00:33:32 Started by upstream project "Trigger" build number 557 00:33:32 originally caused by: 00:33:32 Started by timer 00:33:32 Running as SYSTEM 00:33:32 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server 00:33:32 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11028414181927884709.sh 00:33:32 + source /home/settings.env 00:33:32 ++ OMERO_DB_HOST=pg 00:33:32 ++ OMERO_DB_USER=postgres 00:33:32 ++ OMERO_DB_PASS= 00:33:32 ++ OMERO_ROOT_PASS=omero 00:33:32 ++ OMERO_DATA_DIR=/OMERO 00:33:32 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR 00:33:32 + OMERO_DB_NAME=OMERO-server 00:33:32 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server 00:33:32 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:33:32 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:33:32 + OMERO_DATA_DIR=/home/omero/omero-server-data 00:33:32 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']' 00:33:32 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate 00:33:32 ++ deactivate nondestructive 00:33:32 ++ '[' -n '' ']' 00:33:32 ++ '[' -n '' ']' 00:33:32 ++ hash -r 00:33:32 ++ '[' -n '' ']' 00:33:32 ++ unset VIRTUAL_ENV 00:33:32 ++ unset VIRTUAL_ENV_PROMPT 00:33:32 ++ '[' '!' nondestructive = nondestructive ']' 00:33:32 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3 00:33:32 ++ export VIRTUAL_ENV 00:33:32 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:33:32 ++ 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 00:33:32 ++ export PATH 00:33:32 ++ '[' -n '' ']' 00:33:32 ++ '[' -z '' ']' 00:33:32 ++ _OLD_VIRTUAL_PS1= 00:33:32 ++ PS1='(.venv3) ' 00:33:32 ++ export PS1 00:33:32 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' 00:33:32 ++ export VIRTUAL_ENV_PROMPT 00:33:32 ++ hash -r 00:33:32 + omero admin stop 00:33:33 Waiting on shutdown. Use CTRL-C to exit 00:33:33 .+ sleep 5 00:33:48 + deactivate 00:33:48 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' 00:33:48 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:33:48 + export PATH 00:33:48 + unset _OLD_VIRTUAL_PATH 00:33:48 + '[' -n '' ']' 00:33:48 + hash -r 00:33:48 + '[' -n '' ']' 00:33:48 + unset VIRTUAL_ENV 00:33:48 + unset VIRTUAL_ENV_PROMPT 00:33:48 + '[' '!' '' = nondestructive ']' 00:33:48 + unset -f deactivate 00:33:48 + rm -rf /home/omero/workspace/OMERO-server/.venv3 00:33:49 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3 00:33:53 + '[' false = true ']' 00:33:53 + echo 'Skipping PURGE_DATA:CleanDbAndRepo' 00:33:53 Skipping PURGE_DATA:CleanDbAndRepo 00:33:53 + 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 00:33:55 Copied 1 artifact from "OMERO-build" build number 470 00:33:55 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 463 00:33:55 Copied 2 artifacts from "OMERO-build-build" build number 493 00:33:55 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 2 00:33:55 [OMERO-server] $ /bin/bash -xe /tmp/jenkins9749040392312225462.sh 00:33:55 + source /home/settings.env 00:33:55 ++ OMERO_DB_HOST=pg 00:33:55 ++ OMERO_DB_USER=postgres 00:33:55 ++ OMERO_DB_PASS= 00:33:55 ++ OMERO_ROOT_PASS=omero 00:33:55 ++ OMERO_DATA_DIR=/OMERO 00:33:55 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR 00:33:55 + OMERO_DB_NAME=OMERO-server 00:33:55 + OMERO_DATA_DIR=/home/omero/omero-server-data 00:33:55 + mkdir -p /home/omero/omero-server-data 00:33:55 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server 00:33:55 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:33:55 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:33:55 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip 00:33:55 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip 00:33:55 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties 00:33:55 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties 00:33:55 ++ ls OMERO.server-5.6.3-569-de45fe4b09-ice36-b470.zip 00:33:55 + ZIP=OMERO.server-5.6.3-569-de45fe4b09-ice36-b470.zip 00:33:55 + '[' '!' -z '' ']' 00:33:55 + DIST=OMERO.server-5.6.3-569-de45fe4b09-ice36-b470 00:33:55 + unzip OMERO.server-5.6.3-569-de45fe4b09-ice36-b470.zip 00:33:55 Archive: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470.zip 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/blitz/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/grid/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/profiles/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/error/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/grid/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/luts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/luts/janelia/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/luts/matplotlib/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/luts/ncsa_paledit/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/luts/seaborn/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/luts/wcif/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/analysis_scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/annotation_scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/export_scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/figure_scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/import_scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/scripts/omero/util_scripts/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/server/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/share/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/share/licenses/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/misc/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__1/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__10/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__11/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__2/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__3/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__4/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__5/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__6/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__7/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__8/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__9/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__4/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__5/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__6/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__7/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.1__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.2__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.2__0/t/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.3__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.4__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.0__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.1__1/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.2__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4DEV__1/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4DEV__2/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4DEV__3/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/ 00:33:55 creating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/var/ 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/LICENSE.txt 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/backup.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/blitz/mail-senders.example 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/blitz/mail-server.example 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/build.properties 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/env.bat 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/env.sh 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/hibernate.properties 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/ice.config 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/logback-cli.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/logback-indexing-cli.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/logback-indexing.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/logback.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/mime.types 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/node1.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/node2.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/omero.properties 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/profiles/psql 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/rollover.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/Windows.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/error/maintainance.html 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/grid/README 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/grid/default.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/grid/templates.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/grid/windefault.xml 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/ice.config 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/internal.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/master.cfg 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/templates/robot.template 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/etc/testdropbox.config 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/history.rst 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/OMEZarrReader.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/accessors-smart.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/activation.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/aggdesigner-algorithm.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/aircompressor.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/antlr.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/aopalliance.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/apiguardian-api.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/asm.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/avatica-core.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/avatica-metrics.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/aws-java-sdk-core.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/aws-java-sdk-kms.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/aws-java-sdk-s3.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/base.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-anim.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-awt-util.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-bridge.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-codec.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-constants.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-css.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-dom.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-ext.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-gvt.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-i18n.jar 00:33:55 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/lib/client/batik-parser.jar 00:33:55 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OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/misc/enums.py 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__1/OMERO3__7.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__10/OMERO3A__9.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__11/OMERO3A__10.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__11/OMERO3A__5.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__2/OMERO3A__1.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__3/OMERO3A__2.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__3/OMERO3__5.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__4/OMERO3A__3.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__4/OMERO3__5.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__5/OMERO3A__4.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__6/OMERO3A__5.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__7/OMERO3A__6.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__8/OMERO3A__6.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3A__9/OMERO3A__8.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__4/OMERO3__1.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__5/OMERO3__4.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__6/OMERO3__5.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO3__7/OMERO3__6.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.1__0/OMERO4__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.2__0/OMERO4.1__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.3__0/OMERO4.2__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.4__0/OMERO4.1__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4.4__0/OMERO4.3__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO4__0/OMERO3A__11.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.0__0/OMERO4.4__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.1__1/OMERO5.0__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.1__1/OMERO5.1__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.2__0/OMERO5.1__1.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/OMERO5.2__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/delete-ns-orphans.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/OMERO5.3__0.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/OMERO5.3__1.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/psql-footer.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/psql-header.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/schema.sql 00:33:57 inflating: OMERO.server-5.6.3-569-de45fe4b09-ice36-b470/sql/psql/OMERO5.4__0/views.sql 00:33:57 + rm -f OMERO.server-5.6.3-569-de45fe4b09-ice36-b470.zip 00:33:57 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-569-de45fe4b09-ice36-b470 /home/omero/workspace/OMERO-server/OMERO.server 00:33:57 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:33:57 + JAR=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:33:57 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:33:57 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:33:57 + 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 00:33:57 + 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 00:33:57 --2025-07-17 00:33:57-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar 00:33:57 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:33:57 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:33:57 HTTP request sent, awaiting response... 200 OK 00:33:57 Length: 889211 (868K) [application/java-archive] 00:33:57 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ 00:33:57 00:33:57 0K .......... .......... .......... .......... .......... 5% 3.89M 0s 00:33:57 50K .......... .......... .......... .......... .......... 11% 5.93M 0s 00:33:57 100K .......... .......... .......... .......... .......... 17% 21.8M 0s 00:33:57 150K .......... .......... .......... .......... .......... 23% 23.8M 0s 00:33:57 200K .......... .......... .......... .......... .......... 28% 7.90M 0s 00:33:57 250K .......... .......... .......... .......... .......... 34% 30.1M 0s 00:33:57 300K .......... .......... .......... .......... .......... 40% 44.9M 0s 00:33:57 350K .......... .......... .......... .......... .......... 46% 32.4M 0s 00:33:57 400K .......... .......... .......... .......... .......... 51% 62.5M 0s 00:33:57 450K .......... .......... .......... .......... .......... 57% 8.80M 0s 00:33:57 500K .......... .......... .......... .......... .......... 63% 21.4M 0s 00:33:57 550K .......... .......... .......... .......... .......... 69% 125M 0s 00:33:57 600K .......... .......... .......... .......... .......... 74% 30.3M 0s 00:33:57 650K .......... .......... .......... .......... .......... 80% 33.4M 0s 00:33:57 700K .......... .......... .......... .......... .......... 86% 9.25M 0s 00:33:57 750K .......... .......... .......... .......... .......... 92% 23.5M 0s 00:33:57 800K .......... .......... .......... .......... .......... 97% 29.4M 0s 00:33:57 850K .......... ........ 100% 127M=0.06s 00:33:57 00:33:57 2025-07-17 00:33:57 (15.0 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211] 00:33:57 00:33:57 + 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 00:33:57 --2025-07-17 00:33:57-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar 00:33:58 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:33:58 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:33:58 HTTP request sent, awaiting response... 200 OK 00:33:58 Length: 73309 (72K) [application/java-archive] 00:33:58 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ 00:33:58 00:33:58 0K .......... .......... .......... .......... .......... 69% 4.11M 0s 00:33:58 50K .......... .......... . 100% 8.46M=0.01s 00:33:58 00:33:58 2025-07-17 00:33:58 (4.87 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309] 00:33:58 00:33:58 + 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 00:33:58 --2025-07-17 00:33:58-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar 00:33:58 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:33:58 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:33:58 HTTP request sent, awaiting response... 200 OK 00:33:58 Length: 63303 (62K) [application/java-archive] 00:33:58 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ 00:33:58 00:33:58 0K .......... .......... .......... .......... .......... 80% 4.23M 0s 00:33:58 50K .......... . 100% 11.2M=0.01s 00:33:58 00:33:58 2025-07-17 00:33:58 (4.80 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303] 00:33:58 00:33:58 + 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 00:33:58 --2025-07-17 00:33:58-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar 00:33:58 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:33:58 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:33:58 HTTP request sent, awaiting response... 200 OK 00:33:58 Length: 1271272 (1.2M) [application/java-archive] 00:33:58 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ 00:33:58 00:33:58 0K .......... .......... .......... .......... .......... 4% 4.24M 0s 00:33:58 50K .......... .......... .......... .......... .......... 8% 5.15M 0s 00:33:58 100K .......... .......... .......... .......... .......... 12% 23.8M 0s 00:33:58 150K .......... .......... .......... .......... .......... 16% 21.2M 0s 00:33:58 200K .......... .......... .......... .......... .......... 20% 8.09M 0s 00:33:58 250K .......... .......... .......... .......... .......... 24% 32.6M 0s 00:33:58 300K .......... .......... .......... .......... .......... 28% 56.7M 0s 00:33:58 350K .......... .......... .......... .......... .......... 32% 29.6M 0s 00:33:58 400K .......... .......... .......... .......... .......... 36% 27.2M 0s 00:33:58 450K .......... .......... .......... .......... .......... 40% 9.12M 0s 00:33:58 500K .......... .......... .......... .......... .......... 44% 28.5M 0s 00:33:58 550K .......... .......... .......... .......... .......... 48% 31.8M 0s 00:33:58 600K .......... .......... .......... .......... .......... 52% 104M 0s 00:33:58 650K .......... .......... .......... .......... .......... 56% 30.2M 0s 00:33:58 700K .......... .......... .......... .......... .......... 60% 8.95M 0s 00:33:58 750K .......... .......... .......... .......... .......... 64% 30.6M 0s 00:33:58 800K .......... .......... .......... .......... .......... 68% 33.6M 0s 00:33:58 850K .......... .......... .......... .......... .......... 72% 113M 0s 00:33:58 900K .......... .......... .......... .......... .......... 76% 28.6M 0s 00:33:58 950K .......... .......... .......... .......... .......... 80% 9.07M 0s 00:33:58 1000K .......... .......... .......... .......... .......... 84% 36.3M 0s 00:33:58 1050K .......... .......... .......... .......... .......... 88% 63.6M 0s 00:33:58 1100K .......... .......... .......... .......... .......... 92% 36.4M 0s 00:33:58 1150K .......... .......... .......... .......... .......... 96% 24.0M 0s 00:33:58 1200K .......... .......... .......... .......... . 100% 10.8M=0.07s 00:33:58 00:33:58 2025-07-17 00:33:58 (16.6 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272] 00:33:58 00:33:58 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate 00:33:58 ++ deactivate nondestructive 00:33:58 ++ '[' -n '' ']' 00:33:58 ++ '[' -n '' ']' 00:33:58 ++ hash -r 00:33:58 ++ '[' -n '' ']' 00:33:58 ++ unset VIRTUAL_ENV 00:33:58 ++ unset VIRTUAL_ENV_PROMPT 00:33:58 ++ '[' '!' nondestructive = nondestructive ']' 00:33:58 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3 00:33:58 ++ export VIRTUAL_ENV 00:33:58 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:33:58 ++ 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 00:33:58 ++ export PATH 00:33:58 ++ '[' -n '' ']' 00:33:58 ++ '[' -z '' ']' 00:33:58 ++ _OLD_VIRTUAL_PS1= 00:33:58 ++ PS1='(.venv3) ' 00:33:58 ++ export PS1 00:33:58 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' 00:33:58 ++ export VIRTUAL_ENV_PROMPT 00:33:58 ++ hash -r 00:33:58 + pip install -U pip 00:33:58 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1) 00:33:59 Collecting pip 00:33:59 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB) 00:33:59 Installing collected packages: pip 00:33:59 Attempting uninstall: pip 00:33:59 Found existing installation: pip 22.3.1 00:33:59 Uninstalling pip-22.3.1: 00:33:59 Successfully uninstalled pip-22.3.1 00:34:00 Successfully installed pip-25.1.1 00:34:00 WARNING: There was an error checking the latest version of pip. 00:34:00 + 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 00:34:00 Collecting zeroc-ice==3.6.5 00:34:00 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) 00:34:04 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 10.2 MB/s eta 0:00:00 00:34:04 Installing collected packages: zeroc-ice 00:34:05 Successfully installed zeroc-ice-3.6.5 00:34:05 + pip install markdown 00:34:06 Collecting markdown 00:34:06 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB) 00:34:06 Using cached markdown-3.8.2-py3-none-any.whl (106 kB) 00:34:06 Installing collected packages: markdown 00:34:06 Successfully installed markdown-3.8.2 00:34:06 + pip install reportlab 00:34:06 Collecting reportlab 00:34:06 Using cached reportlab-4.4.2-py3-none-any.whl.metadata (1.8 kB) 00:34:06 Collecting pillow>=9.0.0 (from reportlab) 00:34:06 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) 00:34:07 Collecting charset-normalizer (from reportlab) 00:34:07 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB) 00:34:07 Using cached reportlab-4.4.2-py3-none-any.whl (2.0 MB) 00:34:07 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB) 00:34:07 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB) 00:34:07 Installing collected packages: pillow, charset-normalizer, reportlab 00:34:08 00:34:08 Successfully installed charset-normalizer-3.4.2 pillow-11.3.0 reportlab-4.4.2 00:34:08 + pip install pyarrow 00:34:08 Collecting pyarrow 00:34:08 Using cached pyarrow-20.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB) 00:34:08 Using cached pyarrow-20.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.3 MB) 00:34:08 Installing collected packages: pyarrow 00:34:10 Successfully installed pyarrow-20.0.0 00:34:10 + pip install omego 00:34:10 Collecting omego 00:34:10 Using cached omego-0.7.0-py3-none-any.whl 00:34:10 Collecting future (from omego) 00:34:10 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) 00:34:10 Collecting yaclifw>=0.1.1 (from omego) 00:34:10 Using cached yaclifw-0.2.0-py3-none-any.whl 00:34:10 Collecting six (from yaclifw>=0.1.1->omego) 00:34:10 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) 00:34:10 Using cached future-1.0.0-py3-none-any.whl (491 kB) 00:34:10 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) 00:34:10 Installing collected packages: six, future, yaclifw, omego 00:34:11 00:34:11 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0 00:34:11 + pip install tables 00:34:11 Collecting tables 00:34:11 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB) 00:34:11 Collecting numpy>=1.20.0 (from tables) 00:34:11 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (62 kB) 00:34:11 Collecting numexpr>=2.6.2 (from tables) 00:34:11 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) 00:34:11 Collecting packaging (from tables) 00:34:11 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) 00:34:11 Collecting py-cpuinfo (from tables) 00:34:11 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes) 00:34:12 Collecting blosc2>=2.3.0 (from tables) 00:34:12 Using cached blosc2-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.9 kB) 00:34:12 Collecting typing-extensions>=4.4.0 (from tables) 00:34:12 Using cached typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB) 00:34:12 Collecting ndindex (from blosc2>=2.3.0->tables) 00:34:12 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB) 00:34:12 Collecting msgpack (from blosc2>=2.3.0->tables) 00:34:12 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB) 00:34:12 Collecting platformdirs (from blosc2>=2.3.0->tables) 00:34:12 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB) 00:34:12 Collecting requests (from blosc2>=2.3.0->tables) 00:34:12 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB) 00:34:12 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2) 00:34:12 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables) 00:34:12 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) 00:34:12 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables) 00:34:12 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB) 00:34:13 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables) 00:34:13 Using cached certifi-2025.7.14-py3-none-any.whl.metadata (2.4 kB) 00:34:13 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB) 00:34:13 Using cached blosc2-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB) 00:34:13 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB) 00:34:13 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl (16.9 MB) 00:34:13 Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB) 00:34:13 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB) 00:34:13 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB) 00:34:13 Using cached packaging-25.0-py3-none-any.whl (66 kB) 00:34:13 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB) 00:34:13 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB) 00:34:13 Using cached requests-2.32.4-py3-none-any.whl (64 kB) 00:34:13 Using cached idna-3.10-py3-none-any.whl (70 kB) 00:34:13 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB) 00:34:13 Using cached certifi-2025.7.14-py3-none-any.whl (162 kB) 00:34:13 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables 00:34:16 00:34:16 Successfully installed blosc2-3.5.1 certifi-2025.7.14 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.11.0 numpy-2.3.1 packaging-25.0 platformdirs-4.3.8 py-cpuinfo-9.0.0 requests-2.32.4 tables-3.10.2 typing-extensions-4.14.1 urllib3-2.5.0 00:34:16 + pip install jinja2 00:34:17 Collecting jinja2 00:34:17 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) 00:34:17 Collecting MarkupSafe>=2.0 (from jinja2) 00:34:17 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB) 00:34:17 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB) 00:34:17 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) 00:34:17 Installing collected packages: MarkupSafe, jinja2 00:34:17 00:34:17 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6 00:34:17 + pip install boto3 00:34:18 Collecting boto3 00:34:18 Downloading boto3-1.39.7-py3-none-any.whl.metadata (6.6 kB) 00:34:18 Collecting botocore<1.40.0,>=1.39.7 (from boto3) 00:34:18 Downloading botocore-1.39.7-py3-none-any.whl.metadata (5.7 kB) 00:34:18 Collecting jmespath<2.0.0,>=0.7.1 (from boto3) 00:34:18 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB) 00:34:18 Collecting s3transfer<0.14.0,>=0.13.0 (from boto3) 00:34:18 Using cached s3transfer-0.13.0-py3-none-any.whl.metadata (1.7 kB) 00:34:18 Collecting python-dateutil<3.0.0,>=2.1 (from botocore<1.40.0,>=1.39.7->boto3) 00:34:18 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) 00:34:18 Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.40.0,>=1.39.7->boto3) (2.5.0) 00:34:18 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.40.0,>=1.39.7->boto3) (1.17.0) 00:34:18 Downloading boto3-1.39.7-py3-none-any.whl (139 kB) 00:34:18 Downloading botocore-1.39.7-py3-none-any.whl (13.9 MB) 00:34:19 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.9/13.9 MB 23.1 MB/s eta 0:00:00 00:34:19 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB) 00:34:19 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 00:34:19 Using cached s3transfer-0.13.0-py3-none-any.whl (85 kB) 00:34:19 Installing collected packages: python-dateutil, jmespath, botocore, s3transfer, boto3 00:34:20 00:34:20 Successfully installed boto3-1.39.7 botocore-1.39.7 jmespath-1.0.1 python-dateutil-2.9.0.post0 s3transfer-0.13.0 00:34:20 + pip install smart-open 00:34:20 Collecting smart-open 00:34:20 Using cached smart_open-7.3.0.post1-py3-none-any.whl.metadata (24 kB) 00:34:20 Collecting wrapt (from smart-open) 00:34:20 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) 00:34:20 Using cached smart_open-7.3.0.post1-py3-none-any.whl (61 kB) 00:34:20 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) 00:34:21 Installing collected packages: wrapt, smart-open 00:34:21 00:34:21 Successfully installed smart-open-7.3.0.post1 wrapt-1.17.2 00:34:21 + pip install omero-py 00:34:21 Collecting omero-py 00:34:21 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB) 00:34:21 Collecting urllib3<2 (from omero-py) 00:34:21 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) 00:34:21 Collecting appdirs (from omero-py) 00:34:21 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) 00:34:21 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0) 00:34:21 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.1) 00:34:21 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0) 00:34:21 Collecting PyYAML (from omero-py) 00:34:21 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) 00:34:21 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5) 00:34:21 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4) 00:34:21 Collecting portalocker (from omero-py) 00:34:21 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB) 00:34:21 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2) 00:34:21 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10) 00:34:21 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.7.14) 00:34:21 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB) 00:34:21 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) 00:34:21 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) 00:34:21 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB) 00:34:21 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB) 00:34:21 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, omero-py 00:34:21 Attempting uninstall: urllib3 00:34:21 Found existing installation: urllib3 2.5.0 00:34:21 Uninstalling urllib3-2.5.0: 00:34:21 Successfully uninstalled urllib3-2.5.0 00:34:23 00:34:23 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20 00:34:23 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata 00:34:24 Collecting omero-metadata 00:34:24 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-628xphsx/omero-metadata_352b5a71f6c9435681fc889c3032600e 00:34:24 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-628xphsx/omero-metadata_352b5a71f6c9435681fc889c3032600e 00:34:24 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 58e97342cd5a659fec6a56edcdf6d84e8faa04b4 00:34:24 Installing build dependencies: started 00:34:25 Installing build dependencies: finished with status 'done' 00:34:25 Getting requirements to build wheel: started 00:34:26 Getting requirements to build wheel: finished with status 'done' 00:34:26 Preparing metadata (pyproject.toml): started 00:34:26 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:26 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0) 00:34:26 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2) 00:34:26 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6) 00:34:26 Collecting pandas (from omero-metadata) 00:34:26 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB) 00:34:26 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20) 00:34:26 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4) 00:34:26 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0) 00:34:26 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.1) 00:34:26 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) 00:34:26 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5) 00:34:26 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4) 00:34:26 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0) 00:34:26 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2) 00:34:26 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0) 00:34:26 Collecting pytz>=2020.1 (from pandas->omero-metadata) 00:34:26 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) 00:34:26 Collecting tzdata>=2022.7 (from pandas->omero-metadata) 00:34:26 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB) 00:34:26 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) 00:34:26 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) 00:34:26 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) 00:34:26 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.7.14) 00:34:26 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB) 00:34:26 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) 00:34:26 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB) 00:34:26 Building wheels for collected packages: omero-metadata 00:34:26 Building wheel for omero-metadata (pyproject.toml): started 00:34:26 Building wheel for omero-metadata (pyproject.toml): finished with status 'done' 00:34:26 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=283a11df3166ffe7ae5be8409d102b7d72df42539e71ac34406b14e4e9019b35 00:34:26 Stored in directory: /tmp/pip-ephem-wheel-cache-nlu6fft6/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b 00:34:26 Successfully built omero-metadata 00:34:27 Installing collected packages: pytz, tzdata, pandas, omero-metadata 00:34:33 00:34:33 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.1 pytz-2025.2 tzdata-2025.2 00:34:33 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render 00:34:33 Collecting omero-cli-render 00:34:33 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-aj9j5x15/omero-cli-render_d3922b91cd0e486a910b8f6f0fc27ad0 00:34:33 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-aj9j5x15/omero-cli-render_d3922b91cd0e486a910b8f6f0fc27ad0 00:34:34 Running command git checkout -b merge_ci --track origin/merge_ci 00:34:34 Switched to a new branch 'merge_ci' 00:34:34 branch 'merge_ci' set up to track 'origin/merge_ci'. 00:34:34 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 6eb55374d1a03c7da725d90de9333347db463bef 00:34:34 Installing build dependencies: started 00:34:35 Installing build dependencies: finished with status 'done' 00:34:35 Getting requirements to build wheel: started 00:34:35 Getting requirements to build wheel: finished with status 'done' 00:34:35 Preparing metadata (pyproject.toml): started 00:34:36 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:36 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2) 00:34:36 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0) 00:34:36 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20) 00:34:36 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4) 00:34:36 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0) 00:34:36 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.1) 00:34:36 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) 00:34:36 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5) 00:34:36 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4) 00:34:36 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0) 00:34:36 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.2) 00:34:36 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.10) 00:34:36 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.7.14) 00:34:36 Building wheels for collected packages: omero-cli-render 00:34:36 Building wheel for omero-cli-render (pyproject.toml): started 00:34:36 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done' 00:34:36 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=f0361b0d4dedcd6c5989f9f986e48c92585b399159af4651de1f9f57923bd50c 00:34:36 Stored in directory: /tmp/pip-ephem-wheel-cache-jip67nd9/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee 00:34:36 Successfully built omero-cli-render 00:34:36 Installing collected packages: omero-cli-render 00:34:36 Successfully installed omero-cli-render-0.8.2.dev0 00:34:36 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate 00:34:36 Collecting omero-cli-duplicate 00:34:36 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-pkh3dovd/omero-cli-duplicate_17d9caf12d5e4b3fa09196d649d619f0 00:34:36 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-pkh3dovd/omero-cli-duplicate_17d9caf12d5e4b3fa09196d649d619f0 00:34:37 Running command git checkout -b merge_ci --track origin/merge_ci 00:34:37 Switched to a new branch 'merge_ci' 00:34:37 branch 'merge_ci' set up to track 'origin/merge_ci'. 00:34:37 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 9e47726787dbc8e2b13df34a482c08521c21a182 00:34:37 Installing build dependencies: started 00:34:38 Installing build dependencies: finished with status 'done' 00:34:38 Getting requirements to build wheel: started 00:34:39 Getting requirements to build wheel: finished with status 'done' 00:34:39 Preparing metadata (pyproject.toml): started 00:34:39 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:39 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0) 00:34:39 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20) 00:34:39 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4) 00:34:39 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0) 00:34:39 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.1) 00:34:39 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) 00:34:39 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2) 00:34:39 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5) 00:34:39 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4) 00:34:39 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0) 00:34:39 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.2) 00:34:39 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.10) 00:34:39 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.7.14) 00:34:39 Building wheels for collected packages: omero-cli-duplicate 00:34:39 Building wheel for omero-cli-duplicate (pyproject.toml): started 00:34:39 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done' 00:34:39 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=bc9fdc42b68d603e493a25b3d0f4a8262cefad96e63dd2c3eda4708640769ddd 00:34:39 Stored in directory: /tmp/pip-ephem-wheel-cache-c37fgr9g/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46 00:34:39 Successfully built omero-cli-duplicate 00:34:39 Installing collected packages: omero-cli-duplicate 00:34:39 Successfully installed omero-cli-duplicate-0.4.1.dev0 00:34:39 + pip install omero-certificates 00:34:40 Collecting omero-certificates 00:34:40 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB) 00:34:40 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0) 00:34:40 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20) 00:34:40 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4) 00:34:40 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0) 00:34:40 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.1) 00:34:40 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) 00:34:40 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2) 00:34:40 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) 00:34:40 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4) 00:34:40 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0) 00:34:40 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) 00:34:40 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) 00:34:40 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.7.14) 00:34:40 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB) 00:34:40 Installing collected packages: omero-certificates 00:34:40 Successfully installed omero-certificates-0.4.0 00:34:40 + for x in *.tar.gz 00:34:40 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz 00:34:40 Processing ./omero_dropbox-5.7.1.dev0.tar.gz 00:34:40 Installing build dependencies: started 00:34:41 Installing build dependencies: finished with status 'done' 00:34:41 Getting requirements to build wheel: started 00:34:41 Getting requirements to build wheel: finished with status 'done' 00:34:41 Preparing metadata (pyproject.toml): started 00:34:42 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:42 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0) 00:34:42 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20) 00:34:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4) 00:34:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0) 00:34:42 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.1) 00:34:42 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) 00:34:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2) 00:34:42 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5) 00:34:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4) 00:34:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0) 00:34:42 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.2) 00:34:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10) 00:34:42 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.7.14) 00:34:42 Building wheels for collected packages: omero-dropbox 00:34:42 Building wheel for omero-dropbox (pyproject.toml): started 00:34:42 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done' 00:34:42 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=a283f6de9faf94c4c97226d310a44fea36ce5bf39518a9341b4a5fe259f14f5d 00:34:42 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92 00:34:42 Successfully built omero-dropbox 00:34:42 Installing collected packages: omero-dropbox 00:34:42 Successfully installed omero-dropbox-5.7.1.dev0 00:34:42 + for x in *.tar.gz 00:34:42 + pip install -U omero_marshal-0.9.1.dev0.tar.gz 00:34:42 Processing ./omero_marshal-0.9.1.dev0.tar.gz 00:34:42 Installing build dependencies: started 00:34:43 Installing build dependencies: finished with status 'done' 00:34:43 Getting requirements to build wheel: started 00:34:44 Getting requirements to build wheel: finished with status 'done' 00:34:44 Preparing metadata (pyproject.toml): started 00:34:44 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:44 Building wheels for collected packages: omero_marshal 00:34:44 Building wheel for omero_marshal (pyproject.toml): started 00:34:44 Building wheel for omero_marshal (pyproject.toml): finished with status 'done' 00:34:44 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=2594b8baab99b574a30e9e45120e728e7ea694792916557b31345498660c23a1 00:34:44 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18 00:34:44 Successfully built omero_marshal 00:34:44 Installing collected packages: omero_marshal 00:34:44 Successfully installed omero_marshal-0.9.1.dev0 00:34:44 + for x in *.tar.gz 00:34:44 + pip install -U omero_py-5.21.1.dev0.tar.gz 00:34:45 Processing ./omero_py-5.21.1.dev0.tar.gz 00:34:45 Installing build dependencies: started 00:34:46 Installing build dependencies: finished with status 'done' 00:34:46 Getting requirements to build wheel: started 00:34:46 Getting requirements to build wheel: finished with status 'done' 00:34:46 Preparing metadata (pyproject.toml): started 00:34:47 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:47 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20) 00:34:47 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4) 00:34:47 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0) 00:34:47 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.1) 00:34:47 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0) 00:34:47 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2) 00:34:47 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) 00:34:47 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4) 00:34:47 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0) 00:34:47 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) 00:34:47 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10) 00:34:47 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.7.14) 00:34:47 Building wheels for collected packages: omero-py 00:34:47 Building wheel for omero-py (pyproject.toml): started 00:34:48 Building wheel for omero-py (pyproject.toml): finished with status 'done' 00:34:48 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783499 sha256=03ffdbbe0266929153fc77df1b51095fa1a62481b0cf2027bb1d5642967c70e1 00:34:48 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d 00:34:48 Successfully built omero-py 00:34:48 Installing collected packages: omero-py 00:34:48 Attempting uninstall: omero-py 00:34:48 Found existing installation: omero-py 5.21.0 00:34:48 Uninstalling omero-py-5.21.0: 00:34:48 Successfully uninstalled omero-py-5.21.0 00:34:50 Successfully installed omero-py-5.21.1.dev0 00:34:50 + for x in *.tar.gz 00:34:50 + pip install -U omero_scripts-5.9.2.dev0.tar.gz 00:34:51 Processing ./omero_scripts-5.9.2.dev0.tar.gz 00:34:51 Installing build dependencies: started 00:34:52 Installing build dependencies: finished with status 'done' 00:34:52 Getting requirements to build wheel: started 00:34:52 Getting requirements to build wheel: finished with status 'done' 00:34:52 Preparing metadata (pyproject.toml): started 00:34:52 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:52 Building wheels for collected packages: omero-scripts 00:34:52 Building wheel for omero-scripts (pyproject.toml): started 00:34:52 Building wheel for omero-scripts (pyproject.toml): finished with status 'done' 00:34:52 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=9d91ae225706373ab1caf07ffaab79ebe481b914e5aad29bce5b857eab55371f 00:34:52 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850 00:34:52 Successfully built omero-scripts 00:34:53 Installing collected packages: omero-scripts 00:34:53 Successfully installed omero-scripts-5.9.2.dev0 00:34:53 + for x in *.tar.gz 00:34:53 + pip install -U omero_web-5.29.2.dev0.tar.gz 00:34:53 Processing ./omero_web-5.29.2.dev0.tar.gz 00:34:53 Installing build dependencies: started 00:34:54 Installing build dependencies: finished with status 'done' 00:34:54 Getting requirements to build wheel: started 00:34:55 Getting requirements to build wheel: finished with status 'done' 00:34:55 Preparing metadata (pyproject.toml): started 00:34:55 Preparing metadata (pyproject.toml): finished with status 'done' 00:34:55 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) 00:34:55 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0) 00:34:55 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB) 00:34:55 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0) 00:34:55 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB) 00:34:55 Collecting django-pipeline (from omero-web==5.29.2.dev0) 00:34:55 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB) 00:34:55 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0) 00:34:55 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB) 00:34:55 Collecting django-csp (from omero-web==5.29.2.dev0) 00:34:55 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB) 00:34:55 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0) 00:34:55 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB) 00:34:55 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0) 00:34:55 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB) 00:34:55 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) 00:34:55 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.3.0) 00:34:55 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2) 00:34:55 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0) 00:34:55 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0) 00:34:55 Collecting importlib-resources (from omero-web==5.29.2.dev0) 00:34:55 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB) 00:34:55 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0) 00:34:55 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB) 00:34:55 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0) 00:34:55 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB) 00:34:55 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) 00:34:55 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) 00:34:55 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) 00:34:55 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.3.1) 00:34:55 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) 00:34:55 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.6.5) 00:34:55 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) 00:34:55 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1) 00:34:55 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0) 00:34:55 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB) 00:34:55 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.4.2) 00:34:55 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.10) 00:34:55 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (2025.7.14) 00:34:56 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB) 00:34:56 Using cached django-4.2.23-py3-none-any.whl (8.0 MB) 00:34:56 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB) 00:34:56 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB) 00:34:56 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB) 00:34:56 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB) 00:34:56 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB) 00:34:56 Using cached django_csp-4.0-py3-none-any.whl (25 kB) 00:34:56 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB) 00:34:56 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB) 00:34:56 Using cached wheel-0.45.1-py3-none-any.whl (72 kB) 00:34:56 Building wheels for collected packages: omero-web 00:34:56 Building wheel for omero-web (pyproject.toml): started 00:34:57 Building wheel for omero-web (pyproject.toml): finished with status 'done' 00:34:57 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=79a12e554992a53c57d51e8a42f0704526fbbfe10eda483b76a280ad0d6c1720 00:34:57 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c 00:34:57 Successfully built omero-web 00:34:57 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web 00:35:01 00:35:01 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 00:35:01 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py 00:35:01 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file. 00:35:01 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled. 00:35:01 --2025-07-17 00:35:01-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py 00:35:01 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ... 00:35:01 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected. 00:35:01 HTTP request sent, awaiting response... 200 OK 00:35:01 Length: 125072 (122K) [text/plain] 00:35:01 Saving to: ‘Figure_To_Pdf.py’ 00:35:01 00:35:01 0K .......... .......... .......... .......... .......... 40% 3.90M 0s 00:35:01 50K .......... .......... .......... .......... .......... 81% 12.1M 0s 00:35:01 100K .......... .......... .. 100% 4.93M=0.02s 00:35:01 00:35:01 2025-07-17 00:35:01 (5.70 MB/s) - ‘Figure_To_Pdf.py’ saved [125072/125072] 00:35:01 00:35:01 + chmod 755 Figure_To_Pdf.py 00:35:01 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts 00:35:01 + omero config set omero.db.name OMERO-server 00:35:03 + omero config set omero.db.host pg 00:35:04 + omero config set omero.db.user postgres 00:35:05 + omero config set omero.data.dir /home/omero/omero-server-data 00:35:07 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time% 00:35:08 + omero config set omero.db.poolsize 25 00:35:09 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts 00:35:10 + omero config set omero.security.trustStorePassword changeit 00:35:12 + omero config set omero.mail.config true 00:35:13 + omero config set omero.mail.from qa@openmicroscopy.org.uk 00:35:14 + omero config set omero.mail.host smtp.dundee.ac.uk 00:35:15 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0 00:35:17 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED' 00:35:18 + omero certificates 00:35:19 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024) 00:35:19 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12 00:35:19 + '[' false = true ']' 00:35:19 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade' 00:35:19 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade 00:35:19 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG dbcommand => upgrade 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG dbhost => localhost 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG dbname => OMERO-server 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG dbpass => omero 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG dbuser => omero 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG rootpass => omero 00:35:19 2025-07-17 00:35:19,742 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server 00:35:19 2025-07-17 00:35:19,742 [omego.extern] INFO Executing : omero version 00:35:20 OMERO.py version: 00:35:20 OMERO.server version: 00:35:20 5.6.3-569-de45fe4b09-ice36-b470 00:35:20 5.21.1.dev0 00:35:21 2025-07-17 00:35:21,020 [omego.extern] INFO Completed [1.278 s] 00:35:21 2025-07-17 00:35:21,021 [omego.extern] DEBUG Using omero CLI from omero 00:35:21 2025-07-17 00:35:21,021 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ... 00:35:21 2025-07-17 00:35:21,021 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:35:21 2025-07-17 00:35:21,021 [omego.extern] INFO Executing : omero config get --show-password 00:35:22 2025-07-17 00:35:22,257 [omego.extern] INFO Completed [1.236 s] 00:35:22 2025-07-17 00:35:22,257 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:35:22 2025-07-17 00:35:22,257 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version 00:35:22 2025-07-17 00:35:22,263 [omego.extern] INFO Completed [0.006 s] 00:35:22 2025-07-17 00:35:22,264 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n' 00:35:22 2025-07-17 00:35:22,264 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9 00:35:22 00:35:22 2025-07-17 00:35:22,264 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:35:22 2025-07-17 00:35:22,264 [omego.extern] INFO Executing : omero config get --show-password 00:35:23 2025-07-17 00:35:23,490 [omego.extern] INFO Completed [1.226 s] 00:35:23 2025-07-17 00:35:23,490 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:35:23 2025-07-17 00:35:23,490 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo 00:35:23 2025-07-17 00:35:23,500 [omego.extern] INFO Completed [0.010 s] 00:35:23 2025-07-17 00:35:23,500 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.9") at port "5432".\n' 00:35:23 2025-07-17 00:35:23,500 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1 00:35:23 2025-07-17 00:35:23,500 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:35:23 2025-07-17 00:35:23,500 [omego.extern] INFO Executing : omero config get --show-password 00:35:24 2025-07-17 00:35:24,726 [omego.extern] INFO Completed [1.226 s] 00:35:24 2025-07-17 00:35:24,726 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:35:24 2025-07-17 00:35:24,726 [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 00:35:24 2025-07-17 00:35:24,737 [omego.extern] INFO Completed [0.011 s] 00:35:24 2025-07-17 00:35:24,737 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n' 00:35:24 2025-07-17 00:35:24,737 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0') 00:35:24 2025-07-17 00:35:24,739 [ omego.db] INFO Database is already at OMERO5.4__0 00:35:24 + export LANG=en_US.UTF-8 00:35:24 + LANG=en_US.UTF-8 00:35:24 + export LANGUAGE=en_US:en 00:35:24 + LANGUAGE=en_US:en 00:35:24 + export LC_ALL=en_US.UTF-8 00:35:24 + LC_ALL=en_US.UTF-8 00:35:24 + BUILD_ID=DONT_KILL_ME 00:35:24 + omero admin start 00:35:29 No descriptor given. Using etc/grid/default.xml 00:35:38 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master 00:35:38 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log 00:35:38 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry 00:35:38 Waiting on startup. Use CTRL-C to exit 00:35:38 + omero admin waitup 00:35:39 Waiting on startup. Use CTRL-C to exit 00:35:39 + omero admin diagnostics 00:35:41 00:35:41 ================================================================================ 00:35:41 OMERO Diagnostics (admin) 00:35:41 ================================================================================ 00:35:41 00:35:41 Commands: java -version 11.0.25 (/usr/bin/java) 00:35:41 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python) 00:35:41 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode) 00:35:41 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin) 00:35:41 Commands: psql --version 16.9 (/usr/bin/psql) 00:35:41 Commands: openssl version 3.2.24 (/usr/bin/openssl) 00:35:41 00:35:41 Component: OMERO.py 5.21.1.dev0 00:35:41 Component: OMERO.server 5.6.3-569-de45fe4b09-ice36-b470 00:35:41 00:35:41 Server: icegridnode running 00:35:41 Server: Blitz-0 active (pid = 22151, enabled) 00:35:41 Server: Indexer-0 activating (enabled) 00:35:41 Server: OMERO.Glacier2 active (pid = 22183, enabled) 00:35:41 Server: OMERO.IceStorm active (pid = 22210, enabled) 00:35:41 Server: Processor-0 active (pid = 22190, enabled) 00:35:41 Server: Tables-0 active (pid = 22206, enabled) 00:35:41 00:35:41 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists 00:35:41 Log files: Blitz-0.log 33.1 KB errors=0 warnings=1 00:35:41 Log files: DropBox.log n/a 00:35:41 Log files: FileServer.log n/a 00:35:41 Log files: Indexer-0.log 238 B 00:35:41 Log files: MonitorServer.log n/a 00:35:41 Log files: Processor-0.log 735 B 00:35:41 Log files: Tables-0.log 961 B 00:35:41 Log files: TestDropBox.log n/a 00:35:41 Log files: master.err empty 00:35:41 Log files: master.out 30.5 KB 00:35:41 Log files: Total size 0.07 MB 00:35:41 00:35:41 00:35:41 Environment:OMERO_HOME=(unset) 00:35:41 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:35:41 Environment:OMERO_NODE=(unset) 00:35:41 Environment:OMERO_MASTER=(unset) 00:35:41 Environment:OMERO_USERDIR=(unset) 00:35:41 Environment:OMERO_TMPDIR=(unset) 00:35:41 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 00:35:41 Environment:PYTHONPATH=(unset) 00:35:41 Environment:ICE_HOME=/opt/ice-3.6.5 00:35:41 Environment:LD_LIBRARY_PATH=(unset) 00:35:41 Environment:DYLD_LIBRARY_PATH=(unset) 00:35:41 00:35:41 OMERO SSL port:4064 00:35:41 OMERO TCP port:4063 00:35:41 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True 00:35:41 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0) 00:35:41 00:35:41 JVM settings: Blitz-${index} -Xmx7200m 00:35:41 JVM settings: Indexer-${index} -Xmx4800m 00:35:41 JVM settings: PixelData-${index} -Xmx7200m 00:35:41 JVM settings: Repository-${index} -Xmx4800m 00:35:41 00:35:41 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 17 July 2025 70c8fb5754b4b70f57f87d5c17d7d4d31df3e0f5 00:35:41 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 17 July 2025 70c8fb5754b4b70f57f87d5c17d7d4d31df3e0f5 00:35:41 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 17 July 2025 70c8fb5754b4b70f57f87d5c17d7d4d31df3e0f5 00:35:41 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 17 July 2025 c363992eaea6c1ab0db3439fcca24457facfac06 00:35:41 Jar: lib/server/ome-common.jar OME Common Java 6.0.27-SNAPSHOT 17 July 2025 c363992eaea6c1ab0db3439fcca24457facfac06 00:35:41 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 17 July 2025 c363992eaea6c1ab0db3439fcca24457facfac06 00:35:41 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 17 July 2025 c363992eaea6c1ab0db3439fcca24457facfac06 00:35:41 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 17 July 2025 c363992eaea6c1ab0db3439fcca24457facfac06 00:35:41 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 17 July 2025 c363992eaea6c1ab0db3439fcca24457facfac06 00:35:41 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT 00:35:41 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT 485ee4acdeb20e319644ff233a77d84870f52b8a 00:35:41 + deactivate 00:35:41 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' 00:35:41 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:35:41 + export PATH 00:35:41 + unset _OLD_VIRTUAL_PATH 00:35:41 + '[' -n '' ']' 00:35:41 + hash -r 00:35:41 + '[' -n '' ']' 00:35:41 + unset VIRTUAL_ENV 00:35:41 + unset VIRTUAL_ENV_PROMPT 00:35:41 + '[' '!' '' = nondestructive ']' 00:35:41 + unset -f deactivate 00:35:41 Finished: SUCCESS