00:43:04 Started by upstream project "Trigger" build number 625
00:43:04 originally caused by:
00:43:04 Started by timer
00:43:04 Running as SYSTEM
00:43:04 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:43:04 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13549138299128272333.sh
00:43:04 + source /home/settings.env
00:43:04 ++ OMERO_DB_HOST=pg
00:43:04 ++ OMERO_DB_USER=postgres
00:43:04 ++ OMERO_DB_PASS=
00:43:04 ++ OMERO_ROOT_PASS=omero
00:43:04 ++ OMERO_DATA_DIR=/OMERO
00:43:04 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:43:04 + OMERO_DB_NAME=OMERO-server
00:43:04 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:43:04 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:43:04 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:43:04 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:43:04 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:43:04 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:43:04 ++ deactivate nondestructive
00:43:04 ++ '[' -n '' ']'
00:43:04 ++ '[' -n '' ']'
00:43:04 ++ hash -r
00:43:04 ++ '[' -n '' ']'
00:43:04 ++ unset VIRTUAL_ENV
00:43:04 ++ unset VIRTUAL_ENV_PROMPT
00:43:04 ++ '[' '!' nondestructive = nondestructive ']'
00:43:04 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:43:04 ++ export VIRTUAL_ENV
00:43:04 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:43:04 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:43:04 ++ export PATH
00:43:04 ++ '[' -n '' ']'
00:43:04 ++ '[' -z '' ']'
00:43:04 ++ _OLD_VIRTUAL_PS1=
00:43:04 ++ PS1='(.venv3) '
00:43:04 ++ export PS1
00:43:04 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:43:04 ++ export VIRTUAL_ENV_PROMPT
00:43:04 ++ hash -r
00:43:04 + omero admin stop
00:43:05 Waiting on shutdown. Use CTRL-C to exit
00:43:05 .+ sleep 5
00:43:20 + deactivate
00:43:20 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:43:20 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:43:20 + export PATH
00:43:20 + unset _OLD_VIRTUAL_PATH
00:43:20 + '[' -n '' ']'
00:43:20 + hash -r
00:43:20 + '[' -n '' ']'
00:43:20 + unset VIRTUAL_ENV
00:43:20 + unset VIRTUAL_ENV_PROMPT
00:43:20 + '[' '!' '' = nondestructive ']'
00:43:20 + unset -f deactivate
00:43:20 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:43:21 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:43:24 + '[' false = true ']'
00:43:24 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:43:24 Skipping PURGE_DATA:CleanDbAndRepo
00:43:24 + 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-5.21.2.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-5.29.3.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:43:26 Copied 1 artifact from "OMERO-build" build number 529
00:43:26 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 522
00:43:26 Copied 2 artifacts from "OMERO-build-build" build number 556
00:43:26 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 61
00:43:26 [OMERO-server] $ /bin/bash -xe /tmp/jenkins10823428401332106866.sh
00:43:26 + source /home/settings.env
00:43:26 ++ OMERO_DB_HOST=pg
00:43:26 ++ OMERO_DB_USER=postgres
00:43:26 ++ OMERO_DB_PASS=
00:43:26 ++ OMERO_ROOT_PASS=omero
00:43:26 ++ OMERO_DATA_DIR=/OMERO
00:43:26 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:43:26 + OMERO_DB_NAME=OMERO-server
00:43:26 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:43:26 + mkdir -p /home/omero/omero-server-data
00:43:26 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:43:26 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:43:26 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:43:26 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:43:26 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:43:26 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:43:26 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:43:26 ++ ls OMERO.server-5.6.3-574-f644878cec-ice36-b529.zip
00:43:26 + ZIP=OMERO.server-5.6.3-574-f644878cec-ice36-b529.zip
00:43:26 + '[' '!' -z '' ']'
00:43:26 + DIST=OMERO.server-5.6.3-574-f644878cec-ice36-b529
00:43:26 + unzip OMERO.server-5.6.3-574-f644878cec-ice36-b529.zip
00:43:26 Archive: OMERO.server-5.6.3-574-f644878cec-ice36-b529.zip
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/blitz/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/grid/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/profiles/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/error/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/grid/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/luts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/luts/janelia/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/luts/matplotlib/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/luts/ncsa_paledit/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/luts/seaborn/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/luts/wcif/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/analysis_scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/annotation_scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/export_scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/figure_scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/import_scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/scripts/omero/util_scripts/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/server/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/share/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/share/licenses/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/misc/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__1/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__10/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__11/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__2/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__3/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__4/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__5/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__6/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__7/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__8/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3A__9/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3__4/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3__5/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3__6/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO3__7/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO4.1__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO4.2__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO4.2__0/t/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO4.3__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO4.4__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO4__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.0__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.1__1/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.2__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.3__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4DEV__1/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4DEV__2/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4DEV__3/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/
00:43:26 creating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/var/
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/LICENSE.txt
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/backup.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/blitz/mail-senders.example
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/blitz/mail-server.example
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/build.properties
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/env.bat
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/env.sh
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/hibernate.properties
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/ice.config
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/logback-cli.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/logback-indexing-cli.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/logback-indexing.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/logback.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/mime.types
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/node1.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/node2.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/omero.properties
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/profiles/psql
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/rollover.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/Windows.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/error/maintainance.html
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/grid/README
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/grid/default.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/grid/templates.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/grid/windefault.xml
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/ice.config
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/internal.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/master.cfg
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/templates/robot.template
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/etc/testdropbox.config
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/history.rst
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/OMEZarrReader.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/accessors-smart.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/activation.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/aggdesigner-algorithm.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/aircompressor.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/antlr.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/aopalliance.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/apiguardian-api.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/asm.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/avatica-core.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/avatica-metrics.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/aws-java-sdk-core.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/aws-java-sdk-kms.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/aws-java-sdk-s3.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/base.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-anim.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-awt-util.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-bridge.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-codec.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-constants.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-css.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-dom.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-ext.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-gvt.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-i18n.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-parser.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-script.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-shared-resources.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-svg-dom.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-svggen.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-transcoder.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-util.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/batik-xml.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/btm.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/calcite-core.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/calcite-linq4j.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/cdm-core.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/checker-qual.jar
00:43:26 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/lib/client/commons-beanutils.jar
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00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/psql-footer.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/psql-header.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/schema.sql
00:43:28 inflating: OMERO.server-5.6.3-574-f644878cec-ice36-b529/sql/psql/OMERO5.4__0/views.sql
00:43:28 + rm -f OMERO.server-5.6.3-574-f644878cec-ice36-b529.zip
00:43:28 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-574-f644878cec-ice36-b529 /home/omero/workspace/OMERO-server/OMERO.server
00:43:28 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:43:28 + JAR=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:43:28 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:43:28 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:43:28 + 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
00:43:28 + 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
00:43:28 --2025-09-21 00:43:28-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:43:28 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:43:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:43:29 HTTP request sent, awaiting response... 200 OK
00:43:29 Length: 889211 (868K) [application/java-archive]
00:43:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:43:29
00:43:29 0K .......... .......... .......... .......... .......... 5% 3.79M 0s
00:43:29 50K .......... .......... .......... .......... .......... 11% 5.96M 0s
00:43:29 100K .......... .......... .......... .......... .......... 17% 22.3M 0s
00:43:29 150K .......... .......... .......... .......... .......... 23% 16.6M 0s
00:43:29 200K .......... .......... .......... .......... .......... 28% 8.68M 0s
00:43:29 250K .......... .......... .......... .......... .......... 34% 42.0M 0s
00:43:29 300K .......... .......... .......... .......... .......... 40% 27.5M 0s
00:43:29 350K .......... .......... .......... .......... .......... 46% 43.7M 0s
00:43:29 400K .......... .......... .......... .......... .......... 51% 38.6M 0s
00:43:29 450K .......... .......... .......... .......... .......... 57% 7.94M 0s
00:43:29 500K .......... .......... .......... .......... .......... 63% 39.6M 0s
00:43:29 550K .......... .......... .......... .......... .......... 69% 28.7M 0s
00:43:29 600K .......... .......... .......... .......... .......... 74% 180M 0s
00:43:29 650K .......... .......... .......... .......... .......... 80% 31.6M 0s
00:43:29 700K .......... .......... .......... .......... .......... 86% 8.68M 0s
00:43:29 750K .......... .......... .......... .......... .......... 92% 29.5M 0s
00:43:29 800K .......... .......... .......... .......... .......... 97% 34.4M 0s
00:43:29 850K .......... ........ 100% 107M=0.06s
00:43:29
00:43:29 2025-09-21 00:43:29 (14.9 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:43:29
00:43:29 + 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
00:43:29 --2025-09-21 00:43:29-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:43:29 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:43:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:43:29 HTTP request sent, awaiting response... 200 OK
00:43:29 Length: 73309 (72K) [application/java-archive]
00:43:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:43:29
00:43:29 0K .......... .......... .......... .......... .......... 69% 3.71M 0s
00:43:29 50K .......... .......... . 100% 23.9M=0.01s
00:43:29
00:43:29 2025-09-21 00:43:29 (4.98 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:43:29
00:43:29 + 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
00:43:29 --2025-09-21 00:43:29-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:43:29 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:43:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:43:29 HTTP request sent, awaiting response... 200 OK
00:43:29 Length: 63303 (62K) [application/java-archive]
00:43:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:43:29
00:43:29 0K .......... .......... .......... .......... .......... 80% 4.18M 0s
00:43:29 50K .......... . 100% 11.3M=0.01s
00:43:29
00:43:29 2025-09-21 00:43:29 (4.76 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:43:29
00:43:29 + 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
00:43:29 --2025-09-21 00:43:29-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:43:29 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:43:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:43:29 HTTP request sent, awaiting response... 200 OK
00:43:29 Length: 1271272 (1.2M) [application/java-archive]
00:43:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:43:29
00:43:29 0K .......... .......... .......... .......... .......... 4% 3.78M 0s
00:43:29 50K .......... .......... .......... .......... .......... 8% 9.21M 0s
00:43:29 100K .......... .......... .......... .......... .......... 12% 7.85M 0s
00:43:29 150K .......... .......... .......... .......... .......... 16% 27.7M 0s
00:43:29 200K .......... .......... .......... .......... .......... 20% 7.56M 0s
00:43:29 250K .......... .......... .......... .......... .......... 24% 34.1M 0s
00:43:29 300K .......... .......... .......... .......... .......... 28% 25.8M 0s
00:43:29 350K .......... .......... .......... .......... .......... 32% 93.4M 0s
00:43:29 400K .......... .......... .......... .......... .......... 36% 76.9M 0s
00:43:29 450K .......... .......... .......... .......... .......... 40% 8.02M 0s
00:43:29 500K .......... .......... .......... .......... .......... 44% 23.9M 0s
00:43:29 550K .......... .......... .......... .......... .......... 48% 185M 0s
00:43:29 600K .......... .......... .......... .......... .......... 52% 30.4M 0s
00:43:29 650K .......... .......... .......... .......... .......... 56% 28.8M 0s
00:43:29 700K .......... .......... .......... .......... .......... 60% 8.79M 0s
00:43:29 750K .......... .......... .......... .......... .......... 64% 38.1M 0s
00:43:29 800K .......... .......... .......... .......... .......... 68% 87.1M 0s
00:43:29 850K .......... .......... .......... .......... .......... 72% 32.8M 0s
00:43:29 900K .......... .......... .......... .......... .......... 76% 26.1M 0s
00:43:29 950K .......... .......... .......... .......... .......... 80% 8.91M 0s
00:43:29 1000K .......... .......... .......... .......... .......... 84% 34.7M 0s
00:43:29 1050K .......... .......... .......... .......... .......... 88% 114M 0s
00:43:29 1100K .......... .......... .......... .......... .......... 92% 32.9M 0s
00:43:29 1150K .......... .......... .......... .......... .......... 96% 23.3M 0s
00:43:29 1200K .......... .......... .......... .......... . 100% 10.6M=0.07s
00:43:29
00:43:29 2025-09-21 00:43:29 (16.3 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:43:29
00:43:29 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:43:29 ++ deactivate nondestructive
00:43:29 ++ '[' -n '' ']'
00:43:29 ++ '[' -n '' ']'
00:43:29 ++ hash -r
00:43:29 ++ '[' -n '' ']'
00:43:29 ++ unset VIRTUAL_ENV
00:43:29 ++ unset VIRTUAL_ENV_PROMPT
00:43:29 ++ '[' '!' nondestructive = nondestructive ']'
00:43:29 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:43:29 ++ export VIRTUAL_ENV
00:43:29 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:43:29 ++ 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
00:43:29 ++ export PATH
00:43:29 ++ '[' -n '' ']'
00:43:29 ++ '[' -z '' ']'
00:43:29 ++ _OLD_VIRTUAL_PS1=
00:43:29 ++ PS1='(.venv3) '
00:43:29 ++ export PS1
00:43:29 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:43:29 ++ export VIRTUAL_ENV_PROMPT
00:43:29 ++ hash -r
00:43:29 + pip install -U pip
00:43:30 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:43:30 Collecting pip
00:43:30 Using cached pip-25.2-py3-none-any.whl (1.8 MB)
00:43:30 Installing collected packages: pip
00:43:30 Attempting uninstall: pip
00:43:30 Found existing installation: pip 22.3.1
00:43:30 Uninstalling pip-22.3.1:
00:43:30 Successfully uninstalled pip-22.3.1
00:43:31 Successfully installed pip-25.2
00:43:31 WARNING: There was an error checking the latest version of pip.
00:43:31 + 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
00:43:31 Collecting zeroc-ice==3.6.5
00:43:32 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)
00:43:35 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 9.8 MB/s 0:00:03
00:43:35 Installing collected packages: zeroc-ice
00:43:36 Successfully installed zeroc-ice-3.6.5
00:43:36 + pip install markdown
00:43:37 Collecting markdown
00:43:37 Using cached markdown-3.9-py3-none-any.whl.metadata (5.1 kB)
00:43:37 Using cached markdown-3.9-py3-none-any.whl (107 kB)
00:43:37 Installing collected packages: markdown
00:43:37 Successfully installed markdown-3.9
00:43:37 + pip install reportlab
00:43:37 Collecting reportlab
00:43:37 Using cached reportlab-4.4.4-py3-none-any.whl.metadata (1.7 kB)
00:43:38 Collecting pillow>=9.0.0 (from reportlab)
00:43:38 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:43:38 Collecting charset-normalizer (from reportlab)
00:43:38 Using cached charset_normalizer-3.4.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (36 kB)
00:43:38 Using cached reportlab-4.4.4-py3-none-any.whl (2.0 MB)
00:43:38 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:43:38 Using cached charset_normalizer-3.4.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (150 kB)
00:43:38 Installing collected packages: pillow, charset-normalizer, reportlab
00:43:39
00:43:39 Successfully installed charset-normalizer-3.4.3 pillow-11.3.0 reportlab-4.4.4
00:43:39 + pip install pyarrow
00:43:39 Collecting pyarrow
00:43:39 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
00:43:39 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
00:43:39 Installing collected packages: pyarrow
00:43:41 Successfully installed pyarrow-21.0.0
00:43:41 + pip install omego
00:43:41 Collecting omego
00:43:41 Using cached omego-0.7.0-py3-none-any.whl
00:43:41 Collecting future (from omego)
00:43:41 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:43:41 Collecting yaclifw>=0.1.1 (from omego)
00:43:41 Using cached yaclifw-0.2.0-py3-none-any.whl
00:43:41 Collecting six (from yaclifw>=0.1.1->omego)
00:43:41 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:43:41 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:43:41 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:43:41 Installing collected packages: six, future, yaclifw, omego
00:43:42
00:43:42 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:43:42 + pip install tables
00:43:42 Collecting tables
00:43:42 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:43:42 Collecting numpy>=1.20.0 (from tables)
00:43:42 Using cached numpy-2.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
00:43:42 Collecting numexpr>=2.6.2 (from tables)
00:43:42 Using cached numexpr-2.12.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:43:42 Collecting packaging (from tables)
00:43:42 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:43:42 Collecting py-cpuinfo (from tables)
00:43:42 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:43:43 Collecting blosc2>=2.3.0 (from tables)
00:43:43 Using cached blosc2-3.8.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
00:43:43 Collecting typing-extensions>=4.4.0 (from tables)
00:43:43 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
00:43:43 Collecting ndindex (from blosc2>=2.3.0->tables)
00:43:43 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:43:43 Collecting msgpack (from blosc2>=2.3.0->tables)
00:43:43 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:43:43 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:43:43 Using cached platformdirs-4.4.0-py3-none-any.whl.metadata (12 kB)
00:43:43 Collecting requests (from blosc2>=2.3.0->tables)
00:43:43 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
00:43:43 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.3)
00:43:43 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:43:43 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:43:43 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:43:43 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
00:43:43 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:43:43 Using cached certifi-2025.8.3-py3-none-any.whl.metadata (2.4 kB)
00:43:43 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:43:43 Using cached blosc2-3.8.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
00:43:43 Using cached numexpr-2.12.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (411 kB)
00:43:43 Using cached numpy-2.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
00:43:43 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
00:43:43 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
00:43:43 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:43:43 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:43:43 Using cached platformdirs-4.4.0-py3-none-any.whl (18 kB)
00:43:43 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:43:43 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
00:43:43 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:43:43 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
00:43:43 Using cached certifi-2025.8.3-py3-none-any.whl (161 kB)
00:43:43 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:43:46
00:43:46 Successfully installed blosc2-3.8.0 certifi-2025.8.3 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.12.1 numpy-2.3.3 packaging-25.0 platformdirs-4.4.0 py-cpuinfo-9.0.0 requests-2.32.5 tables-3.10.2 typing-extensions-4.15.0 urllib3-2.5.0
00:43:46 + pip install jinja2
00:43:47 Collecting jinja2
00:43:47 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:43:47 Collecting MarkupSafe>=2.0 (from jinja2)
00:43:47 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:43:47 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:43:47 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
00:43:47 Installing collected packages: MarkupSafe, jinja2
00:43:47
00:43:47 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
00:43:47 + pip install zarr
00:43:47 Collecting zarr
00:43:47 Using cached zarr-3.1.3-py3-none-any.whl.metadata (10 kB)
00:43:47 Collecting donfig>=0.8 (from zarr)
00:43:47 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
00:43:48 Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr)
00:43:48 Using cached numcodecs-0.16.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.3 kB)
00:43:48 Requirement already satisfied: numpy>=1.26 in ./.venv3/lib64/python3.11/site-packages (from zarr) (2.3.3)
00:43:48 Requirement already satisfied: packaging>=22.0 in ./.venv3/lib64/python3.11/site-packages (from zarr) (25.0)
00:43:48 Requirement already satisfied: typing-extensions>=4.9 in ./.venv3/lib64/python3.11/site-packages (from zarr) (4.15.0)
00:43:48 Collecting pyyaml (from donfig>=0.8->zarr)
00:43:48 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:43:48 Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr)
00:43:48 Using cached crc32c-2.7.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.3 kB)
00:43:48 Using cached zarr-3.1.3-py3-none-any.whl (276 kB)
00:43:48 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
00:43:48 Using cached numcodecs-0.16.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.9 MB)
00:43:48 Using cached crc32c-2.7.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (53 kB)
00:43:48 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
00:43:48 Installing collected packages: pyyaml, numcodecs, crc32c, donfig, zarr
00:43:50
00:43:50 Successfully installed crc32c-2.7.1 donfig-0.8.1.post1 numcodecs-0.16.3 pyyaml-6.0.2 zarr-3.1.3
00:43:50 + pip install fsspec requests aiohttp s3fs
00:43:50 Collecting fsspec
00:43:50 Using cached fsspec-2025.9.0-py3-none-any.whl.metadata (10 kB)
00:43:50 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (2.32.5)
00:43:51 Collecting aiohttp
00:43:51 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)
00:43:51 Collecting s3fs
00:43:51 Using cached s3fs-2025.9.0-py3-none-any.whl.metadata (1.4 kB)
00:43:51 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests) (3.4.3)
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00:43:51 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests) (2025.8.3)
00:43:51 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp)
00:43:51 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
00:43:51 Collecting aiosignal>=1.4.0 (from aiohttp)
00:43:51 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
00:43:51 Collecting attrs>=17.3.0 (from aiohttp)
00:43:51 Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)
00:43:51 Collecting frozenlist>=1.1.1 (from aiohttp)
00:43:51 Using cached frozenlist-1.7.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
00:43:51 Collecting multidict<7.0,>=4.5 (from aiohttp)
00:43:51 Using cached multidict-6.6.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
00:43:51 Collecting propcache>=0.2.0 (from aiohttp)
00:43:51 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
00:43:52 Collecting yarl<2.0,>=1.17.0 (from aiohttp)
00:43:52 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB)
00:43:52 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs)
00:43:52 Using cached aiobotocore-2.24.2-py3-none-any.whl.metadata (25 kB)
00:43:52 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:43:52 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
00:43:52 Collecting botocore<1.40.19,>=1.40.15 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:43:52 Using cached botocore-1.40.18-py3-none-any.whl.metadata (5.7 kB)
00:43:52 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:43:52 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:43:52 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:43:52 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
00:43:52 Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:43:52 Using cached wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (6.4 kB)
00:43:52 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->aiobotocore<3.0.0,>=2.5.4->s3fs) (1.17.0)
00:43:52 Requirement already satisfied: typing-extensions>=4.2 in ./.venv3/lib64/python3.11/site-packages (from aiosignal>=1.4.0->aiohttp) (4.15.0)
00:43:52 Using cached fsspec-2025.9.0-py3-none-any.whl (199 kB)
00:43:52 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB)
00:43:52 Using cached multidict-6.6.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
00:43:52 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (348 kB)
00:43:52 Using cached s3fs-2025.9.0-py3-none-any.whl (30 kB)
00:43:52 Using cached aiobotocore-2.24.2-py3-none-any.whl (85 kB)
00:43:52 Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB)
00:43:52 Using cached botocore-1.40.18-py3-none-any.whl (14.0 MB)
00:43:52 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
00:43:52 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:43:52 Using cached wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (82 kB)
00:43:52 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
00:43:52 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
00:43:52 Using cached attrs-25.3.0-py3-none-any.whl (63 kB)
00:43:52 Using cached frozenlist-1.7.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (235 kB)
00:43:52 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB)
00:43:53 Installing collected packages: wrapt, python-dateutil, propcache, multidict, jmespath, fsspec, frozenlist, attrs, aioitertools, aiohappyeyeballs, yarl, botocore, aiosignal, aiohttp, aiobotocore, s3fs
00:43:54
00:43:54 Successfully installed aiobotocore-2.24.2 aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aioitertools-0.12.0 aiosignal-1.4.0 attrs-25.3.0 botocore-1.40.18 frozenlist-1.7.0 fsspec-2025.9.0 jmespath-1.0.1 multidict-6.6.4 propcache-0.3.2 python-dateutil-2.9.0.post0 s3fs-2025.9.0 wrapt-1.17.3 yarl-1.20.1
00:43:54 + pip install omero-py
00:43:54 Collecting omero-py
00:43:54 Using cached omero_py-5.21.1-py3-none-any.whl.metadata (6.5 kB)
00:43:54 Collecting appdirs (from omero-py)
00:43:54 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:43:54 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:43:54 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.3)
00:43:54 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
00:43:54 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.2)
00:43:54 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:43:54 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
00:43:54 Collecting portalocker (from omero-py)
00:43:54 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:43:54 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.3)
00:43:54 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
00:43:54 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.5.0)
00:43:54 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.8.3)
00:43:54 Using cached omero_py-5.21.1-py3-none-any.whl (2.8 MB)
00:43:54 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:43:54 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:43:55 Installing collected packages: appdirs, portalocker, omero-py
00:43:56
00:43:56 Successfully installed appdirs-1.4.4 omero-py-5.21.1 portalocker-3.2.0
00:43:56 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:43:57 Collecting omero-metadata
00:43:57 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-uxe0eix0/omero-metadata_f378e0ec159b45de91bbf4040044da60
00:43:57 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-uxe0eix0/omero-metadata_f378e0ec159b45de91bbf4040044da60
00:43:58 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 374fba59a6887bc466643fa298f3213bbb78cbe2
00:43:58 Installing build dependencies: started
00:43:58 Installing build dependencies: finished with status 'done'
00:43:58 Getting requirements to build wheel: started
00:43:59 Getting requirements to build wheel: finished with status 'done'
00:43:59 Preparing metadata (pyproject.toml): started
00:43:59 Preparing metadata (pyproject.toml): finished with status 'done'
00:43:59 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.1)
00:43:59 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
00:43:59 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:43:59 Collecting pandas (from omero-metadata)
00:43:59 Using cached pandas-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
00:43:59 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:43:59 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:43:59 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.3)
00:43:59 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)
00:43:59 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
00:43:59 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
00:43:59 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:43:59 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
00:43:59 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:43:59 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:43:59 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:43:59 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:43:59 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:43:59 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil>=2.8.2->pandas->omero-metadata) (1.17.0)
00:43:59 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.3)
00:43:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.10)
00:43:59 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.5.0)
00:43:59 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.8.3)
00:43:59 Using cached pandas-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
00:43:59 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:43:59 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:43:59 Building wheels for collected packages: omero-metadata
00:43:59 Building wheel for omero-metadata (pyproject.toml): started
00:44:00 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:44:00 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=638e8b1526c81fa217afe220f0b24b48fb082026c1fc3b5b5c3d1bf4b2011852
00:44:00 Stored in directory: /tmp/pip-ephem-wheel-cache-qxupqalv/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:44:00 Successfully built omero-metadata
00:44:00 Installing collected packages: pytz, tzdata, pandas, omero-metadata
00:44:04
00:44:04 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.2 pytz-2025.2 tzdata-2025.2
00:44:04 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:44:05 Collecting omero-cli-render
00:44:05 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-9fiiwfx3/omero-cli-render_bb976a9faef4453eb8d4515bace3b450
00:44:05 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-9fiiwfx3/omero-cli-render_bb976a9faef4453eb8d4515bace3b450
00:44:05 Running command git checkout -b merge_ci --track origin/merge_ci
00:44:06 Switched to a new branch 'merge_ci'
00:44:06 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:44:06 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 987f954cfa712918357c343248810be79f4bce39
00:44:06 Installing build dependencies: started
00:44:07 Installing build dependencies: finished with status 'done'
00:44:07 Getting requirements to build wheel: started
00:44:07 Getting requirements to build wheel: finished with status 'done'
00:44:07 Preparing metadata (pyproject.toml): started
00:44:07 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:07 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
00:44:07 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.1)
00:44:07 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:44:07 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:44:07 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.3)
00:44:07 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)
00:44:07 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)
00:44:07 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
00:44:07 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:44:07 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.3)
00:44:07 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)
00:44:07 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) (2.5.0)
00:44:07 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.8.3)
00:44:07 Building wheels for collected packages: omero-cli-render
00:44:07 Building wheel for omero-cli-render (pyproject.toml): started
00:44:07 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:44:07 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=3c1d736ad98fe0d191abd4f8d5a849f2e4573a8d30828486ca304ba4d5777aa1
00:44:07 Stored in directory: /tmp/pip-ephem-wheel-cache-q5ov92go/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:44:07 Successfully built omero-cli-render
00:44:07 Installing collected packages: omero-cli-render
00:44:07 Successfully installed omero-cli-render-0.8.2.dev0
00:44:08 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:44:08 Collecting omero-cli-duplicate
00:44:08 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-et487rae/omero-cli-duplicate_4fbb4a4c6879413595210c36555d90b2
00:44:08 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-et487rae/omero-cli-duplicate_4fbb4a4c6879413595210c36555d90b2
00:44:09 Running command git checkout -b merge_ci --track origin/merge_ci
00:44:09 Switched to a new branch 'merge_ci'
00:44:09 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:44:09 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit d35dea796db18fc4d2c3954c97161facd31154c1
00:44:09 Installing build dependencies: started
00:44:10 Installing build dependencies: finished with status 'done'
00:44:10 Getting requirements to build wheel: started
00:44:10 Getting requirements to build wheel: finished with status 'done'
00:44:10 Preparing metadata (pyproject.toml): started
00:44:10 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:10 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.1)
00:44:10 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:44:10 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:44:10 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.3)
00:44:10 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)
00:44:10 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:44:10 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)
00:44:10 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
00:44:10 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:44:10 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.3)
00:44:10 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)
00:44:10 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.5.0)
00:44:10 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.8.3)
00:44:10 Building wheels for collected packages: omero-cli-duplicate
00:44:10 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:44:11 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:44:11 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=36e064c4c93bbb58f8cae0575f77be39a66d6240c1f7d3a38f6c80ba657c21f7
00:44:11 Stored in directory: /tmp/pip-ephem-wheel-cache-tf9hgets/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:44:11 Successfully built omero-cli-duplicate
00:44:11 Installing collected packages: omero-cli-duplicate
00:44:11 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:44:11 + pip install omero-certificates
00:44:11 Collecting omero-certificates
00:44:11 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:44:11 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.1)
00:44:11 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:44:11 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:44:11 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.3)
00:44:11 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)
00:44:11 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:44:11 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)
00:44:11 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
00:44:11 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:44:11 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.3)
00:44:11 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)
00:44:11 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.5.0)
00:44:11 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.8.3)
00:44:11 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:44:11 Installing collected packages: omero-certificates
00:44:11 Successfully installed omero-certificates-0.4.0
00:44:11 + for x in *.tar.gz
00:44:11 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:44:12 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:44:12 Installing build dependencies: started
00:44:12 Installing build dependencies: finished with status 'done'
00:44:12 Getting requirements to build wheel: started
00:44:13 Getting requirements to build wheel: finished with status 'done'
00:44:13 Preparing metadata (pyproject.toml): started
00:44:13 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:13 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.1)
00:44:13 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:44:13 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:44:13 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.3)
00:44:13 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)
00:44:13 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:44:13 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)
00:44:13 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
00:44:13 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:44:13 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.3)
00:44:13 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)
00:44:13 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) (2.5.0)
00:44:13 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.8.3)
00:44:13 Building wheels for collected packages: omero-dropbox
00:44:13 Building wheel for omero-dropbox (pyproject.toml): started
00:44:13 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:44:13 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=20653511526a70aa4d300692facde458949eba1b19718d7a793034610ad28e9d
00:44:13 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:44:13 Successfully built omero-dropbox
00:44:13 Installing collected packages: omero-dropbox
00:44:13 Successfully installed omero-dropbox-5.7.1.dev0
00:44:13 + for x in *.tar.gz
00:44:13 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:44:14 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:44:14 Installing build dependencies: started
00:44:15 Installing build dependencies: finished with status 'done'
00:44:15 Getting requirements to build wheel: started
00:44:15 Getting requirements to build wheel: finished with status 'done'
00:44:15 Preparing metadata (pyproject.toml): started
00:44:15 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:15 Building wheels for collected packages: omero_marshal
00:44:15 Building wheel for omero_marshal (pyproject.toml): started
00:44:15 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:44:15 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=049c4251a9172c976fb04b5435bb801fdb720688d3c8ac1cee45f30254805e95
00:44:15 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:44:15 Successfully built omero_marshal
00:44:16 Installing collected packages: omero_marshal
00:44:16 Successfully installed omero_marshal-0.9.1.dev0
00:44:16 + for x in *.tar.gz
00:44:16 + pip install -U omero_py-5.21.2.dev0.tar.gz
00:44:16 Processing ./omero_py-5.21.2.dev0.tar.gz
00:44:16 Installing build dependencies: started
00:44:17 Installing build dependencies: finished with status 'done'
00:44:17 Getting requirements to build wheel: started
00:44:17 Getting requirements to build wheel: finished with status 'done'
00:44:17 Preparing metadata (pyproject.toml): started
00:44:18 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:18 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (1.4.4)
00:44:18 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (1.0.0)
00:44:18 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (2.3.3)
00:44:18 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (11.3.0)
00:44:18 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (6.0.2)
00:44:18 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (3.6.5)
00:44:18 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (2.32.5)
00:44:18 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.2.dev0) (3.2.0)
00:44:18 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.2.dev0) (3.4.3)
00:44:18 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.2.dev0) (3.10)
00:44:18 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.2.dev0) (2.5.0)
00:44:18 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.2.dev0) (2025.8.3)
00:44:18 Building wheels for collected packages: omero-py
00:44:18 Building wheel for omero-py (pyproject.toml): started
00:44:19 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:44:19 Created wheel for omero-py: filename=omero_py-5.21.2.dev0-py3-none-any.whl size=2783448 sha256=472baea5b8de801dbd52e995c840b31f9573323139a83ad0f9d65364a1c290f2
00:44:19 Stored in directory: /home/omero/.cache/pip/wheels/f3/91/03/43dba9c5cbf305bc3731f08db7b7193b750bf8d4c8e5f42e09
00:44:19 Successfully built omero-py
00:44:19 Installing collected packages: omero-py
00:44:19 Attempting uninstall: omero-py
00:44:19 Found existing installation: omero-py 5.21.1
00:44:19 Uninstalling omero-py-5.21.1:
00:44:19 Successfully uninstalled omero-py-5.21.1
00:44:21 Successfully installed omero-py-5.21.2.dev0
00:44:21 + for x in *.tar.gz
00:44:21 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:44:21 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:44:21 Installing build dependencies: started
00:44:22 Installing build dependencies: finished with status 'done'
00:44:22 Getting requirements to build wheel: started
00:44:23 Getting requirements to build wheel: finished with status 'done'
00:44:23 Preparing metadata (pyproject.toml): started
00:44:23 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:23 Building wheels for collected packages: omero-scripts
00:44:23 Building wheel for omero-scripts (pyproject.toml): started
00:44:23 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:44:23 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=219934c5ddf87a5591216c788491a5e70bffc98d8c0462bcc59449227fba0637
00:44:23 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:44:23 Successfully built omero-scripts
00:44:23 Installing collected packages: omero-scripts
00:44:23 Successfully installed omero-scripts-5.9.2.dev0
00:44:23 + for x in *.tar.gz
00:44:23 + pip install -U omero_web-5.29.3.dev0.tar.gz
00:44:24 Processing ./omero_web-5.29.3.dev0.tar.gz
00:44:24 Installing build dependencies: started
00:44:25 Installing build dependencies: finished with status 'done'
00:44:25 Getting requirements to build wheel: started
00:44:25 Getting requirements to build wheel: finished with status 'done'
00:44:25 Preparing metadata (pyproject.toml): started
00:44:25 Preparing metadata (pyproject.toml): finished with status 'done'
00:44:25 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (5.21.2.dev0)
00:44:25 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.3.dev0)
00:44:25 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:44:26 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.3.dev0)
00:44:26 Using cached django-4.2.24-py3-none-any.whl.metadata (4.2 kB)
00:44:26 Collecting django-pipeline (from omero-web==5.29.3.dev0)
00:44:26 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
00:44:26 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.3.dev0)
00:44:26 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:44:26 Collecting django-csp (from omero-web==5.29.3.dev0)
00:44:26 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:44:26 Collecting whitenoise>=5.3.0 (from omero-web==5.29.3.dev0)
00:44:26 Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
00:44:26 Collecting gunicorn>=19.3 (from omero-web==5.29.3.dev0)
00:44:26 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:44:26 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (0.9.1.dev0)
00:44:26 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (11.3.0)
00:44:26 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (2025.2)
00:44:26 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (3.2.0)
00:44:26 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (25.0)
00:44:26 Collecting importlib-resources (from omero-web==5.29.3.dev0)
00:44:26 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:44:26 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:44:26 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB)
00:44:26 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:44:26 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:44:26 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (1.4.4)
00:44:26 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (1.0.0)
00:44:26 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.3.3)
00:44:26 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (6.0.2)
00:44:26 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==5.29.3.dev0) (3.6.5)
00:44:26 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.32.5)
00:44:26 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.3.dev0) (65.5.1)
00:44:26 Collecting wheel (from django-pipeline->omero-web==5.29.3.dev0)
00:44:26 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:44:26 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (3.4.3)
00:44:26 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (3.10)
00:44:26 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.5.0)
00:44:26 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (2025.8.3)
00:44:26 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:44:26 Using cached django-4.2.24-py3-none-any.whl (8.0 MB)
00:44:26 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB)
00:44:26 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:44:26 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:44:26 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:44:26 Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
00:44:26 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:44:26 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
00:44:26 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:44:26 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:44:26 Building wheels for collected packages: omero-web
00:44:26 Building wheel for omero-web (pyproject.toml): started
00:44:27 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:44:27 Created wheel for omero-web: filename=omero_web-5.29.3.dev0-py3-none-any.whl size=2818225 sha256=bfb46a2bf96a8d471542161f4ef6236619b72eee743bad473ed2df1f06819e6b
00:44:27 Stored in directory: /home/omero/.cache/pip/wheels/22/5c/22/7feca3b3e1a26ce9fb6b16848ce79640a0079788b3a7d5450b
00:44:27 Successfully built omero-web
00:44:27 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:44:31
00:44:31 Successfully installed Django-4.2.24 asgiref-3.9.1 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.1.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.3.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.11.0
00:44:31 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:44:31 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:44:31 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:44:31 --2025-09-21 00:44:31-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:44:31 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...
00:44:31 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
00:44:31 HTTP request sent, awaiting response... 200 OK
00:44:31 Length: 125361 (122K) [text/plain]
00:44:31 Saving to: ‘Figure_To_Pdf.py’
00:44:31
00:44:31 0K .......... .......... .......... .......... .......... 40% 4.04M 0s
00:44:31 50K .......... .......... .......... .......... .......... 81% 11.6M 0s
00:44:31 100K .......... .......... .. 100% 4.54M=0.02s
00:44:31
00:44:31 2025-09-21 00:44:31 (5.66 MB/s) - ‘Figure_To_Pdf.py’ saved [125361/125361]
00:44:31
00:44:31 + chmod 755 Figure_To_Pdf.py
00:44:31 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:44:31 + omero config set omero.db.name OMERO-server
00:44:32 + omero config set omero.db.host pg
00:44:34 + omero config set omero.db.user postgres
00:44:35 + omero config set omero.data.dir /home/omero/omero-server-data
00:44:36 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:44:37 + omero config set omero.db.poolsize 25
00:44:38 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:44:40 + omero config set omero.security.trustStorePassword changeit
00:44:41 + omero config set omero.mail.config true
00:44:42 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:44:43 + omero config set omero.mail.host smtp.dundee.ac.uk
00:44:44 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:44:46 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:44:47 + omero certificates
00:44:48 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:44:48 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:44:48 + '[' false = true ']'
00:44:48 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:44:48 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:44:48 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG dbcommand => upgrade
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG dbhost => localhost
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG dbname => OMERO-server
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG dbpass => omero
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG dbuser => omero
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG rootpass => omero
00:44:48 2025-09-21 00:44:48,727 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:44:48 2025-09-21 00:44:48,727 [omego.extern] INFO Executing : omero version
00:44:49 OMERO.py version:
00:44:49 OMERO.server version:
00:44:49 5.6.3-574-f644878cec-ice36-b529
00:44:49 5.21.2.dev0
00:44:49 2025-09-21 00:44:49,974 [omego.extern] INFO Completed [1.247 s]
00:44:49 2025-09-21 00:44:49,974 [omego.extern] DEBUG Using omero CLI from omero
00:44:49 2025-09-21 00:44:49,974 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:44:49 2025-09-21 00:44:49,974 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:44:49 2025-09-21 00:44:49,974 [omego.extern] INFO Executing : omero config get --show-password
00:44:51 2025-09-21 00:44:51,172 [omego.extern] INFO Completed [1.197 s]
00:44:51 2025-09-21 00:44:51,172 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:44:51 2025-09-21 00:44:51,172 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:44:51 2025-09-21 00:44:51,177 [omego.extern] INFO Completed [0.005 s]
00:44:51 2025-09-21 00:44:51,177 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
00:44:51 2025-09-21 00:44:51,177 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
00:44:51
00:44:51 2025-09-21 00:44:51,177 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:44:51 2025-09-21 00:44:51,178 [omego.extern] INFO Executing : omero config get --show-password
00:44:52 2025-09-21 00:44:52,411 [omego.extern] INFO Completed [1.233 s]
00:44:52 2025-09-21 00:44:52,411 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:44:52 2025-09-21 00:44:52,411 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:44:52 2025-09-21 00:44:52,420 [omego.extern] INFO Completed [0.009 s]
00:44:52 2025-09-21 00:44:52,420 [ 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'
00:44:52 2025-09-21 00:44:52,420 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:44:52 2025-09-21 00:44:52,420 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:44:52 2025-09-21 00:44:52,420 [omego.extern] INFO Executing : omero config get --show-password
00:44:53 2025-09-21 00:44:53,648 [omego.extern] INFO Completed [1.228 s]
00:44:53 2025-09-21 00:44:53,648 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:44:53 2025-09-21 00:44:53,648 [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
00:44:53 2025-09-21 00:44:53,659 [omego.extern] INFO Completed [0.011 s]
00:44:53 2025-09-21 00:44:53,659 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:44:53 2025-09-21 00:44:53,659 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:44:53 2025-09-21 00:44:53,660 [ omego.db] INFO Database is already at OMERO5.4__0
00:44:53 + export LANG=en_US.UTF-8
00:44:53 + LANG=en_US.UTF-8
00:44:53 + export LANGUAGE=en_US:en
00:44:53 + LANGUAGE=en_US:en
00:44:53 + export LC_ALL=en_US.UTF-8
00:44:53 + LC_ALL=en_US.UTF-8
00:44:53 + BUILD_ID=DONT_KILL_ME
00:44:53 + omero admin start
00:44:58 No descriptor given. Using etc/grid/default.xml
00:45:07 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:45:07 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:45:07 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:45:07 Waiting on startup. Use CTRL-C to exit
00:45:08 + omero admin waitup
00:45:09 Waiting on startup. Use CTRL-C to exit
00:45:09 + omero admin diagnostics
00:45:10
00:45:10 ================================================================================
00:45:10 OMERO Diagnostics (admin)
00:45:10 ================================================================================
00:45:10
00:45:10 Commands: java -version 11.0.25 (/usr/bin/java)
00:45:10 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:45:10 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:45:10 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:45:10 Commands: psql --version 16.9 (/usr/bin/psql)
00:45:10 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:45:10
00:45:10 Component: OMERO.py 5.21.2.dev0
00:45:10 Component: OMERO.server 5.6.3-574-f644878cec-ice36-b529
00:45:10
00:45:10 Server: icegridnode running
00:45:10 Server: Blitz-0 active (pid = 57359, enabled)
00:45:10 Server: Indexer-0 activating (enabled)
00:45:10 Server: OMERO.Glacier2 active (pid = 57390, enabled)
00:45:10 Server: OMERO.IceStorm active (pid = 57414, enabled)
00:45:10 Server: Processor-0 active (pid = 57416, enabled)
00:45:10 Server: Tables-0 active (pid = 57397, enabled)
00:45:10
00:45:10 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:45:10 Log files: Blitz-0.log 33.2 KB errors=0 warnings=1
00:45:10 Log files: DropBox.log n/a
00:45:10 Log files: FileServer.log n/a
00:45:10 Log files: Indexer-0.log 358 B
00:45:10 Log files: MonitorServer.log n/a
00:45:10 Log files: Processor-0.log 735 B
00:45:10 Log files: Tables-0.log 961 B
00:45:10 Log files: TestDropBox.log n/a
00:45:10 Log files: master.err empty
00:45:10 Log files: master.out 30.5 KB
00:45:10 Log files: Total size 0.07 MB
00:45:10
00:45:10
00:45:10 Environment:OMERO_HOME=(unset)
00:45:10 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:45:10 Environment:OMERO_NODE=(unset)
00:45:10 Environment:OMERO_MASTER=(unset)
00:45:10 Environment:OMERO_USERDIR=(unset)
00:45:10 Environment:OMERO_TMPDIR=(unset)
00:45:10 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
00:45:10 Environment:PYTHONPATH=(unset)
00:45:10 Environment:ICE_HOME=/opt/ice-3.6.5
00:45:10 Environment:LD_LIBRARY_PATH=(unset)
00:45:10 Environment:DYLD_LIBRARY_PATH=(unset)
00:45:10
00:45:10 OMERO SSL port:4064
00:45:10 OMERO TCP port:4063
00:45:10 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:45:10 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:45:10
00:45:10 JVM settings: Blitz-${index} -Xmx7200m
00:45:10 JVM settings: Indexer-${index} -Xmx4800m
00:45:10 JVM settings: PixelData-${index} -Xmx7200m
00:45:10 JVM settings: Repository-${index} -Xmx4800m
00:45:10
00:45:10 Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 21 September 2025 63860c97b0dd8bdef268fe2fbfb902759112a125
00:45:10 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 21 September 2025 63860c97b0dd8bdef268fe2fbfb902759112a125
00:45:10 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 21 September 2025 63860c97b0dd8bdef268fe2fbfb902759112a125
00:45:10 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 21 September 2025 c2e2704e10d1b65d7952bdda47ec2e27d2f65ffa
00:45:10 Jar: lib/server/ome-common.jar OME Common Java 6.1.1-SNAPSHOT 21 September 2025 c2e2704e10d1b65d7952bdda47ec2e27d2f65ffa
00:45:10 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 21 September 2025 c2e2704e10d1b65d7952bdda47ec2e27d2f65ffa
00:45:10 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 21 September 2025 c2e2704e10d1b65d7952bdda47ec2e27d2f65ffa
00:45:10 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 21 September 2025 c2e2704e10d1b65d7952bdda47ec2e27d2f65ffa
00:45:10 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 21 September 2025 c2e2704e10d1b65d7952bdda47ec2e27d2f65ffa
00:45:10 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:45:10 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT c98af6cba6a4362f9d78467f230acb59ad23a9e8
00:45:11 + deactivate
00:45:11 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:45:11 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:45:11 + export PATH
00:45:11 + unset _OLD_VIRTUAL_PATH
00:45:11 + '[' -n '' ']'
00:45:11 + hash -r
00:45:11 + '[' -n '' ']'
00:45:11 + unset VIRTUAL_ENV
00:45:11 + unset VIRTUAL_ENV_PROMPT
00:45:11 + '[' '!' '' = nondestructive ']'
00:45:11 + unset -f deactivate
00:45:11 Finished: SUCCESS
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