00:32:02 Started by upstream project "Trigger" build number 555
00:32:02 originally caused by:
00:32:02 Started by timer
00:32:02 Running as SYSTEM
00:32:02 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:32:02 [OMERO-server] $ /bin/bash -xe /tmp/jenkins3061051663752005781.sh
00:32:02 + source /home/settings.env
00:32:02 ++ OMERO_DB_HOST=pg
00:32:02 ++ OMERO_DB_USER=postgres
00:32:02 ++ OMERO_DB_PASS=
00:32:02 ++ OMERO_ROOT_PASS=omero
00:32:02 ++ OMERO_DATA_DIR=/OMERO
00:32:02 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:32:02 + OMERO_DB_NAME=OMERO-server
00:32:02 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:32:02 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:32:02 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:32:02 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:32:02 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:32:02 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:32:02 ++ deactivate nondestructive
00:32:02 ++ '[' -n '' ']'
00:32:02 ++ '[' -n '' ']'
00:32:02 ++ hash -r
00:32:02 ++ '[' -n '' ']'
00:32:02 ++ unset VIRTUAL_ENV
00:32:02 ++ unset VIRTUAL_ENV_PROMPT
00:32:02 ++ '[' '!' nondestructive = nondestructive ']'
00:32:02 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:32:02 ++ export VIRTUAL_ENV
00:32:02 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:32:02 ++ 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
00:32:02 ++ export PATH
00:32:02 ++ '[' -n '' ']'
00:32:02 ++ '[' -z '' ']'
00:32:02 ++ _OLD_VIRTUAL_PS1=
00:32:02 ++ PS1='(.venv3) '
00:32:02 ++ export PS1
00:32:02 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:32:02 ++ export VIRTUAL_ENV_PROMPT
00:32:02 ++ hash -r
00:32:02 + omero admin stop
00:32:03 Waiting on shutdown. Use CTRL-C to exit
00:32:03 .+ sleep 5
00:32:18 + deactivate
00:32:18 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:32:18 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:32:18 + export PATH
00:32:18 + unset _OLD_VIRTUAL_PATH
00:32:18 + '[' -n '' ']'
00:32:18 + hash -r
00:32:18 + '[' -n '' ']'
00:32:18 + unset VIRTUAL_ENV
00:32:18 + unset VIRTUAL_ENV_PROMPT
00:32:18 + '[' '!' '' = nondestructive ']'
00:32:18 + unset -f deactivate
00:32:18 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:32:19 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:32:24 + '[' false = true ']'
00:32:24 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:32:24 Skipping PURGE_DATA:CleanDbAndRepo
00:32:24 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.4-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.21.1.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
00:32:26 Copied 1 artifact from "OMERO-build" build number 468
00:32:26 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 461
00:32:26 Copied 2 artifacts from "OMERO-build-build" build number 491
00:32:26 [OMERO-server] $ /bin/bash -xe /tmp/jenkins16726321135461042247.sh
00:32:26 + source /home/settings.env
00:32:26 ++ OMERO_DB_HOST=pg
00:32:26 ++ OMERO_DB_USER=postgres
00:32:26 ++ OMERO_DB_PASS=
00:32:26 ++ OMERO_ROOT_PASS=omero
00:32:26 ++ OMERO_DATA_DIR=/OMERO
00:32:26 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:32:26 + OMERO_DB_NAME=OMERO-server
00:32:26 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:32:26 + mkdir -p /home/omero/omero-server-data
00:32:26 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:32:26 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:32:26 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:32:26 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:32:26 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:32:26 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:32:26 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:32:26 ++ ls OMERO.server-5.6.3-569-769e77f47c-ice36-b468.zip
00:32:26 + ZIP=OMERO.server-5.6.3-569-769e77f47c-ice36-b468.zip
00:32:26 + '[' '!' -z '' ']'
00:32:26 + DIST=OMERO.server-5.6.3-569-769e77f47c-ice36-b468
00:32:26 + unzip OMERO.server-5.6.3-569-769e77f47c-ice36-b468.zip
00:32:26 Archive: OMERO.server-5.6.3-569-769e77f47c-ice36-b468.zip
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/blitz/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/grid/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/profiles/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/error/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/grid/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/luts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/luts/janelia/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/luts/matplotlib/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/luts/ncsa_paledit/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/luts/seaborn/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/luts/wcif/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/analysis_scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/annotation_scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/export_scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/figure_scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/import_scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/scripts/omero/util_scripts/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/server/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/share/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/share/licenses/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/misc/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__1/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__10/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__11/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__2/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__3/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__4/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__5/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__6/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__7/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__8/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3A__9/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3__4/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3__5/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3__6/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO3__7/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.1__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.2__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.2__0/t/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.3__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.4__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.0__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.1__1/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.2__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4DEV__1/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4DEV__2/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4DEV__3/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/
00:32:26 creating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/var/
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/LICENSE.txt
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/backup.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/blitz/mail-senders.example
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/blitz/mail-server.example
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/build.properties
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/env.bat
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/env.sh
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/hibernate.properties
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/ice.config
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/logback-cli.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/logback-indexing-cli.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/logback-indexing.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/logback.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/mime.types
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/node1.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/node2.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/omero.properties
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/profiles/psql
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/rollover.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/Windows.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/error/maintainance.html
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/grid/README
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/grid/default.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/grid/templates.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/grid/windefault.xml
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/ice.config
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/internal.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/master.cfg
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/templates/robot.template
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/etc/testdropbox.config
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/history.rst
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/OMEZarrReader.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/accessors-smart.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/activation.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/aggdesigner-algorithm.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/aircompressor.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/antlr.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/aopalliance.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/apiguardian-api.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/asm.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/avatica-core.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/avatica-metrics.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/aws-java-sdk-core.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/aws-java-sdk-kms.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/aws-java-sdk-s3.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/base.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-anim.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-awt-util.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-bridge.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-codec.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-constants.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-css.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-dom.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-ext.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-gvt.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-i18n.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-parser.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-script.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-shared-resources.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-svg-dom.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-svggen.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-transcoder.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-util.jar
00:32:26 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/lib/client/batik-xml.jar
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00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO4__0/OMERO3A__11.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/psql-footer.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/psql-header.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/schema.sql
00:32:28 inflating: OMERO.server-5.6.3-569-769e77f47c-ice36-b468/sql/psql/OMERO5.4__0/views.sql
00:32:28 + rm -f OMERO.server-5.6.3-569-769e77f47c-ice36-b468.zip
00:32:28 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-569-769e77f47c-ice36-b468 /home/omero/workspace/OMERO-server/OMERO.server
00:32:28 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server/ https://artifacts.glencoesoftware.com:443/artifactory/omero-plus/com/glencoesoftware/omero/omero-zarr-pixel-buffer/0.4.1/omero-zarr-pixel-buffer-0.4.1.jar
00:32:28 --2025-07-15 00:32:28-- https://artifacts.glencoesoftware.com/artifactory/omero-plus/com/glencoesoftware/omero/omero-zarr-pixel-buffer/0.4.1/omero-zarr-pixel-buffer-0.4.1.jar
00:32:28 Resolving artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)... 67.205.169.144, 2604:a880:400:d0::19b7:6001
00:32:28 Connecting to artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)|67.205.169.144|:443... connected.
00:32:29 HTTP request sent, awaiting response... 200 OK
00:32:29 Length: 26159 (26K) [application/java-archive]
00:32:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’
00:32:29
00:32:29 0K .......... .......... ..... 100% 217M=0s
00:32:29
00:32:29 2025-07-15 00:32:29 (217 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’ saved [26159/26159]
00:32:29
00:32:29 + 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
00:32:29 --2025-07-15 00:32:29-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:32:29 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:32:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:32:29 HTTP request sent, awaiting response... 200 OK
00:32:29 Length: 889211 (868K) [application/java-archive]
00:32:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:32:29
00:32:29 0K .......... .......... .......... .......... .......... 5% 4.09M 0s
00:32:29 50K .......... .......... .......... .......... .......... 11% 5.23M 0s
00:32:29 100K .......... .......... .......... .......... .......... 17% 22.4M 0s
00:32:29 150K .......... .......... .......... .......... .......... 23% 15.6M 0s
00:32:29 200K .......... .......... .......... .......... .......... 28% 9.45M 0s
00:32:29 250K .......... .......... .......... .......... .......... 34% 36.8M 0s
00:32:29 300K .......... .......... .......... .......... .......... 40% 22.7M 0s
00:32:29 350K .......... .......... .......... .......... .......... 46% 29.8M 0s
00:32:29 400K .......... .......... .......... .......... .......... 51% 97.7M 0s
00:32:29 450K .......... .......... .......... .......... .......... 57% 8.88M 0s
00:32:29 500K .......... .......... .......... .......... .......... 63% 30.5M 0s
00:32:29 550K .......... .......... .......... .......... .......... 69% 29.8M 0s
00:32:29 600K .......... .......... .......... .......... .......... 74% 135M 0s
00:32:29 650K .......... .......... .......... .......... .......... 80% 32.4M 0s
00:32:29 700K .......... .......... .......... .......... .......... 86% 8.76M 0s
00:32:29 750K .......... .......... .......... .......... .......... 92% 33.0M 0s
00:32:29 800K .......... .......... .......... .......... .......... 97% 15.8M 0s
00:32:29 850K .......... ........ 100% 175M=0.06s
00:32:29
00:32:29 2025-07-15 00:32:29 (14.6 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:32:29
00:32:29 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:32:29 --2025-07-15 00:32:29-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:32:29 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:32:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:32:29 HTTP request sent, awaiting response... 200 OK
00:32:29 Length: 73309 (72K) [application/java-archive]
00:32:29 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:32:29
00:32:29 0K .......... .......... .......... .......... .......... 69% 4.18M 0s
00:32:29 50K .......... .......... . 100% 10.1M=0.01s
00:32:29
00:32:29 2025-07-15 00:32:29 (5.07 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:32:29
00:32:29 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:32:29 --2025-07-15 00:32:29-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:32:29 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:32:29 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:32:29 HTTP request sent, awaiting response... 200 OK
00:32:30 Length: 63303 (62K) [application/java-archive]
00:32:30 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:32:30
00:32:30 0K .......... .......... .......... .......... .......... 80% 4.11M 0s
00:32:30 50K .......... . 100% 10.6M=0.01s
00:32:30
00:32:30 2025-07-15 00:32:30 (4.66 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:32:30
00:32:30 + 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
00:32:30 --2025-07-15 00:32:30-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:32:30 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:32:30 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:32:30 HTTP request sent, awaiting response... 200 OK
00:32:30 Length: 1271272 (1.2M) [application/java-archive]
00:32:30 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:32:30
00:32:30 0K .......... .......... .......... .......... .......... 4% 4.14M 0s
00:32:30 50K .......... .......... .......... .......... .......... 8% 5.02M 0s
00:32:30 100K .......... .......... .......... .......... .......... 12% 20.7M 0s
00:32:30 150K .......... .......... .......... .......... .......... 16% 26.9M 0s
00:32:30 200K .......... .......... .......... .......... .......... 20% 25.8M 0s
00:32:30 250K .......... .......... .......... .......... .......... 24% 8.82M 0s
00:32:30 300K .......... .......... .......... .......... .......... 28% 21.7M 0s
00:32:30 350K .......... .......... .......... .......... .......... 32% 72.3M 0s
00:32:30 400K .......... .......... .......... .......... .......... 36% 30.8M 0s
00:32:30 450K .......... .......... .......... .......... .......... 40% 9.88M 0s
00:32:30 500K .......... .......... .......... .......... .......... 44% 19.7M 0s
00:32:30 550K .......... .......... .......... .......... .......... 48% 109M 0s
00:32:30 600K .......... .......... .......... .......... .......... 52% 32.0M 0s
00:32:30 650K .......... .......... .......... .......... .......... 56% 40.0M 0s
00:32:30 700K .......... .......... .......... .......... .......... 60% 7.09M 0s
00:32:30 750K .......... .......... .......... .......... .......... 64% 35.4M 0s
00:32:30 800K .......... .......... .......... .......... .......... 68% 148M 0s
00:32:30 850K .......... .......... .......... .......... .......... 72% 29.5M 0s
00:32:30 900K .......... .......... .......... .......... .......... 76% 97.5M 0s
00:32:30 950K .......... .......... .......... .......... .......... 80% 7.51M 0s
00:32:30 1000K .......... .......... .......... .......... .......... 84% 77.6M 0s
00:32:30 1050K .......... .......... .......... .......... .......... 88% 39.5M 0s
00:32:30 1100K .......... .......... .......... .......... .......... 92% 29.6M 0s
00:32:30 1150K .......... .......... .......... .......... .......... 96% 86.7M 0s
00:32:30 1200K .......... .......... .......... .......... . 100% 182M=0.07s
00:32:30
00:32:30 2025-07-15 00:32:30 (17.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:32:30
00:32:30 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:32:30 ++ deactivate nondestructive
00:32:30 ++ '[' -n '' ']'
00:32:30 ++ '[' -n '' ']'
00:32:30 ++ hash -r
00:32:30 ++ '[' -n '' ']'
00:32:30 ++ unset VIRTUAL_ENV
00:32:30 ++ unset VIRTUAL_ENV_PROMPT
00:32:30 ++ '[' '!' nondestructive = nondestructive ']'
00:32:30 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:32:30 ++ export VIRTUAL_ENV
00:32:30 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:32:30 ++ 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
00:32:30 ++ export PATH
00:32:30 ++ '[' -n '' ']'
00:32:30 ++ '[' -z '' ']'
00:32:30 ++ _OLD_VIRTUAL_PS1=
00:32:30 ++ PS1='(.venv3) '
00:32:30 ++ export PS1
00:32:30 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:32:30 ++ export VIRTUAL_ENV_PROMPT
00:32:30 ++ hash -r
00:32:30 + pip install -U pip
00:32:30 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:32:30 Collecting pip
00:32:30 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
00:32:30 Installing collected packages: pip
00:32:30 Attempting uninstall: pip
00:32:30 Found existing installation: pip 22.3.1
00:32:31 Uninstalling pip-22.3.1:
00:32:31 Successfully uninstalled pip-22.3.1
00:32:31 Successfully installed pip-25.1.1
00:32:31 WARNING: There was an error checking the latest version of pip.
00:32:32 + 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
00:32:32 Collecting zeroc-ice==3.6.5
00:32:32 Downloading https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
00:32:34 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 23.4 MB/s eta 0:00:00
00:32:34 Installing collected packages: zeroc-ice
00:32:35 Successfully installed zeroc-ice-3.6.5
00:32:35 + pip install markdown
00:32:35 Collecting markdown
00:32:35 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB)
00:32:35 Using cached markdown-3.8.2-py3-none-any.whl (106 kB)
00:32:35 Installing collected packages: markdown
00:32:35 Successfully installed markdown-3.8.2
00:32:35 + pip install reportlab
00:32:36 Collecting reportlab
00:32:36 Using cached reportlab-4.4.2-py3-none-any.whl.metadata (1.8 kB)
00:32:36 Collecting pillow>=9.0.0 (from reportlab)
00:32:36 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:32:36 Collecting charset-normalizer (from reportlab)
00:32:36 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
00:32:36 Using cached reportlab-4.4.2-py3-none-any.whl (2.0 MB)
00:32:36 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:32:36 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
00:32:36 Installing collected packages: pillow, charset-normalizer, reportlab
00:32:37
00:32:37 Successfully installed charset-normalizer-3.4.2 pillow-11.3.0 reportlab-4.4.2
00:32:37 + pip install pyarrow
00:32:38 Collecting pyarrow
00:32:38 Using cached pyarrow-20.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
00:32:38 Using cached pyarrow-20.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.3 MB)
00:32:38 Installing collected packages: pyarrow
00:32:39 Successfully installed pyarrow-20.0.0
00:32:39 + pip install omego
00:32:40 Collecting omego
00:32:40 Using cached omego-0.7.0-py3-none-any.whl
00:32:40 Collecting future (from omego)
00:32:40 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:32:40 Collecting yaclifw>=0.1.1 (from omego)
00:32:40 Using cached yaclifw-0.2.0-py3-none-any.whl
00:32:40 Collecting six (from yaclifw>=0.1.1->omego)
00:32:40 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:32:40 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:32:40 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:32:40 Installing collected packages: six, future, yaclifw, omego
00:32:40
00:32:40 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:32:40 + pip install tables
00:32:41 Collecting tables
00:32:41 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:32:41 Collecting numpy>=1.20.0 (from tables)
00:32:41 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (62 kB)
00:32:41 Collecting numexpr>=2.6.2 (from tables)
00:32:41 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:32:41 Collecting packaging (from tables)
00:32:41 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:32:41 Collecting py-cpuinfo (from tables)
00:32:41 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:32:41 Collecting blosc2>=2.3.0 (from tables)
00:32:41 Using cached blosc2-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.9 kB)
00:32:41 Collecting typing-extensions>=4.4.0 (from tables)
00:32:41 Using cached typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB)
00:32:41 Collecting ndindex (from blosc2>=2.3.0->tables)
00:32:41 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:32:41 Collecting msgpack (from blosc2>=2.3.0->tables)
00:32:41 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:32:41 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:32:41 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
00:32:41 Collecting requests (from blosc2>=2.3.0->tables)
00:32:41 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)
00:32:41 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2)
00:32:41 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:32:41 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:32:41 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:32:41 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
00:32:42 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:32:42 Downloading certifi-2025.7.14-py3-none-any.whl.metadata (2.4 kB)
00:32:42 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:32:42 Using cached blosc2-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB)
00:32:42 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB)
00:32:42 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl (16.9 MB)
00:32:42 Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB)
00:32:42 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
00:32:42 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:32:42 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:32:42 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
00:32:42 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:32:42 Using cached requests-2.32.4-py3-none-any.whl (64 kB)
00:32:42 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:32:42 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
00:32:42 Downloading certifi-2025.7.14-py3-none-any.whl (162 kB)
00:32:42 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:32:45
00:32:45 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
00:32:45 + pip install jinja2
00:32:46 Collecting jinja2
00:32:46 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:32:46 Collecting MarkupSafe>=2.0 (from jinja2)
00:32:46 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:32:46 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:32:46 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
00:32:46 Installing collected packages: MarkupSafe, jinja2
00:32:46
00:32:46 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
00:32:46 + pip install boto3
00:32:47 Collecting boto3
00:32:47 Using cached boto3-1.39.4-py3-none-any.whl.metadata (6.6 kB)
00:32:47 Collecting botocore<1.40.0,>=1.39.4 (from boto3)
00:32:47 Using cached botocore-1.39.4-py3-none-any.whl.metadata (5.7 kB)
00:32:47 Collecting jmespath<2.0.0,>=0.7.1 (from boto3)
00:32:47 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
00:32:47 Collecting s3transfer<0.14.0,>=0.13.0 (from boto3)
00:32:47 Using cached s3transfer-0.13.0-py3-none-any.whl.metadata (1.7 kB)
00:32:47 Collecting python-dateutil<3.0.0,>=2.1 (from botocore<1.40.0,>=1.39.4->boto3)
00:32:47 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:32:47 Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.40.0,>=1.39.4->boto3) (2.5.0)
00:32:47 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,>=1.39.4->boto3) (1.17.0)
00:32:47 Using cached boto3-1.39.4-py3-none-any.whl (139 kB)
00:32:47 Using cached botocore-1.39.4-py3-none-any.whl (13.8 MB)
00:32:47 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
00:32:47 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:32:47 Using cached s3transfer-0.13.0-py3-none-any.whl (85 kB)
00:32:48 Installing collected packages: python-dateutil, jmespath, botocore, s3transfer, boto3
00:32:48
00:32:48 Successfully installed boto3-1.39.4 botocore-1.39.4 jmespath-1.0.1 python-dateutil-2.9.0.post0 s3transfer-0.13.0
00:32:48 + pip install smart-open
00:32:49 Collecting smart-open
00:32:49 Using cached smart_open-7.3.0.post1-py3-none-any.whl.metadata (24 kB)
00:32:49 Collecting wrapt (from smart-open)
00:32:49 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)
00:32:49 Using cached smart_open-7.3.0.post1-py3-none-any.whl (61 kB)
00:32:49 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)
00:32:49 Installing collected packages: wrapt, smart-open
00:32:49
00:32:49 Successfully installed smart-open-7.3.0.post1 wrapt-1.17.2
00:32:49 + pip install omero-py
00:32:50 Collecting omero-py
00:32:50 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB)
00:32:50 Collecting urllib3<2 (from omero-py)
00:32:50 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:32:50 Collecting appdirs (from omero-py)
00:32:50 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:32:50 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:32:50 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.1)
00:32:50 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
00:32:50 Collecting PyYAML (from omero-py)
00:32:50 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:32:50 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:32:50 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4)
00:32:50 Collecting portalocker (from omero-py)
00:32:50 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:32:50 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
00:32:50 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
00:32:50 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.7.14)
00:32:50 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB)
00:32:50 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:32:50 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:32:50 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:32:50 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
00:32:50 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, omero-py
00:32:50 Attempting uninstall: urllib3
00:32:50 Found existing installation: urllib3 2.5.0
00:32:50 Uninstalling urllib3-2.5.0:
00:32:50 Successfully uninstalled urllib3-2.5.0
00:32:52
00:32:52 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20
00:32:52 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:32:52 Collecting omero-metadata
00:32:52 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-0za6afck/omero-metadata_044efb544f914e2799a42e6d556f3e4c
00:32:52 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-0za6afck/omero-metadata_044efb544f914e2799a42e6d556f3e4c
00:32:54 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 22eddf307f2d8eef8b0139384cc6e224cd3788f1
00:32:54 Installing build dependencies: started
00:32:55 Installing build dependencies: finished with status 'done'
00:32:55 Getting requirements to build wheel: started
00:32:56 Getting requirements to build wheel: finished with status 'done'
00:32:56 Preparing metadata (pyproject.toml): started
00:32:56 Preparing metadata (pyproject.toml): finished with status 'done'
00:32:56 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0)
00:32:56 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
00:32:56 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:32:56 Collecting pandas (from omero-metadata)
00:32:56 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
00:32:56 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:32:56 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:32:56 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:32:56 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.1)
00:32:56 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)
00:32:56 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)
00:32:56 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4)
00:32:56 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:32:56 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
00:32:56 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:32:56 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:32:56 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:32:56 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:32:56 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:32:56 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)
00:32:56 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)
00:32:56 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)
00:32:56 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)
00:32:56 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
00:32:56 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:32:56 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:32:56 Building wheels for collected packages: omero-metadata
00:32:56 Building wheel for omero-metadata (pyproject.toml): started
00:32:57 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:32:57 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=ced548b0163e236f33be2e86bdeb3b7bbf4a6254f45337cfd828c9f959f3dca3
00:32:57 Stored in directory: /tmp/pip-ephem-wheel-cache-y4smo746/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:32:57 Successfully built omero-metadata
00:32:57 Installing collected packages: pytz, tzdata, pandas, omero-metadata
00:33:01
00:33:01 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.1 pytz-2025.2 tzdata-2025.2
00:33:02 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:33:02 Collecting omero-cli-render
00:33:02 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-xb5r8gcg/omero-cli-render_bbe7c74f40544ed78ceaa144f18dde98
00:33:02 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-xb5r8gcg/omero-cli-render_bbe7c74f40544ed78ceaa144f18dde98
00:33:03 Running command git checkout -b merge_ci --track origin/merge_ci
00:33:03 Switched to a new branch 'merge_ci'
00:33:03 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:33:03 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 647efd0cbd1f6c9a604bbe4358093a17e71be909
00:33:03 Installing build dependencies: started
00:33:04 Installing build dependencies: finished with status 'done'
00:33:04 Getting requirements to build wheel: started
00:33:04 Getting requirements to build wheel: finished with status 'done'
00:33:04 Preparing metadata (pyproject.toml): started
00:33:04 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:04 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
00:33:04 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0)
00:33:04 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:33:04 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:33:04 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:33:04 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.1)
00:33:04 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)
00:33:04 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)
00:33:04 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4)
00:33:04 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:33:05 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)
00:33:05 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)
00:33:05 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)
00:33:05 Building wheels for collected packages: omero-cli-render
00:33:05 Building wheel for omero-cli-render (pyproject.toml): started
00:33:05 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:33:05 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=6dd9d2559b5a469c252e9c3749d29959eb9ce34fa828c0dbe0a0c7f9c202eeb1
00:33:05 Stored in directory: /tmp/pip-ephem-wheel-cache-bsiqh25g/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:33:05 Successfully built omero-cli-render
00:33:05 Installing collected packages: omero-cli-render
00:33:05 Successfully installed omero-cli-render-0.8.2.dev0
00:33:05 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:33:05 Collecting omero-cli-duplicate
00:33:05 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-xf__0ctk/omero-cli-duplicate_828af78fff044e37a63a1c0afacfc721
00:33:05 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-xf__0ctk/omero-cli-duplicate_828af78fff044e37a63a1c0afacfc721
00:33:06 Running command git checkout -b merge_ci --track origin/merge_ci
00:33:07 Switched to a new branch 'merge_ci'
00:33:07 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:33:07 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit cd00e90a99db49965fa0194c58e37566bef214e3
00:33:07 Installing build dependencies: started
00:33:08 Installing build dependencies: finished with status 'done'
00:33:08 Getting requirements to build wheel: started
00:33:08 Getting requirements to build wheel: finished with status 'done'
00:33:08 Preparing metadata (pyproject.toml): started
00:33:09 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:09 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0)
00:33:09 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:33:09 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:33:09 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:33:09 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.1)
00:33:09 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)
00:33:09 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:33:09 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)
00:33:09 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4)
00:33:09 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:33:09 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)
00:33:09 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)
00:33:09 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)
00:33:09 Building wheels for collected packages: omero-cli-duplicate
00:33:09 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:33:09 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:33:09 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=bda7a20bb257ed7172bd56dc3b3836b30b78fb3fbb6a33c50061227216807dfc
00:33:09 Stored in directory: /tmp/pip-ephem-wheel-cache-zd6jccva/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:33:09 Successfully built omero-cli-duplicate
00:33:09 Installing collected packages: omero-cli-duplicate
00:33:09 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:33:09 + pip install omero-certificates
00:33:10 Collecting omero-certificates
00:33:10 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:33:10 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0)
00:33:10 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:33:10 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:33:10 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:33:10 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.1)
00:33:10 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)
00:33:10 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:33:10 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)
00:33:10 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4)
00:33:10 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:33:10 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)
00:33:10 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)
00:33:10 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)
00:33:10 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:33:10 Installing collected packages: omero-certificates
00:33:10 Successfully installed omero-certificates-0.4.0
00:33:10 + for x in *.tar.gz
00:33:10 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:33:10 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:33:10 Installing build dependencies: started
00:33:11 Installing build dependencies: finished with status 'done'
00:33:11 Getting requirements to build wheel: started
00:33:11 Getting requirements to build wheel: finished with status 'done'
00:33:11 Preparing metadata (pyproject.toml): started
00:33:11 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:11 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0)
00:33:11 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
00:33:11 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:33:11 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:33:11 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.1)
00:33:11 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)
00:33:11 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:33:11 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)
00:33:11 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4)
00:33:11 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:33:11 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)
00:33:11 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)
00:33:11 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)
00:33:11 Building wheels for collected packages: omero-dropbox
00:33:11 Building wheel for omero-dropbox (pyproject.toml): started
00:33:12 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:33:12 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=2da42de09c9e490b65e3e4f79e0180f67cebbd1cf381bdd09cb0f7ba9f901b8a
00:33:12 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:33:12 Successfully built omero-dropbox
00:33:12 Installing collected packages: omero-dropbox
00:33:12 Successfully installed omero-dropbox-5.7.1.dev0
00:33:12 + for x in *.tar.gz
00:33:12 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:33:12 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:33:12 Installing build dependencies: started
00:33:16 Installing build dependencies: finished with status 'done'
00:33:16 Getting requirements to build wheel: started
00:33:16 Getting requirements to build wheel: finished with status 'done'
00:33:16 Preparing metadata (pyproject.toml): started
00:33:16 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:16 Building wheels for collected packages: omero_marshal
00:33:16 Building wheel for omero_marshal (pyproject.toml): started
00:33:17 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:33:17 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=4e0019a412f179cab8beec17d9945ef53e31dd8323ebfe9146932e762059ffe1
00:33:17 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:33:17 Successfully built omero_marshal
00:33:17 Installing collected packages: omero_marshal
00:33:17 Successfully installed omero_marshal-0.9.1.dev0
00:33:17 + for x in *.tar.gz
00:33:17 + pip install -U omero_py-5.21.1.dev0.tar.gz
00:33:17 Processing ./omero_py-5.21.1.dev0.tar.gz
00:33:18 Installing build dependencies: started
00:33:18 Installing build dependencies: finished with status 'done'
00:33:18 Getting requirements to build wheel: started
00:33:19 Getting requirements to build wheel: finished with status 'done'
00:33:19 Preparing metadata (pyproject.toml): started
00:33:19 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:19 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20)
00:33:19 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4)
00:33:19 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0)
00:33:19 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.1)
00:33:19 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0)
00:33:19 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2)
00:33:19 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)
00:33:19 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4)
00:33:19 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0)
00:33:19 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)
00:33:19 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10)
00:33:19 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)
00:33:19 Building wheels for collected packages: omero-py
00:33:19 Building wheel for omero-py (pyproject.toml): started
00:33:20 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:33:20 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783499 sha256=2679685cdeb05379c8740cbecb9b7191ded97ad94e2b1e2d19fa8fafb1f615c6
00:33:20 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d
00:33:20 Successfully built omero-py
00:33:20 Installing collected packages: omero-py
00:33:20 Attempting uninstall: omero-py
00:33:20 Found existing installation: omero-py 5.21.0
00:33:20 Uninstalling omero-py-5.21.0:
00:33:21 Successfully uninstalled omero-py-5.21.0
00:33:23 Successfully installed omero-py-5.21.1.dev0
00:33:23 + for x in *.tar.gz
00:33:23 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:33:23 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:33:23 Installing build dependencies: started
00:33:24 Installing build dependencies: finished with status 'done'
00:33:24 Getting requirements to build wheel: started
00:33:24 Getting requirements to build wheel: finished with status 'done'
00:33:24 Preparing metadata (pyproject.toml): started
00:33:25 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:25 Building wheels for collected packages: omero-scripts
00:33:25 Building wheel for omero-scripts (pyproject.toml): started
00:33:25 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:33:25 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=7bb9a798b6a2bbc895f73c3a8edbdb64524240baca170f127e63dbaf272af11a
00:33:25 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:33:25 Successfully built omero-scripts
00:33:25 Installing collected packages: omero-scripts
00:33:25 Successfully installed omero-scripts-5.9.2.dev0
00:33:25 + for x in *.tar.gz
00:33:25 + pip install -U omero_web-5.29.2.dev0.tar.gz
00:33:25 Processing ./omero_web-5.29.2.dev0.tar.gz
00:33:26 Installing build dependencies: started
00:33:27 Installing build dependencies: finished with status 'done'
00:33:27 Getting requirements to build wheel: started
00:33:27 Getting requirements to build wheel: finished with status 'done'
00:33:27 Preparing metadata (pyproject.toml): started
00:33:27 Preparing metadata (pyproject.toml): finished with status 'done'
00:33:27 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)
00:33:27 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0)
00:33:27 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:33:27 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0)
00:33:27 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB)
00:33:28 Collecting django-pipeline (from omero-web==5.29.2.dev0)
00:33:28 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
00:33:28 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0)
00:33:28 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:33:28 Collecting django-csp (from omero-web==5.29.2.dev0)
00:33:28 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:33:28 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0)
00:33:28 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
00:33:28 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0)
00:33:28 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:33:28 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)
00:33:28 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.3.0)
00:33:28 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2)
00:33:28 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0)
00:33:28 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0)
00:33:28 Collecting importlib-resources (from omero-web==5.29.2.dev0)
00:33:28 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:33:28 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
00:33:28 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB)
00:33:28 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
00:33:28 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:33:28 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)
00:33:28 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)
00:33:28 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)
00:33:28 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)
00:33:28 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)
00:33:28 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)
00:33:28 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)
00:33:28 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1)
00:33:28 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0)
00:33:28 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:33:28 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)
00:33:28 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)
00:33:28 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)
00:33:28 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:33:28 Using cached django-4.2.23-py3-none-any.whl (8.0 MB)
00:33:28 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB)
00:33:28 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:33:28 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:33:28 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:33:28 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
00:33:28 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:33:28 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
00:33:28 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:33:28 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:33:28 Building wheels for collected packages: omero-web
00:33:28 Building wheel for omero-web (pyproject.toml): started
00:33:29 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:33:29 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=fb0521cb39b61845f9659c55a3c42484ef11a02941c9b6d3f05e4275964768d3
00:33:29 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c
00:33:29 Successfully built omero-web
00:33:29 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:33:32
00:33:32 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
00:33:32 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:33:32 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:33:32 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:33:32 --2025-07-15 00:33:32-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:33:32 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.110.133, ...
00:33:32 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
00:33:32 HTTP request sent, awaiting response... 200 OK
00:33:33 Length: 125072 (122K) [text/plain]
00:33:33 Saving to: ‘Figure_To_Pdf.py’
00:33:33
00:33:33 0K .......... .......... .......... .......... .......... 40% 3.91M 0s
00:33:33 50K .......... .......... .......... .......... .......... 81% 13.7M 0s
00:33:33 100K .......... .......... .. 100% 4.28M=0.02s
00:33:33
00:33:33 2025-07-15 00:33:33 (5.66 MB/s) - ‘Figure_To_Pdf.py’ saved [125072/125072]
00:33:33
00:33:33 + chmod 755 Figure_To_Pdf.py
00:33:33 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:33:33 + omero config set omero.db.name OMERO-server
00:33:34 + omero config set omero.db.host pg
00:33:35 + omero config set omero.db.user postgres
00:33:36 + omero config set omero.data.dir /home/omero/omero-server-data
00:33:38 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:33:39 + omero config set omero.db.poolsize 25
00:33:40 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:33:41 + omero config set omero.security.trustStorePassword changeit
00:33:43 + omero config set omero.mail.config true
00:33:44 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:33:45 + omero config set omero.mail.host smtp.dundee.ac.uk
00:33:46 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:33:48 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:33:49 + omero certificates
00:33:50 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:33:50 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:33:50 + '[' false = true ']'
00:33:50 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:33:50 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:33:50 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:33:50 2025-07-15 00:33:50,878 [ omego.db] DEBUG dbcommand => upgrade
00:33:50 2025-07-15 00:33:50,879 [ omego.db] DEBUG dbhost => localhost
00:33:50 2025-07-15 00:33:50,879 [ omego.db] DEBUG dbname => OMERO-server
00:33:50 2025-07-15 00:33:50,879 [ omego.db] DEBUG dbpass => omero
00:33:50 2025-07-15 00:33:50,879 [ omego.db] DEBUG dbuser => omero
00:33:50 2025-07-15 00:33:50,879 [ omego.db] DEBUG rootpass => omero
00:33:50 2025-07-15 00:33:50,879 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:33:50 2025-07-15 00:33:50,879 [omego.extern] INFO Executing : omero version
00:33:52 OMERO.py version:
00:33:52 OMERO.server version:
00:33:52 5.6.3-569-769e77f47c-ice36-b468
00:33:52 5.21.1.dev0
00:33:52 2025-07-15 00:33:52,225 [omego.extern] INFO Completed [1.346 s]
00:33:52 2025-07-15 00:33:52,226 [omego.extern] DEBUG Using omero CLI from omero
00:33:52 2025-07-15 00:33:52,226 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:33:52 2025-07-15 00:33:52,226 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:33:52 2025-07-15 00:33:52,226 [omego.extern] INFO Executing : omero config get --show-password
00:33:53 2025-07-15 00:33:53,468 [omego.extern] INFO Completed [1.242 s]
00:33:53 2025-07-15 00:33:53,468 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:33:53 2025-07-15 00:33:53,468 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:33:53 2025-07-15 00:33:53,474 [omego.extern] INFO Completed [0.006 s]
00:33:53 2025-07-15 00:33:53,475 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
00:33:53 2025-07-15 00:33:53,475 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
00:33:53
00:33:53 2025-07-15 00:33:53,475 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:33:53 2025-07-15 00:33:53,475 [omego.extern] INFO Executing : omero config get --show-password
00:33:54 2025-07-15 00:33:54,722 [omego.extern] INFO Completed [1.248 s]
00:33:54 2025-07-15 00:33:54,723 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:33:54 2025-07-15 00:33:54,723 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:33:54 2025-07-15 00:33:54,732 [omego.extern] INFO Completed [0.010 s]
00:33:54 2025-07-15 00:33:54,733 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.6") at port "5432".\n'
00:33:54 2025-07-15 00:33:54,733 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:33:54 2025-07-15 00:33:54,733 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:33:54 2025-07-15 00:33:54,733 [omego.extern] INFO Executing : omero config get --show-password
00:33:56 2025-07-15 00:33:56,026 [omego.extern] INFO Completed [1.293 s]
00:33:56 2025-07-15 00:33:56,026 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:33:56 2025-07-15 00:33:56,026 [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
00:33:56 2025-07-15 00:33:56,037 [omego.extern] INFO Completed [0.011 s]
00:33:56 2025-07-15 00:33:56,037 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:33:56 2025-07-15 00:33:56,037 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:33:56 2025-07-15 00:33:56,039 [ omego.db] INFO Database is already at OMERO5.4__0
00:33:56 + export LANG=en_US.UTF-8
00:33:56 + LANG=en_US.UTF-8
00:33:56 + export LANGUAGE=en_US:en
00:33:56 + LANGUAGE=en_US:en
00:33:56 + export LC_ALL=en_US.UTF-8
00:33:56 + LC_ALL=en_US.UTF-8
00:33:56 + BUILD_ID=DONT_KILL_ME
00:33:56 + omero admin start
00:34:00 No descriptor given. Using etc/grid/default.xml
00:34:08 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:34:08 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:34:08 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:34:08 Waiting on startup. Use CTRL-C to exit
00:34:09 + omero admin waitup
00:34:10 Waiting on startup. Use CTRL-C to exit
00:34:10 + omero admin diagnostics
00:34:12
00:34:12 ================================================================================
00:34:12 OMERO Diagnostics (admin)
00:34:12 ================================================================================
00:34:12
00:34:12 Commands: java -version 11.0.25 (/usr/bin/java)
00:34:12 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:34:12 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:34:12 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:34:12 Commands: psql --version 16.9 (/usr/bin/psql)
00:34:12 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:34:12
00:34:12 Component: OMERO.py 5.21.1.dev0
00:34:12 Component: OMERO.server 5.6.3-569-769e77f47c-ice36-b468
00:34:12
00:34:12 Server: icegridnode running
00:34:12 Server: Blitz-0 active (pid = 82771, enabled)
00:34:12 Server: Indexer-0 activating (enabled)
00:34:12 Server: OMERO.Glacier2 active (pid = 82799, enabled)
00:34:12 Server: OMERO.IceStorm active (pid = 82817, enabled)
00:34:12 Server: Processor-0 active (pid = 82829, enabled)
00:34:12 Server: Tables-0 active (pid = 82810, enabled)
00:34:12
00:34:12 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:34:12 Log files: Blitz-0.log 33.2 KB errors=0 warnings=1
00:34:12 Log files: DropBox.log n/a
00:34:12 Log files: FileServer.log n/a
00:34:12 Log files: Indexer-0.log 238 B
00:34:12 Log files: MonitorServer.log n/a
00:34:12 Log files: Processor-0.log 735 B
00:34:12 Log files: Tables-0.log 961 B
00:34:12 Log files: TestDropBox.log n/a
00:34:12 Log files: master.err empty
00:34:12 Log files: master.out 30.5 KB
00:34:12 Log files: Total size 0.07 MB
00:34:12
00:34:12
00:34:12 Environment:OMERO_HOME=(unset)
00:34:12 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:34:12 Environment:OMERO_NODE=(unset)
00:34:12 Environment:OMERO_MASTER=(unset)
00:34:12 Environment:OMERO_USERDIR=(unset)
00:34:12 Environment:OMERO_TMPDIR=(unset)
00:34:12 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
00:34:12 Environment:PYTHONPATH=(unset)
00:34:12 Environment:ICE_HOME=/opt/ice-3.6.5
00:34:12 Environment:LD_LIBRARY_PATH=(unset)
00:34:12 Environment:DYLD_LIBRARY_PATH=(unset)
00:34:12
00:34:12 OMERO SSL port:4064
00:34:12 OMERO TCP port:4063
00:34:12 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:34:12 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:34:12
00:34:12 JVM settings: Blitz-${index} -Xmx7200m
00:34:12 JVM settings: Indexer-${index} -Xmx4800m
00:34:12 JVM settings: PixelData-${index} -Xmx7200m
00:34:12 JVM settings: Repository-${index} -Xmx4800m
00:34:12
00:34:12 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 15 July 2025 06d4137dffb6ef8e5c0ce736f7bc87d39b0b6a6c
00:34:12 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 15 July 2025 06d4137dffb6ef8e5c0ce736f7bc87d39b0b6a6c
00:34:12 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 15 July 2025 06d4137dffb6ef8e5c0ce736f7bc87d39b0b6a6c
00:34:12 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 15 July 2025 5ce01a2723e21c56d93ef9809c360c4d366df71c
00:34:12 Jar: lib/server/ome-common.jar OME Common Java 6.0.27-SNAPSHOT 15 July 2025 5ce01a2723e21c56d93ef9809c360c4d366df71c
00:34:12 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 15 July 2025 5ce01a2723e21c56d93ef9809c360c4d366df71c
00:34:12 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 15 July 2025 5ce01a2723e21c56d93ef9809c360c4d366df71c
00:34:12 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 15 July 2025 5ce01a2723e21c56d93ef9809c360c4d366df71c
00:34:12 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 15 July 2025 5ce01a2723e21c56d93ef9809c360c4d366df71c
00:34:12 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:34:12 Jar: lib/server/omero-zarr-pixel-buffer-0.4.1.jar OMERO Zarr Pixel Buffer 0.4.1 7c2d45bab0b51137dada7abda144282d6dcc76e1
00:34:12 + deactivate
00:34:12 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:34:12 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:34:12 + export PATH
00:34:12 + unset _OLD_VIRTUAL_PATH
00:34:12 + '[' -n '' ']'
00:34:12 + hash -r
00:34:12 + '[' -n '' ']'
00:34:12 + unset VIRTUAL_ENV
00:34:12 + unset VIRTUAL_ENV_PROMPT
00:34:12 + '[' '!' '' = nondestructive ']'
00:34:12 + unset -f deactivate
00:34:12 Finished: SUCCESS
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