01:06:20 Started by upstream project "Trigger" build number 578
01:06:20 originally caused by:
01:06:20 Started by timer
01:06:20 Running as SYSTEM
01:06:22 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
01:06:23 [OMERO-server] $ /bin/bash -xe /tmp/jenkins14652953141744008102.sh
01:06:23 + source /home/settings.env
01:06:23 ++ OMERO_DB_HOST=pg
01:06:23 ++ OMERO_DB_USER=postgres
01:06:23 ++ OMERO_DB_PASS=
01:06:23 ++ OMERO_ROOT_PASS=omero
01:06:23 ++ OMERO_DATA_DIR=/OMERO
01:06:23 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
01:06:23 + OMERO_DB_NAME=OMERO-server
01:06:23 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
01:06:23 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:06:23 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:06:23 + OMERO_DATA_DIR=/home/omero/omero-server-data
01:06:23 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
01:06:23 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
01:06:23 ++ deactivate nondestructive
01:06:23 ++ '[' -n '' ']'
01:06:23 ++ '[' -n '' ']'
01:06:23 ++ hash -r
01:06:23 ++ '[' -n '' ']'
01:06:23 ++ unset VIRTUAL_ENV
01:06:23 ++ unset VIRTUAL_ENV_PROMPT
01:06:23 ++ '[' '!' nondestructive = nondestructive ']'
01:06:23 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
01:06:23 ++ export VIRTUAL_ENV
01:06:23 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:06:23 ++ 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
01:06:23 ++ export PATH
01:06:23 ++ '[' -n '' ']'
01:06:23 ++ '[' -z '' ']'
01:06:23 ++ _OLD_VIRTUAL_PS1=
01:06:23 ++ PS1='(.venv3) '
01:06:23 ++ export PS1
01:06:23 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
01:06:23 ++ export VIRTUAL_ENV_PROMPT
01:06:23 ++ hash -r
01:06:23 + omero admin stop
01:07:02 Server not running
01:07:02 + echo not running
01:07:02 not running
01:07:02 + sleep 5
01:07:07 + deactivate
01:07:07 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
01:07:07 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:07:07 + export PATH
01:07:07 + unset _OLD_VIRTUAL_PATH
01:07:07 + '[' -n '' ']'
01:07:07 + hash -r
01:07:07 + '[' -n '' ']'
01:07:07 + unset VIRTUAL_ENV
01:07:07 + unset VIRTUAL_ENV_PROMPT
01:07:07 + '[' '!' '' = nondestructive ']'
01:07:07 + unset -f deactivate
01:07:07 + rm -rf /home/omero/workspace/OMERO-server/.venv3
01:07:08 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
01:07:14 + '[' false = true ']'
01:07:14 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
01:07:14 Skipping PURGE_DATA:CleanDbAndRepo
01:07:14 + 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
01:07:16 Copied 1 artifact from "OMERO-build" build number 487
01:07:16 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 480
01:07:16 Copied 2 artifacts from "OMERO-build-build" build number 514
01:07:16 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 20
01:07:16 [OMERO-server] $ /bin/bash -xe /tmp/jenkins1640759179282628596.sh
01:07:16 + source /home/settings.env
01:07:16 ++ OMERO_DB_HOST=pg
01:07:16 ++ OMERO_DB_USER=postgres
01:07:16 ++ OMERO_DB_PASS=
01:07:16 ++ OMERO_ROOT_PASS=omero
01:07:16 ++ OMERO_DATA_DIR=/OMERO
01:07:16 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
01:07:16 + OMERO_DB_NAME=OMERO-server
01:07:16 + OMERO_DATA_DIR=/home/omero/omero-server-data
01:07:16 + mkdir -p /home/omero/omero-server-data
01:07:16 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
01:07:16 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:07:16 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:07:16 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
01:07:16 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
01:07:16 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
01:07:16 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
01:07:16 ++ ls OMERO.server-5.6.3-574-fbdee10c54-ice36-b487.zip
01:07:16 + ZIP=OMERO.server-5.6.3-574-fbdee10c54-ice36-b487.zip
01:07:16 + '[' '!' -z '' ']'
01:07:16 + DIST=OMERO.server-5.6.3-574-fbdee10c54-ice36-b487
01:07:16 + unzip OMERO.server-5.6.3-574-fbdee10c54-ice36-b487.zip
01:07:16 Archive: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487.zip
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/blitz/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/grid/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/profiles/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/error/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/grid/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/luts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/luts/janelia/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/luts/matplotlib/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/luts/ncsa_paledit/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/luts/seaborn/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/luts/wcif/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/analysis_scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/annotation_scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/export_scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/figure_scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/import_scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/scripts/omero/util_scripts/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/server/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/share/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/share/licenses/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/misc/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__1/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__10/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__11/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__2/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__3/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__4/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__5/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__6/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__7/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__8/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3A__9/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3__4/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3__5/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3__6/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO3__7/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO4.1__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO4.2__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO4.2__0/t/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO4.3__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO4.4__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO4__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.0__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.1__1/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.2__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.3__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4DEV__1/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4DEV__2/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4DEV__3/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4__0/
01:07:16 creating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/var/
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/LICENSE.txt
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/backup.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/blitz/mail-senders.example
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/blitz/mail-server.example
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/build.properties
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/env.bat
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/env.sh
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/hibernate.properties
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/ice.config
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/logback-cli.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/logback-indexing-cli.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/logback-indexing.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/logback.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/mime.types
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/node1.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/node2.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/omero.properties
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/profiles/psql
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/rollover.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/Windows.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/error/maintainance.html
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/grid/README
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/grid/default.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/grid/templates.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/grid/windefault.xml
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/ice.config
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/internal.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/master.cfg
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/templates/robot.template
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/etc/testdropbox.config
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/history.rst
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/OMEZarrReader.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/accessors-smart.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/activation.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/aggdesigner-algorithm.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/aircompressor.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/antlr.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/aopalliance.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/apiguardian-api.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/asm.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/avatica-core.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/avatica-metrics.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/aws-java-sdk-core.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/aws-java-sdk-kms.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/aws-java-sdk-s3.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/base.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-anim.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-awt-util.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-bridge.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-codec.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-constants.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-css.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-dom.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-ext.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-gvt.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-i18n.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-parser.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-script.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-shared-resources.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-svg-dom.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-svggen.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-transcoder.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-util.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/batik-xml.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/btm.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/calcite-core.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/calcite-linq4j.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/cdm-core.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/checker-qual.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/commons-beanutils.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/commons-codec.jar
01:07:16 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/lib/client/commons-collections.jar
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01:07:18 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4__0/psql-footer.sql
01:07:18 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4__0/psql-header.sql
01:07:18 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4__0/schema.sql
01:07:18 inflating: OMERO.server-5.6.3-574-fbdee10c54-ice36-b487/sql/psql/OMERO5.4__0/views.sql
01:07:18 + rm -f OMERO.server-5.6.3-574-fbdee10c54-ice36-b487.zip
01:07:18 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-574-fbdee10c54-ice36-b487 /home/omero/workspace/OMERO-server/OMERO.server
01:07:18 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
01:07:18 + JAR=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
01:07:18 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
01:07:19 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
01:07:19 + 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
01:07:19 + 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
01:07:19 --2025-08-06 01:07:19-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
01:07:20 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
01:07:20 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
01:07:20 HTTP request sent, awaiting response... 200 OK
01:07:20 Length: 889211 (868K) [application/java-archive]
01:07:20 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
01:07:20
01:07:20 0K .......... .......... .......... .......... .......... 5% 3.89M 0s
01:07:20 50K .......... .......... .......... .......... .......... 11% 5.88M 0s
01:07:20 100K .......... .......... .......... .......... .......... 17% 21.7M 0s
01:07:20 150K .......... .......... .......... .......... .......... 23% 24.5M 0s
01:07:20 200K .......... .......... .......... .......... .......... 28% 7.86M 0s
01:07:20 250K .......... .......... .......... .......... .......... 34% 34.0M 0s
01:07:20 300K .......... .......... .......... .......... .......... 40% 44.5M 0s
01:07:20 350K .......... .......... .......... .......... .......... 46% 34.2M 0s
01:07:20 400K .......... .......... .......... .......... .......... 51% 64.8M 0s
01:07:20 450K .......... .......... .......... .......... .......... 57% 7.81M 0s
01:07:20 500K .......... .......... .......... .......... .......... 63% 24.3M 0s
01:07:20 550K .......... .......... .......... .......... .......... 69% 141M 0s
01:07:20 600K .......... .......... .......... .......... .......... 74% 36.3M 0s
01:07:20 650K .......... .......... .......... .......... .......... 80% 30.5M 0s
01:07:20 700K .......... .......... .......... .......... .......... 86% 9.13M 0s
01:07:20 750K .......... .......... .......... .......... .......... 92% 29.6M 0s
01:07:20 800K .......... .......... .......... .......... .......... 97% 28.3M 0s
01:07:20 850K .......... ........ 100% 226M=0.06s
01:07:20
01:07:20 2025-08-06 01:07:20 (15.0 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
01:07:20
01:07:20 + 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
01:07:20 --2025-08-06 01:07:20-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
01:07:20 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
01:07:20 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
01:07:20 HTTP request sent, awaiting response... 200 OK
01:07:20 Length: 73309 (72K) [application/java-archive]
01:07:20 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
01:07:20
01:07:20 0K .......... .......... .......... .......... .......... 69% 4.09M 0s
01:07:20 50K .......... .......... . 100% 10.5M=0.01s
01:07:20
01:07:20 2025-08-06 01:07:20 (5.01 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
01:07:20
01:07:20 + 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
01:07:20 --2025-08-06 01:07:20-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
01:07:20 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
01:07:20 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
01:07:20 HTTP request sent, awaiting response... 200 OK
01:07:20 Length: 63303 (62K) [application/java-archive]
01:07:20 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
01:07:20
01:07:20 0K .......... .......... .......... .......... .......... 80% 4.14M 0s
01:07:20 50K .......... . 100% 11.3M=0.01s
01:07:20
01:07:20 2025-08-06 01:07:20 (4.71 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
01:07:20
01:07:20 + 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
01:07:20 --2025-08-06 01:07:20-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
01:07:20 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
01:07:20 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
01:07:20 HTTP request sent, awaiting response... 200 OK
01:07:20 Length: 1271272 (1.2M) [application/java-archive]
01:07:20 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
01:07:20
01:07:20 0K .......... .......... .......... .......... .......... 4% 4.19M 0s
01:07:20 50K .......... .......... .......... .......... .......... 8% 10.8M 0s
01:07:20 100K .......... .......... .......... .......... .......... 12% 6.77M 0s
01:07:20 150K .......... .......... .......... .......... .......... 16% 24.7M 0s
01:07:20 200K .......... .......... .......... .......... .......... 20% 8.04M 0s
01:07:20 250K .......... .......... .......... .......... .......... 24% 32.0M 0s
01:07:20 300K .......... .......... .......... .......... .......... 28% 19.6M 0s
01:07:20 350K .......... .......... .......... .......... .......... 32% 109M 0s
01:07:20 400K .......... .......... .......... .......... .......... 36% 40.6M 0s
01:07:20 450K .......... .......... .......... .......... .......... 40% 10.0M 0s
01:07:20 500K .......... .......... .......... .......... .......... 44% 21.5M 0s
01:07:20 550K .......... .......... .......... .......... .......... 48% 142M 0s
01:07:20 600K .......... .......... .......... .......... .......... 52% 22.9M 0s
01:07:20 650K .......... .......... .......... .......... .......... 56% 30.3M 0s
01:07:20 700K .......... .......... .......... .......... .......... 60% 9.68M 0s
01:07:20 750K .......... .......... .......... .......... .......... 64% 30.0M 0s
01:07:20 800K .......... .......... .......... .......... .......... 68% 148M 0s
01:07:20 850K .......... .......... .......... .......... .......... 72% 23.8M 0s
01:07:20 900K .......... .......... .......... .......... .......... 76% 33.8M 0s
01:07:20 950K .......... .......... .......... .......... .......... 80% 9.50M 0s
01:07:20 1000K .......... .......... .......... .......... .......... 84% 116M 0s
01:07:20 1050K .......... .......... .......... .......... .......... 88% 31.6M 0s
01:07:20 1100K .......... .......... .......... .......... .......... 92% 24.0M 0s
01:07:20 1150K .......... .......... .......... .......... .......... 96% 9.40M 0s
01:07:20 1200K .......... .......... .......... .......... . 100% 171M=0.07s
01:07:20
01:07:20 2025-08-06 01:07:20 (16.5 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
01:07:20
01:07:20 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
01:07:20 ++ deactivate nondestructive
01:07:20 ++ '[' -n '' ']'
01:07:20 ++ '[' -n '' ']'
01:07:20 ++ hash -r
01:07:20 ++ '[' -n '' ']'
01:07:20 ++ unset VIRTUAL_ENV
01:07:20 ++ unset VIRTUAL_ENV_PROMPT
01:07:20 ++ '[' '!' nondestructive = nondestructive ']'
01:07:20 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
01:07:20 ++ export VIRTUAL_ENV
01:07:20 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:07:20 ++ 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
01:07:20 ++ export PATH
01:07:20 ++ '[' -n '' ']'
01:07:20 ++ '[' -z '' ']'
01:07:20 ++ _OLD_VIRTUAL_PS1=
01:07:20 ++ PS1='(.venv3) '
01:07:20 ++ export PS1
01:07:20 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
01:07:20 ++ export VIRTUAL_ENV_PROMPT
01:07:20 ++ hash -r
01:07:20 + pip install -U pip
01:07:21 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
01:07:21 Collecting pip
01:07:21 Using cached pip-25.2-py3-none-any.whl (1.8 MB)
01:07:21 Installing collected packages: pip
01:07:21 Attempting uninstall: pip
01:07:21 Found existing installation: pip 22.3.1
01:07:21 Uninstalling pip-22.3.1:
01:07:21 Successfully uninstalled pip-22.3.1
01:07:22 Successfully installed pip-25.2
01:07:22 WARNING: There was an error checking the latest version of pip.
01:07:22 + 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
01:07:23 Collecting zeroc-ice==3.6.5
01:07:23 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)
01:07:25 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 20.0 MB/s 0:00:01
01:07:25 Installing collected packages: zeroc-ice
01:07:26 Successfully installed zeroc-ice-3.6.5
01:07:26 + pip install markdown
01:07:27 Collecting markdown
01:07:27 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB)
01:07:27 Using cached markdown-3.8.2-py3-none-any.whl (106 kB)
01:07:27 Installing collected packages: markdown
01:07:27 Successfully installed markdown-3.8.2
01:07:27 + pip install reportlab
01:07:28 Collecting reportlab
01:07:28 Using cached reportlab-4.4.3-py3-none-any.whl.metadata (1.7 kB)
01:07:28 Collecting pillow>=9.0.0 (from reportlab)
01:07:28 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
01:07:28 Collecting charset-normalizer (from reportlab)
01:07:28 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
01:07:28 Using cached reportlab-4.4.3-py3-none-any.whl (2.0 MB)
01:07:28 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
01:07:29 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
01:07:29 Installing collected packages: pillow, charset-normalizer, reportlab
01:07:30
01:07:30 Successfully installed charset-normalizer-3.4.2 pillow-11.3.0 reportlab-4.4.3
01:07:30 + pip install pyarrow
01:07:30 Collecting pyarrow
01:07:30 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
01:07:30 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
01:07:31 Installing collected packages: pyarrow
01:07:33 Successfully installed pyarrow-21.0.0
01:07:33 + pip install omego
01:07:33 Collecting omego
01:07:33 Using cached omego-0.7.0-py3-none-any.whl
01:07:33 Collecting future (from omego)
01:07:33 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
01:07:33 Collecting yaclifw>=0.1.1 (from omego)
01:07:33 Using cached yaclifw-0.2.0-py3-none-any.whl
01:07:33 Collecting six (from yaclifw>=0.1.1->omego)
01:07:33 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
01:07:33 Using cached future-1.0.0-py3-none-any.whl (491 kB)
01:07:34 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
01:07:34 Installing collected packages: six, future, yaclifw, omego
01:07:34
01:07:34 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
01:07:34 + pip install tables
01:07:34 Collecting tables
01:07:34 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
01:07:35 Collecting numpy>=1.20.0 (from tables)
01:07:35 Using cached numpy-2.3.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
01:07:35 Collecting numexpr>=2.6.2 (from tables)
01:07:35 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
01:07:35 Collecting packaging (from tables)
01:07:35 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
01:07:35 Collecting py-cpuinfo (from tables)
01:07:35 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
01:07:35 Collecting blosc2>=2.3.0 (from tables)
01:07:35 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.0 kB)
01:07:35 Collecting typing-extensions>=4.4.0 (from tables)
01:07:35 Using cached typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB)
01:07:35 Collecting ndindex (from blosc2>=2.3.0->tables)
01:07:35 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
01:07:35 Collecting msgpack (from blosc2>=2.3.0->tables)
01:07:36 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
01:07:36 Collecting platformdirs (from blosc2>=2.3.0->tables)
01:07:36 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
01:07:36 Collecting requests (from blosc2>=2.3.0->tables)
01:07:36 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)
01:07:36 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2)
01:07:36 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
01:07:36 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
01:07:36 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
01:07:36 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
01:07:36 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
01:07:36 Using cached certifi-2025.8.3-py3-none-any.whl.metadata (2.4 kB)
01:07:36 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
01:07:37 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB)
01:07:37 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB)
01:07:37 Using cached numpy-2.3.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
01:07:37 Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB)
01:07:37 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
01:07:37 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
01:07:37 Using cached packaging-25.0-py3-none-any.whl (66 kB)
01:07:37 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
01:07:38 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
01:07:38 Using cached requests-2.32.4-py3-none-any.whl (64 kB)
01:07:38 Using cached idna-3.10-py3-none-any.whl (70 kB)
01:07:38 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
01:07:38 Using cached certifi-2025.8.3-py3-none-any.whl (161 kB)
01:07:38 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
01:07:41
01:07:41 Successfully installed blosc2-3.6.1 certifi-2025.8.3 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.11.0 numpy-2.3.2 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
01:07:41 + pip install jinja2
01:07:42 Collecting jinja2
01:07:42 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
01:07:42 Collecting MarkupSafe>=2.0 (from jinja2)
01:07:42 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
01:07:42 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
01:07:42 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
01:07:42 Installing collected packages: MarkupSafe, jinja2
01:07:42
01:07:42 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
01:07:42 + pip install zarr
01:07:43 Collecting zarr
01:07:43 Using cached zarr-3.1.1-py3-none-any.whl.metadata (10 kB)
01:07:43 Collecting donfig>=0.8 (from zarr)
01:07:43 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
01:07:43 Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr)
01:07:43 Using cached numcodecs-0.16.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.3 kB)
01:07:43 Requirement already satisfied: numpy>=1.26 in ./.venv3/lib64/python3.11/site-packages (from zarr) (2.3.2)
01:07:43 Requirement already satisfied: packaging>=22.0 in ./.venv3/lib64/python3.11/site-packages (from zarr) (25.0)
01:07:43 Requirement already satisfied: typing-extensions>=4.9 in ./.venv3/lib64/python3.11/site-packages (from zarr) (4.14.1)
01:07:43 Collecting pyyaml (from donfig>=0.8->zarr)
01:07:43 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
01:07:43 Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr)
01:07:43 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)
01:07:44 Using cached zarr-3.1.1-py3-none-any.whl (255 kB)
01:07:44 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
01:07:44 Using cached numcodecs-0.16.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.8 MB)
01:07:44 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)
01:07:44 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
01:07:45 Installing collected packages: pyyaml, numcodecs, crc32c, donfig, zarr
01:07:45
01:07:45 Successfully installed crc32c-2.7.1 donfig-0.8.1.post1 numcodecs-0.16.1 pyyaml-6.0.2 zarr-3.1.1
01:07:45 + pip install fsspec requests aiohttp s3fs
01:07:46 Collecting fsspec
01:07:46 Using cached fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB)
01:07:46 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (2.32.4)
01:07:46 Collecting aiohttp
01:07:46 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)
01:07:47 Collecting s3fs
01:07:47 Using cached s3fs-2025.7.0-py3-none-any.whl.metadata (1.4 kB)
01:07:47 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests) (3.4.2)
01:07:47 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests) (3.10)
01:07:47 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests) (2.5.0)
01:07:47 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests) (2025.8.3)
01:07:47 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp)
01:07:47 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
01:07:47 Collecting aiosignal>=1.4.0 (from aiohttp)
01:07:47 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
01:07:47 Collecting attrs>=17.3.0 (from aiohttp)
01:07:47 Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)
01:07:47 Collecting frozenlist>=1.1.1 (from aiohttp)
01:07:47 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)
01:07:48 Collecting multidict<7.0,>=4.5 (from aiohttp)
01:07:48 Using cached multidict-6.6.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
01:07:48 Collecting propcache>=0.2.0 (from aiohttp)
01:07:48 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
01:07:48 Collecting yarl<2.0,>=1.17.0 (from aiohttp)
01:07:48 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB)
01:07:48 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs)
01:07:48 Using cached aiobotocore-2.23.2-py3-none-any.whl.metadata (25 kB)
01:07:48 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
01:07:48 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
01:07:49 Collecting botocore<1.39.9,>=1.39.7 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
01:07:49 Using cached botocore-1.39.8-py3-none-any.whl.metadata (5.7 kB)
01:07:49 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
01:07:49 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
01:07:49 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
01:07:49 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
01:07:50 Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
01:07:50 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)
01:07:50 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)
01:07:50 Requirement already satisfied: typing-extensions>=4.2 in ./.venv3/lib64/python3.11/site-packages (from aiosignal>=1.4.0->aiohttp) (4.14.1)
01:07:50 Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB)
01:07:50 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB)
01:07:50 Using cached multidict-6.6.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
01:07:50 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (348 kB)
01:07:50 Using cached s3fs-2025.7.0-py3-none-any.whl (30 kB)
01:07:50 Using cached aiobotocore-2.23.2-py3-none-any.whl (84 kB)
01:07:50 Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB)
01:07:50 Using cached botocore-1.39.8-py3-none-any.whl (13.9 MB)
01:07:51 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
01:07:51 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
01:07:51 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)
01:07:51 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
01:07:51 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
01:07:51 Using cached attrs-25.3.0-py3-none-any.whl (63 kB)
01:07:51 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 (235 kB)
01:07:51 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB)
01:07:51 Installing collected packages: wrapt, python-dateutil, propcache, multidict, jmespath, fsspec, frozenlist, attrs, aioitertools, aiohappyeyeballs, yarl, botocore, aiosignal, aiohttp, aiobotocore, s3fs
01:07:53
01:07:53 Successfully installed aiobotocore-2.23.2 aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aioitertools-0.12.0 aiosignal-1.4.0 attrs-25.3.0 botocore-1.39.8 frozenlist-1.7.0 fsspec-2025.7.0 jmespath-1.0.1 multidict-6.6.3 propcache-0.3.2 python-dateutil-2.9.0.post0 s3fs-2025.7.0 wrapt-1.17.2 yarl-1.20.1
01:07:53 + pip install omero-py
01:07:53 Collecting omero-py
01:07:53 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB)
01:07:53 Collecting urllib3<2 (from omero-py)
01:07:53 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
01:07:53 Collecting appdirs (from omero-py)
01:07:53 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
01:07:53 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
01:07:53 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.2)
01:07:53 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
01:07:53 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.2)
01:07:53 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
01:07:53 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4)
01:07:54 Collecting portalocker (from omero-py)
01:07:54 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
01:07:54 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
01:07:54 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
01:07:54 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.8.3)
01:07:54 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB)
01:07:54 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
01:07:54 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
01:07:54 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
01:07:54 Installing collected packages: appdirs, urllib3, portalocker, omero-py
01:07:54 Attempting uninstall: urllib3
01:07:54 Found existing installation: urllib3 2.5.0
01:07:54 Uninstalling urllib3-2.5.0:
01:07:54 Successfully uninstalled urllib3-2.5.0
01:07:56
01:07:56 Successfully installed appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20
01:07:56 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
01:07:56 Collecting omero-metadata
01:07:56 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-bnnpjadi/omero-metadata_2a6396ab17da431a88fdeb0493341ec3
01:07:56 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-bnnpjadi/omero-metadata_2a6396ab17da431a88fdeb0493341ec3
01:07:58 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 462e8acaa9d574df967c5a5c2c8be1693d9e18a2
01:07:58 Installing build dependencies: started
01:07:59 Installing build dependencies: finished with status 'done'
01:07:59 Getting requirements to build wheel: started
01:08:00 Getting requirements to build wheel: finished with status 'done'
01:08:00 Preparing metadata (pyproject.toml): started
01:08:00 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:00 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0)
01:08:00 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
01:08:00 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
01:08:00 Collecting pandas (from omero-metadata)
01:08:00 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
01:08:00 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
01:08:00 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
01:08:00 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
01:08:00 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.2)
01:08:00 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)
01:08:00 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)
01:08:00 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4)
01:08:00 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
01:08:00 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
01:08:00 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
01:08:00 Collecting pytz>=2020.1 (from pandas->omero-metadata)
01:08:00 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
01:08:01 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
01:08:01 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
01:08:01 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)
01:08:01 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)
01:08:01 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)
01:08:01 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)
01:08:01 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
01:08:01 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
01:08:01 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
01:08:01 Building wheels for collected packages: omero-metadata
01:08:01 Building wheel for omero-metadata (pyproject.toml): started
01:08:01 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
01:08:01 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=0be5caf5734e53ca80d878b35642b97a2ff6c8c9ce7a19347a2a2148338f5dcd
01:08:01 Stored in directory: /tmp/pip-ephem-wheel-cache-ce5s4b1x/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
01:08:01 Successfully built omero-metadata
01:08:01 Installing collected packages: pytz, tzdata, pandas, omero-metadata
01:08:06
01:08:06 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.1 pytz-2025.2 tzdata-2025.2
01:08:06 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
01:08:07 Collecting omero-cli-render
01:08:07 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-no4_f5gl/omero-cli-render_fd700114c0d74304ad15884a6dd22558
01:08:07 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-no4_f5gl/omero-cli-render_fd700114c0d74304ad15884a6dd22558
01:08:07 Running command git checkout -b merge_ci --track origin/merge_ci
01:08:08 Switched to a new branch 'merge_ci'
01:08:08 branch 'merge_ci' set up to track 'origin/merge_ci'.
01:08:08 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 2d97958b194c28b98008ac142c40ac32766b5097
01:08:08 Installing build dependencies: started
01:08:09 Installing build dependencies: finished with status 'done'
01:08:09 Getting requirements to build wheel: started
01:08:09 Getting requirements to build wheel: finished with status 'done'
01:08:09 Preparing metadata (pyproject.toml): started
01:08:09 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:09 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
01:08:09 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0)
01:08:09 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
01:08:09 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
01:08:09 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
01:08:09 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.2)
01:08:09 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)
01:08:09 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)
01:08:09 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4)
01:08:09 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
01:08:09 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)
01:08:09 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)
01:08:09 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)
01:08:09 Building wheels for collected packages: omero-cli-render
01:08:09 Building wheel for omero-cli-render (pyproject.toml): started
01:08:09 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
01:08:09 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=56d8be6f34568693d8b690b274f87c903bba807f45383c1118d639111cc070cb
01:08:09 Stored in directory: /tmp/pip-ephem-wheel-cache-1trhmkfk/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
01:08:09 Successfully built omero-cli-render
01:08:10 Installing collected packages: omero-cli-render
01:08:10 Successfully installed omero-cli-render-0.8.2.dev0
01:08:10 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
01:08:10 Collecting omero-cli-duplicate
01:08:10 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-rxsl0azw/omero-cli-duplicate_6a43f8533554439ea1c8698b3279f239
01:08:10 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-rxsl0azw/omero-cli-duplicate_6a43f8533554439ea1c8698b3279f239
01:08:11 Running command git checkout -b merge_ci --track origin/merge_ci
01:08:11 Switched to a new branch 'merge_ci'
01:08:11 branch 'merge_ci' set up to track 'origin/merge_ci'.
01:08:11 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 77c1a871c7dfeee89f73061725c580be8e0779e2
01:08:11 Installing build dependencies: started
01:08:12 Installing build dependencies: finished with status 'done'
01:08:12 Getting requirements to build wheel: started
01:08:12 Getting requirements to build wheel: finished with status 'done'
01:08:12 Preparing metadata (pyproject.toml): started
01:08:13 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:13 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0)
01:08:13 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
01:08:13 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
01:08:13 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
01:08:13 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.2)
01:08:13 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)
01:08:13 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
01:08:13 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)
01:08:13 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4)
01:08:13 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
01:08:13 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)
01:08:13 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)
01:08:13 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)
01:08:13 Building wheels for collected packages: omero-cli-duplicate
01:08:13 Building wheel for omero-cli-duplicate (pyproject.toml): started
01:08:13 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
01:08:13 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=474524eea8085846d95623e8fac8b95e8052a9c840973a0ccae46595e89dcbbd
01:08:13 Stored in directory: /tmp/pip-ephem-wheel-cache-m093mdcg/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
01:08:13 Successfully built omero-cli-duplicate
01:08:13 Installing collected packages: omero-cli-duplicate
01:08:13 Successfully installed omero-cli-duplicate-0.4.1.dev0
01:08:13 + pip install omero-certificates
01:08:14 Collecting omero-certificates
01:08:14 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
01:08:14 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0)
01:08:14 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
01:08:14 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
01:08:14 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
01:08:14 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.2)
01:08:14 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)
01:08:14 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
01:08:14 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)
01:08:14 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4)
01:08:14 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
01:08:14 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)
01:08:14 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)
01:08:14 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)
01:08:14 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
01:08:14 Installing collected packages: omero-certificates
01:08:14 Successfully installed omero-certificates-0.4.0
01:08:14 + for x in *.tar.gz
01:08:14 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
01:08:14 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
01:08:14 Installing build dependencies: started
01:08:15 Installing build dependencies: finished with status 'done'
01:08:15 Getting requirements to build wheel: started
01:08:15 Getting requirements to build wheel: finished with status 'done'
01:08:15 Preparing metadata (pyproject.toml): started
01:08:15 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:15 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0)
01:08:15 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
01:08:15 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
01:08:15 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
01:08:15 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.2)
01:08:15 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)
01:08:15 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
01:08:15 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)
01:08:15 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4)
01:08:15 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
01:08:16 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)
01:08:16 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)
01:08:16 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)
01:08:16 Building wheels for collected packages: omero-dropbox
01:08:16 Building wheel for omero-dropbox (pyproject.toml): started
01:08:16 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
01:08:16 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=6a8d671333b5854be26efccace92b6827bf1f7332999f0b44f11ab4294fb1cc3
01:08:16 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
01:08:16 Successfully built omero-dropbox
01:08:16 Installing collected packages: omero-dropbox
01:08:16 Successfully installed omero-dropbox-5.7.1.dev0
01:08:16 + for x in *.tar.gz
01:08:16 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
01:08:16 Processing ./omero_marshal-0.9.1.dev0.tar.gz
01:08:16 Installing build dependencies: started
01:08:17 Installing build dependencies: finished with status 'done'
01:08:17 Getting requirements to build wheel: started
01:08:18 Getting requirements to build wheel: finished with status 'done'
01:08:18 Preparing metadata (pyproject.toml): started
01:08:18 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:18 Building wheels for collected packages: omero_marshal
01:08:18 Building wheel for omero_marshal (pyproject.toml): started
01:08:18 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
01:08:18 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=f717c923fc5bc7e15fb10c67588b898f9a1c666bfd95ffebb792fb129266b761
01:08:18 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
01:08:18 Successfully built omero_marshal
01:08:18 Installing collected packages: omero_marshal
01:08:19 Successfully installed omero_marshal-0.9.1.dev0
01:08:19 + for x in *.tar.gz
01:08:19 + pip install -U omero_py-5.21.1.dev0.tar.gz
01:08:19 Processing ./omero_py-5.21.1.dev0.tar.gz
01:08:19 Installing build dependencies: started
01:08:20 Installing build dependencies: finished with status 'done'
01:08:20 Getting requirements to build wheel: started
01:08:21 Getting requirements to build wheel: finished with status 'done'
01:08:21 Preparing metadata (pyproject.toml): started
01:08:21 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:21 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20)
01:08:21 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4)
01:08:21 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0)
01:08:21 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.2)
01:08:21 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0)
01:08:21 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2)
01:08:21 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)
01:08:21 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4)
01:08:21 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0)
01:08:21 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)
01:08:21 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10)
01:08:21 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.8.3)
01:08:21 Building wheels for collected packages: omero-py
01:08:21 Building wheel for omero-py (pyproject.toml): started
01:08:22 Building wheel for omero-py (pyproject.toml): finished with status 'done'
01:08:22 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783541 sha256=37154119e9fa1e19952327826059e1d3095e28de70ed61f709067e86df33aac1
01:08:22 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d
01:08:22 Successfully built omero-py
01:08:22 Installing collected packages: omero-py
01:08:22 Attempting uninstall: omero-py
01:08:22 Found existing installation: omero-py 5.21.0
01:08:22 Uninstalling omero-py-5.21.0:
01:08:23 Successfully uninstalled omero-py-5.21.0
01:08:25 Successfully installed omero-py-5.21.1.dev0
01:08:25 + for x in *.tar.gz
01:08:25 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
01:08:25 Processing ./omero_scripts-5.9.2.dev0.tar.gz
01:08:25 Installing build dependencies: started
01:08:26 Installing build dependencies: finished with status 'done'
01:08:26 Getting requirements to build wheel: started
01:08:26 Getting requirements to build wheel: finished with status 'done'
01:08:26 Preparing metadata (pyproject.toml): started
01:08:26 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:26 Building wheels for collected packages: omero-scripts
01:08:26 Building wheel for omero-scripts (pyproject.toml): started
01:08:27 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
01:08:27 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=7d1fe5077f0596a752a862cdcfbd00c19b943a50d9feac8c2511c5545bd492e8
01:08:27 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
01:08:27 Successfully built omero-scripts
01:08:27 Installing collected packages: omero-scripts
01:08:27 Successfully installed omero-scripts-5.9.2.dev0
01:08:27 + for x in *.tar.gz
01:08:27 + pip install -U omero_web-5.29.2.dev0.tar.gz
01:08:27 Processing ./omero_web-5.29.2.dev0.tar.gz
01:08:28 Installing build dependencies: started
01:08:29 Installing build dependencies: finished with status 'done'
01:08:29 Getting requirements to build wheel: started
01:08:29 Getting requirements to build wheel: finished with status 'done'
01:08:29 Preparing metadata (pyproject.toml): started
01:08:29 Preparing metadata (pyproject.toml): finished with status 'done'
01:08:29 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)
01:08:30 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0)
01:08:30 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
01:08:30 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0)
01:08:30 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB)
01:08:30 Collecting django-pipeline (from omero-web==5.29.2.dev0)
01:08:30 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
01:08:30 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0)
01:08:30 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
01:08:30 Collecting django-csp (from omero-web==5.29.2.dev0)
01:08:30 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
01:08:30 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0)
01:08:30 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
01:08:30 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0)
01:08:30 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
01:08:30 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)
01:08:30 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.3.0)
01:08:30 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2)
01:08:30 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0)
01:08:30 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0)
01:08:30 Collecting importlib-resources (from omero-web==5.29.2.dev0)
01:08:30 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
01:08:30 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
01:08:30 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB)
01:08:30 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
01:08:31 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
01:08:31 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)
01:08:31 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)
01:08:31 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)
01:08:31 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.3.2)
01:08:31 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)
01:08:31 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)
01:08:31 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)
01:08:31 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1)
01:08:31 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0)
01:08:31 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
01:08:31 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)
01:08:31 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)
01:08:31 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) (2025.8.3)
01:08:31 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
01:08:31 Using cached django-4.2.23-py3-none-any.whl (8.0 MB)
01:08:31 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB)
01:08:31 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
01:08:31 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
01:08:31 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
01:08:31 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
01:08:31 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
01:08:31 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
01:08:31 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
01:08:31 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
01:08:31 Building wheels for collected packages: omero-web
01:08:31 Building wheel for omero-web (pyproject.toml): started
01:08:33 Building wheel for omero-web (pyproject.toml): finished with status 'done'
01:08:33 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=51a48eb78357d3777f47ce977aa83775d040f2c429a66689de2da6e51d71f33e
01:08:33 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c
01:08:33 Successfully built omero-web
01:08:33 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
01:08:36
01:08:36 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
01:08:36 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
01:08:36 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
01:08:36 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
01:08:36 --2025-08-06 01:08:36-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
01:08:36 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
01:08:36 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
01:08:36 HTTP request sent, awaiting response... 200 OK
01:08:36 Length: 125081 (122K) [text/plain]
01:08:36 Saving to: ‘Figure_To_Pdf.py’
01:08:36
01:08:36 0K .......... .......... .......... .......... .......... 40% 3.87M 0s
01:08:36 50K .......... .......... .......... .......... .......... 81% 5.98M 0s
01:08:36 100K .......... .......... .. 100% 45.0M=0.02s
01:08:36
01:08:36 2025-08-06 01:08:36 (5.61 MB/s) - ‘Figure_To_Pdf.py’ saved [125081/125081]
01:08:36
01:08:36 + chmod 755 Figure_To_Pdf.py
01:08:36 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
01:08:36 + omero config set omero.db.name OMERO-server
01:08:38 + omero config set omero.db.host pg
01:08:39 + omero config set omero.db.user postgres
01:08:40 + omero config set omero.data.dir /home/omero/omero-server-data
01:08:41 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
01:08:43 + omero config set omero.db.poolsize 25
01:08:44 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
01:08:45 + omero config set omero.security.trustStorePassword changeit
01:08:47 + omero config set omero.mail.config true
01:08:48 + omero config set omero.mail.from qa@openmicroscopy.org.uk
01:08:49 + omero config set omero.mail.host smtp.dundee.ac.uk
01:08:50 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
01:08:52 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
01:08:53 + omero certificates
01:08:54 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
01:08:54 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
01:08:54 + '[' false = true ']'
01:08:54 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
01:08:54 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
01:08:54 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
01:08:54 2025-08-06 01:08:54,887 [ omego.db] DEBUG dbcommand => upgrade
01:08:54 2025-08-06 01:08:54,887 [ omego.db] DEBUG dbhost => localhost
01:08:54 2025-08-06 01:08:54,887 [ omego.db] DEBUG dbname => OMERO-server
01:08:54 2025-08-06 01:08:54,887 [ omego.db] DEBUG dbpass => omero
01:08:54 2025-08-06 01:08:54,888 [ omego.db] DEBUG dbuser => omero
01:08:54 2025-08-06 01:08:54,888 [ omego.db] DEBUG rootpass => omero
01:08:54 2025-08-06 01:08:54,888 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
01:08:54 2025-08-06 01:08:54,888 [omego.extern] INFO Executing : omero version
01:08:55 OMERO.py version:
01:08:56 OMERO.server version:
01:08:56 5.6.3-574-fbdee10c54-ice36-b487
01:08:56 5.21.1.dev0
01:08:56 2025-08-06 01:08:56,170 [omego.extern] INFO Completed [1.282 s]
01:08:56 2025-08-06 01:08:56,170 [omego.extern] DEBUG Using omero CLI from omero
01:08:56 2025-08-06 01:08:56,170 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
01:08:56 2025-08-06 01:08:56,170 [omego.extern] INFO Running [current environment]: omero config get --show-password
01:08:56 2025-08-06 01:08:56,170 [omego.extern] INFO Executing : omero config get --show-password
01:08:57 2025-08-06 01:08:57,400 [omego.extern] INFO Completed [1.230 s]
01:08:57 2025-08-06 01:08:57,401 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
01:08:57 2025-08-06 01:08:57,401 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
01:08:57 2025-08-06 01:08:57,646 [omego.extern] INFO Completed [0.245 s]
01:08:57 2025-08-06 01:08:57,646 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
01:08:57 2025-08-06 01:08:57,646 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
01:08:57
01:08:57 2025-08-06 01:08:57,646 [omego.extern] INFO Running [current environment]: omero config get --show-password
01:08:57 2025-08-06 01:08:57,646 [omego.extern] INFO Executing : omero config get --show-password
01:08:58 2025-08-06 01:08:58,932 [omego.extern] INFO Completed [1.286 s]
01:08:58 2025-08-06 01:08:58,932 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
01:08:58 2025-08-06 01:08:58,932 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
01:08:59 2025-08-06 01:08:59,072 [omego.extern] INFO Completed [0.141 s]
01:08:59 2025-08-06 01:08:59,073 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.5") at port "5432".\n'
01:08:59 2025-08-06 01:08:59,073 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
01:08:59 2025-08-06 01:08:59,073 [omego.extern] INFO Running [current environment]: omero config get --show-password
01:08:59 2025-08-06 01:08:59,073 [omego.extern] INFO Executing : omero config get --show-password
01:09:00 2025-08-06 01:09:00,305 [omego.extern] INFO Completed [1.233 s]
01:09:00 2025-08-06 01:09:00,306 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
01:09:00 2025-08-06 01:09:00,306 [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
01:09:01 2025-08-06 01:09:01,153 [omego.extern] INFO Completed [0.847 s]
01:09:01 2025-08-06 01:09:01,153 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
01:09:01 2025-08-06 01:09:01,153 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
01:09:01 2025-08-06 01:09:01,155 [ omego.db] INFO Database is already at OMERO5.4__0
01:09:01 + export LANG=en_US.UTF-8
01:09:01 + LANG=en_US.UTF-8
01:09:01 + export LANGUAGE=en_US:en
01:09:01 + LANGUAGE=en_US:en
01:09:01 + export LC_ALL=en_US.UTF-8
01:09:01 + LC_ALL=en_US.UTF-8
01:09:01 + BUILD_ID=DONT_KILL_ME
01:09:01 + omero admin start
01:09:07 No descriptor given. Using etc/grid/default.xml
01:09:19 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
01:09:19 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
01:09:19 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
01:09:19 Waiting on startup. Use CTRL-C to exit
01:09:20 + omero admin waitup
01:09:21 Waiting on startup. Use CTRL-C to exit
01:09:21 + omero admin diagnostics
01:09:22
01:09:22 ================================================================================
01:09:22 OMERO Diagnostics (admin)
01:09:22 ================================================================================
01:09:22
01:09:22 Commands: java -version 11.0.25 (/usr/bin/java)
01:09:22 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
01:09:22 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
01:09:22 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
01:09:22 Commands: psql --version 16.9 (/usr/bin/psql)
01:09:22 Commands: openssl version 3.2.24 (/usr/bin/openssl)
01:09:22
01:09:22 Component: OMERO.py 5.21.1.dev0
01:09:22 Component: OMERO.server 5.6.3-574-fbdee10c54-ice36-b487
01:09:22
01:09:22 Server: icegridnode running
01:09:22 Server: Blitz-0 active (pid = 2371, enabled)
01:09:22 Server: Indexer-0 activating (enabled)
01:09:22 Server: OMERO.Glacier2 active (pid = 2397, enabled)
01:09:22 Server: OMERO.IceStorm active (pid = 2421, enabled)
01:09:22 Server: Processor-0 activating (enabled)
01:09:22 Server: Tables-0 activating (enabled)
01:09:22
01:09:22 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
01:09:22 Log files: Blitz-0.log 14.0 KB errors=0 warnings=1
01:09:22 Log files: DropBox.log n/a
01:09:22 Log files: FileServer.log n/a
01:09:22 Log files: Indexer-0.log 2.1 KB
01:09:22 Log files: MonitorServer.log n/a
01:09:22 Log files: Processor-0.log 592 B
01:09:22 Log files: Tables-0.log 841 B
01:09:22 Log files: TestDropBox.log n/a
01:09:22 Log files: master.err empty
01:09:22 Log files: master.out 30.5 KB
01:09:22 Log files: Total size 0.05 MB
01:09:22
01:09:22
01:09:22 Environment:OMERO_HOME=(unset)
01:09:22 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:09:22 Environment:OMERO_NODE=(unset)
01:09:22 Environment:OMERO_MASTER=(unset)
01:09:22 Environment:OMERO_USERDIR=(unset)
01:09:22 Environment:OMERO_TMPDIR=(unset)
01:09:22 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
01:09:22 Environment:PYTHONPATH=(unset)
01:09:22 Environment:ICE_HOME=/opt/ice-3.6.5
01:09:22 Environment:LD_LIBRARY_PATH=(unset)
01:09:22 Environment:DYLD_LIBRARY_PATH=(unset)
01:09:22
01:09:22 OMERO SSL port:4064
01:09:22 OMERO TCP port:4063
01:09:22 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
01:09:22 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
01:09:22
01:09:22 JVM settings: Blitz-${index} -Xmx7200m
01:09:22 JVM settings: Indexer-${index} -Xmx4800m
01:09:22 JVM settings: PixelData-${index} -Xmx7200m
01:09:22 JVM settings: Repository-${index} -Xmx4800m
01:09:22
01:09:22 Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 6 August 2025 748e13fdc890f223b724d68d3620412abd94d99b
01:09:22 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 6 August 2025 748e13fdc890f223b724d68d3620412abd94d99b
01:09:22 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 6 August 2025 748e13fdc890f223b724d68d3620412abd94d99b
01:09:22 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 6 August 2025 92c7961c2c8ff8fd6149679b5b4e92bec2255d96
01:09:22 Jar: lib/server/ome-common.jar OME Common Java 6.1.1-SNAPSHOT 6 August 2025 92c7961c2c8ff8fd6149679b5b4e92bec2255d96
01:09:22 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 6 August 2025 92c7961c2c8ff8fd6149679b5b4e92bec2255d96
01:09:22 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 6 August 2025 92c7961c2c8ff8fd6149679b5b4e92bec2255d96
01:09:22 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 6 August 2025 92c7961c2c8ff8fd6149679b5b4e92bec2255d96
01:09:22 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 6 August 2025 92c7961c2c8ff8fd6149679b5b4e92bec2255d96
01:09:22 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
01:09:22 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT 3708e6072d898cfb0b70daaab15dd46141466dda
01:09:23 + deactivate
01:09:23 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
01:09:23 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:09:23 + export PATH
01:09:23 + unset _OLD_VIRTUAL_PATH
01:09:23 + '[' -n '' ']'
01:09:23 + hash -r
01:09:23 + '[' -n '' ']'
01:09:23 + unset VIRTUAL_ENV
01:09:23 + unset VIRTUAL_ENV_PROMPT
01:09:23 + '[' '!' '' = nondestructive ']'
01:09:23 + unset -f deactivate
01:09:23 Finished: SUCCESS
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