MB/s) - ‘Figure_To_Pdf.py’ saved [125072/125072]
12:42:53
12:42:53 + chmod 755 Figure_To_Pdf.py
12:42:53 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
12:42:53 + omero config set omero.db.name OMERO-server
12:42:55 + omero config set omero.db.host pg
12:42:56 + omero config set omero.db.user postgres
12:42:57 + omero config set omero.data.dir /home/omero/omero-server-data
12:42:58 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
12:43:00 + omero config set omero.db.poolsize 25
12:43:01 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
12:43:02 + omero config set omero.security.trustStorePassword changeit
12:43:03 + omero config set omero.mail.config true
12:43:05 + omero config set omero.mail.from qa@openmicroscopy.org.uk
12:43:06 + omero config set omero.mail.host smtp.dundee.ac.uk
12:43:07 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
12:43:08 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
12:43:10 + omero certificates
12:43:11 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
12:43:11 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
12:43:11 + '[' false = true ']'
12:43:11 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
12:43:11 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
12:43:11 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG dbcommand => upgrade
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG dbhost => localhost
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG dbname => OMERO-server
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG dbpass => omero
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG dbuser => omero
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG rootpass => omero
12:43:11 2025-07-18 12:43:11,705 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
12:43:11 2025-07-18 12:43:11,705 [omego.extern] INFO Executing : omero version
12:43:12 OMERO.py version:
12:43:12 OMERO.server version:
12:43:12 5.6.3-571-fbdab3a624-ice36-b471
12:43:12 5.21.1.dev0
12:43:13 2025-07-18 12:43:13,009 [omego.extern] INFO Completed [1.303 s]
12:43:13 2025-07-18 12:43:13,009 [omego.extern] DEBUG Using omero CLI from omero
12:43:13 2025-07-18 12:43:13,009 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
12:43:13 2025-07-18 12:43:13,009 [omego.extern] INFO Running [current environment]: omero config get --show-password
12:43:13 2025-07-18 12:43:13,009 [omego.extern] INFO Executing : omero config get --show-password
12:43:14 2025-07-18 12:43:14,252 [omego.extern] INFO Completed [1.243 s]
12:43:14 2025-07-18 12:43:14,252 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
12:43:14 2025-07-18 12:43:14,252 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
12:43:14 2025-07-18 12:43:14,259 [omego.extern] INFO Completed [0.006 s]
12:43:14 2025-07-18 12:43:14,259 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
12:43:14 2025-07-18 12:43:14,259 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
12:43:14
12:43:14 2025-07-18 12:43:14,259 [omego.extern] INFO Running [current environment]: omero config get --show-password
12:43:14 2025-07-18 12:43:14,259 [omego.extern] INFO Executing : omero config get --show-password
12:43:15 2025-07-18 12:43:15,508 [omego.extern] INFO Completed [1.249 s]
12:43:15 2025-07-18 12:43:15,508 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
12:43:15 2025-07-18 12:43:15,508 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
12:43:15 2025-07-18 12:43:15,518 [omego.extern] INFO Completed [0.010 s]
12:43:15 2025-07-18 12:43:15,518 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.9") at port "5432".\n'
12:43:15 2025-07-18 12:43:15,519 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
12:43:15 2025-07-18 12:43:15,519 [omego.extern] INFO Running [current environment]: omero config get --show-password
12:43:15 2025-07-18 12:43:15,519 [omego.extern] INFO Executing : omero config get --show-password
12:43:16 2025-07-18 12:43:16,804 [omego.extern] INFO Completed [1.285 s]
12:43:16 2025-07-18 12:43:16,804 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
12:43:16 2025-07-18 12:43:16,804 [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
12:43:16 2025-07-18 12:43:16,815 [omego.extern] INFO Completed [0.011 s]
12:43:16 2025-07-18 12:43:16,815 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
12:43:16 2025-07-18 12:43:16,815 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
12:43:16 2025-07-18 12:43:16,817 [ omego.db] INFO Database is already at OMERO5.4__0
12:43:16 + export LANG=en_US.UTF-8
12:43:16 + LANG=en_US.UTF-8
12:43:16 + export LANGUAGE=en_US:en
12:43:16 + LANGUAGE=en_US:en
12:43:16 + export LC_ALL=en_US.UTF-8
12:43:16 + LC_ALL=en_US.UTF-8
12:43:16 + BUILD_ID=DONT_KILL_ME
12:43:16 + omero admin start
12:43:21 No descriptor given. Using etc/grid/default.xml
12:43:29 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
12:43:29 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
12:43:29 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
12:43:29 Waiting on startup. Use CTRL-C to exit
12:43:29 + omero admin waitup
12:43:30 Waiting on startup. Use CTRL-C to exit
12:43:31 + omero admin diagnostics
12:43:32
12:43:32 ================================================================================
12:43:32 OMERO Diagnostics (admin)
12:43:32 ================================================================================
12:43:32
12:43:32 Commands: java -version 11.0.25 (/usr/bin/java)
12:43:32 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
12:43:32 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
12:43:32 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
12:43:32 Commands: psql --version 16.9 (/usr/bin/psql)
12:43:32 Commands: openssl version 3.2.24 (/usr/bin/openssl)
12:43:32
12:43:32 Component: OMERO.py 5.21.1.dev0
12:43:32 Component: OMERO.server 5.6.3-571-fbdab3a624-ice36-b471
12:43:32
12:43:32 Server: icegridnode running
12:43:32 Server: Blitz-0 active (pid = 47454, enabled)
12:43:32 Server: Indexer-0 activating (enabled)
12:43:32 Server: OMERO.Glacier2 active (pid = 47504, enabled)
12:43:32 Server: OMERO.IceStorm active (pid = 47502, enabled)
12:43:32 Server: Processor-0 activating (enabled)
12:43:32 Server: Tables-0 activating (enabled)
12:43:32
12:43:32 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
12:43:32 Log files: Blitz-0.log 22.7 KB errors=0 warnings=1
12:43:32 Log files: DropBox.log n/a
12:43:32 Log files: FileServer.log n/a
12:43:32 Log files: Indexer-0.log 114 B
12:43:32 Log files: MonitorServer.log n/a
12:43:32 Log files: Processor-0.log 281 B
12:43:32 Log files: Tables-0.log 281 B
12:43:32 Log files: TestDropBox.log n/a
12:43:32 Log files: master.err empty
12:43:32 Log files: master.out 30.5 KB
12:43:32 Log files: Total size 0.05 MB
12:43:32
12:43:32
12:43:32 Environment:OMERO_HOME=(unset)
12:43:32 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:43:32 Environment:OMERO_NODE=(unset)
12:43:32 Environment:OMERO_MASTER=(unset)
12:43:32 Environment:OMERO_USERDIR=(unset)
12:43:32 Environment:OMERO_TMPDIR=(unset)
12:43:32 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
12:43:32 Environment:PYTHONPATH=(unset)
12:43:32 Environment:ICE_HOME=/opt/ice-3.6.5
12:43:32 Environment:LD_LIBRARY_PATH=(unset)
12:43:32 Environment:DYLD_LIBRARY_PATH=(unset)
12:43:32
12:43:32 OMERO SSL port:4064
12:43:32 OMERO TCP port:4063
12:43:32 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
12:43:32 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
12:43:32
12:43:32 JVM settings: Blitz-${index} -Xmx7200m
12:43:32 JVM settings: Indexer-${index} -Xmx4800m
12:43:32 JVM settings: PixelData-${index} -Xmx7200m
12:43:32 JVM settings: Repository-${index} -Xmx4800m
12:43:32
12:43:32 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 18 July 2025 60d8f4b5e1d73f82e727298dfd07d638605a3f64
12:43:32 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 18 July 2025 60d8f4b5e1d73f82e727298dfd07d638605a3f64
12:43:32 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 18 July 2025 60d8f4b5e1d73f82e727298dfd07d638605a3f64
12:43:32 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 18 July 2025 3f7b177dd4ca862e1da8913ef8d94885e29f6d19
12:43:32 Jar: lib/server/ome-common.jar OME Common Java 6.0.27-SNAPSHOT 18 July 2025 3f7b177dd4ca862e1da8913ef8d94885e29f6d19
12:43:32 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 18 July 2025 3f7b177dd4ca862e1da8913ef8d94885e29f6d19
12:43:32 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 18 July 2025 3f7b177dd4ca862e1da8913ef8d94885e29f6d19
12:43:32 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 18 July 2025 3f7b177dd4ca862e1da8913ef8d94885e29f6d19
12:43:32 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 18 July 2025 3f7b177dd4ca862e1da8913ef8d94885e29f6d19
12:43:32 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
12:43:32 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT 054df919f1f46dfe9fee5045242198e05b4dda1c
12:43:32 + deactivate
12:43:32 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
12:43:32 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:43:32 + export PATH
12:43:32 + unset _OLD_VIRTUAL_PATH
12:43:32 + '[' -n '' ']'
12:43:32 + hash -r
12:43:32 + '[' -n '' ']'
12:43:32 + unset VIRTUAL_ENV
12:43:32 + unset VIRTUAL_ENV_PROMPT
12:43:32 + '[' '!' '' = nondestructive ']'
12:43:32 + unset -f deactivate
12:43:32 Finished: SUCCESS
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