09:31:09 Started by upstream project "Trigger" build number 536
09:31:09 originally caused by:
09:31:09 Started by user devspace
09:31:09 Running as SYSTEM
09:31:09 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
09:31:10 [OMERO-server] $ /bin/bash -xe /tmp/jenkins2536948256922951385.sh
09:31:10 + source /home/settings.env
09:31:10 ++ OMERO_DB_HOST=pg
09:31:10 ++ OMERO_DB_USER=postgres
09:31:10 ++ OMERO_DB_PASS=
09:31:10 ++ OMERO_ROOT_PASS=omero
09:31:10 ++ OMERO_DATA_DIR=/OMERO
09:31:10 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:31:10 + OMERO_DB_NAME=OMERO-server
09:31:10 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:31:10 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:31:10 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:31:10 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:31:10 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
09:31:10 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:31:10 ++ deactivate nondestructive
09:31:10 ++ '[' -n '' ']'
09:31:10 ++ '[' -n '' ']'
09:31:10 ++ hash -r
09:31:10 ++ '[' -n '' ']'
09:31:10 ++ unset VIRTUAL_ENV
09:31:10 ++ unset VIRTUAL_ENV_PROMPT
09:31:10 ++ '[' '!' nondestructive = nondestructive ']'
09:31:10 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:31:10 ++ export VIRTUAL_ENV
09:31:10 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:31:10 ++ 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
09:31:10 ++ export PATH
09:31:10 ++ '[' -n '' ']'
09:31:10 ++ '[' -z '' ']'
09:31:10 ++ _OLD_VIRTUAL_PS1=
09:31:10 ++ PS1='(.venv3) '
09:31:10 ++ export PS1
09:31:10 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
09:31:10 ++ export VIRTUAL_ENV_PROMPT
09:31:10 ++ hash -r
09:31:10 + omero admin stop
09:31:11 Waiting on shutdown. Use CTRL-C to exit
09:31:11 .+ sleep 5
09:31:27 + deactivate
09:31:27 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:31:27 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:31:27 + export PATH
09:31:27 + unset _OLD_VIRTUAL_PATH
09:31:27 + '[' -n '' ']'
09:31:27 + hash -r
09:31:27 + '[' -n '' ']'
09:31:27 + unset VIRTUAL_ENV
09:31:27 + unset VIRTUAL_ENV_PROMPT
09:31:27 + '[' '!' '' = nondestructive ']'
09:31:27 + unset -f deactivate
09:31:27 + rm -rf /home/omero/workspace/OMERO-server/.venv3
09:31:28 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
09:31:32 + '[' false = true ']'
09:31:32 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
09:31:32 Skipping PURGE_DATA:CleanDbAndRepo
09:31:32 + 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
09:31:35 Copied 1 artifact from "OMERO-build" build number 451
09:31:35 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 444
09:31:35 Copied 2 artifacts from "OMERO-build-build" build number 474
09:31:35 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11228085230033417595.sh
09:31:35 + source /home/settings.env
09:31:35 ++ OMERO_DB_HOST=pg
09:31:35 ++ OMERO_DB_USER=postgres
09:31:35 ++ OMERO_DB_PASS=
09:31:35 ++ OMERO_ROOT_PASS=omero
09:31:35 ++ OMERO_DATA_DIR=/OMERO
09:31:35 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:31:35 + OMERO_DB_NAME=OMERO-server
09:31:35 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:31:35 + mkdir -p /home/omero/omero-server-data
09:31:35 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:31:35 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:31:35 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:31:35 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:31:35 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:31:35 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:31:35 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:31:35 ++ ls OMERO.server-5.6.3-569-4523d266fe-ice36-b451.zip
09:31:35 + ZIP=OMERO.server-5.6.3-569-4523d266fe-ice36-b451.zip
09:31:35 + '[' '!' -z '' ']'
09:31:35 + DIST=OMERO.server-5.6.3-569-4523d266fe-ice36-b451
09:31:35 + unzip OMERO.server-5.6.3-569-4523d266fe-ice36-b451.zip
09:31:35 Archive: OMERO.server-5.6.3-569-4523d266fe-ice36-b451.zip
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/blitz/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/grid/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/profiles/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/error/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/grid/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/luts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/luts/janelia/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/luts/matplotlib/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/luts/ncsa_paledit/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/luts/seaborn/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/luts/wcif/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/analysis_scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/annotation_scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/export_scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/figure_scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/import_scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/scripts/omero/util_scripts/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/server/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/share/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/share/licenses/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/misc/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__1/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__10/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__11/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__2/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__3/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__4/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__5/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__6/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__7/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__8/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3A__9/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3__4/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3__5/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3__6/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO3__7/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO4.1__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO4.2__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO4.2__0/t/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO4.3__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO4.4__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO4__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.0__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.1__1/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.2__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.3__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4DEV__1/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4DEV__2/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4DEV__3/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/
09:31:35 creating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/var/
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/LICENSE.txt
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/backup.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/blitz/mail-senders.example
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/blitz/mail-server.example
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/build.properties
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/env.bat
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/env.sh
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/hibernate.properties
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/ice.config
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/logback-cli.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/logback-indexing-cli.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/logback-indexing.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/logback.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/mime.types
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/node1.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/node2.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/omero.properties
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/profiles/psql
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/rollover.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/Windows.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/error/maintainance.html
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/grid/README
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/grid/default.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/grid/templates.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/grid/windefault.xml
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/ice.config
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/internal.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/master.cfg
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/templates/robot.template
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/etc/testdropbox.config
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/history.rst
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/OMEZarrReader.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/accessors-smart.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/activation.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/aggdesigner-algorithm.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/aircompressor.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/antlr.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/aopalliance.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/apiguardian-api.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/asm.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/avatica-core.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/avatica-metrics.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/aws-java-sdk-core.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/aws-java-sdk-kms.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/aws-java-sdk-s3.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/base.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-anim.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-awt-util.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-bridge.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-codec.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-constants.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-css.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-dom.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-ext.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-gvt.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-i18n.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-parser.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-script.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-shared-resources.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-svg-dom.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-svggen.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-transcoder.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-util.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/batik-xml.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/btm.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/calcite-core.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/calcite-linq4j.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/cdm-core.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/checker-qual.jar
09:31:35 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/lib/client/commons-beanutils.jar
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09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/psql-footer.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/psql-header.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/schema.sql
09:31:37 inflating: OMERO.server-5.6.3-569-4523d266fe-ice36-b451/sql/psql/OMERO5.4__0/views.sql
09:31:37 + rm -f OMERO.server-5.6.3-569-4523d266fe-ice36-b451.zip
09:31:37 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-569-4523d266fe-ice36-b451 /home/omero/workspace/OMERO-server/OMERO.server
09:31:37 + 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
09:31:37 --2025-06-26 09:31:37-- 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
09:31:38 Resolving artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)... 67.205.169.144, 2604:a880:400:d0::19b7:6001
09:31:38 Connecting to artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)|67.205.169.144|:443... connected.
09:31:38 HTTP request sent, awaiting response... 200 OK
09:31:39 Length: 26159 (26K) [application/java-archive]
09:31:39 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’
09:31:39
09:31:39 0K .......... .......... ..... 100% 129M=0s
09:31:39
09:31:39 2025-06-26 09:31:39 (129 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’ saved [26159/26159]
09:31:39
09:31:39 + 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
09:31:39 --2025-06-26 09:31:39-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
09:31:39 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
09:31:39 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
09:31:39 HTTP request sent, awaiting response... 200 OK
09:31:39 Length: 889211 (868K) [application/java-archive]
09:31:39 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
09:31:39
09:31:39 0K .......... .......... .......... .......... .......... 5% 3.76M 0s
09:31:39 50K .......... .......... .......... .......... .......... 11% 11.4M 0s
09:31:39 100K .......... .......... .......... .......... .......... 17% 7.80M 0s
09:31:39 150K .......... .......... .......... .......... .......... 23% 27.2M 0s
09:31:39 200K .......... .......... .......... .......... .......... 28% 7.74M 0s
09:31:39 250K .......... .......... .......... .......... .......... 34% 34.0M 0s
09:31:39 300K .......... .......... .......... .......... .......... 40% 52.0M 0s
09:31:39 350K .......... .......... .......... .......... .......... 46% 35.8M 0s
09:31:39 400K .......... .......... .......... .......... .......... 51% 77.3M 0s
09:31:39 450K .......... .......... .......... .......... .......... 57% 7.81M 0s
09:31:39 500K .......... .......... .......... .......... .......... 63% 21.3M 0s
09:31:39 550K .......... .......... .......... .......... .......... 69% 104M 0s
09:31:39 600K .......... .......... .......... .......... .......... 74% 45.2M 0s
09:31:39 650K .......... .......... .......... .......... .......... 80% 28.4M 0s
09:31:39 700K .......... .......... .......... .......... .......... 86% 9.05M 0s
09:31:39 750K .......... .......... .......... .......... .......... 92% 25.9M 0s
09:31:39 800K .......... .......... .......... .......... .......... 97% 38.1M 0s
09:31:39 850K .......... ........ 100% 178M=0.06s
09:31:39
09:31:39 2025-06-26 09:31:39 (15.0 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
09:31:39
09:31:39 + 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
09:31:39 --2025-06-26 09:31:39-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
09:31:39 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
09:31:39 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
09:31:39 HTTP request sent, awaiting response... 200 OK
09:31:39 Length: 73309 (72K) [application/java-archive]
09:31:39 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
09:31:39
09:31:39 0K .......... .......... .......... .......... .......... 69% 3.55M 0s
09:31:39 50K .......... .......... . 100% 25.2M=0.01s
09:31:39
09:31:39 2025-06-26 09:31:39 (4.79 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
09:31:39
09:31:39 + 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
09:31:39 --2025-06-26 09:31:39-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
09:31:39 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
09:31:39 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
09:31:39 HTTP request sent, awaiting response... 200 OK
09:31:39 Length: 63303 (62K) [application/java-archive]
09:31:39 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
09:31:39
09:31:39 0K .......... .......... .......... .......... .......... 80% 3.83M 0s
09:31:39 50K .......... . 100% 16.4M=0.01s
09:31:39
09:31:39 2025-06-26 09:31:39 (4.49 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
09:31:39
09:31:39 + 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
09:31:39 --2025-06-26 09:31:39-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
09:31:39 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
09:31:39 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
09:31:39 HTTP request sent, awaiting response... 200 OK
09:31:40 Length: 1271272 (1.2M) [application/java-archive]
09:31:40 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
09:31:40
09:31:40 0K .......... .......... .......... .......... .......... 4% 3.89M 0s
09:31:40 50K .......... .......... .......... .......... .......... 8% 5.44M 0s
09:31:40 100K .......... .......... .......... .......... .......... 12% 21.5M 0s
09:31:40 150K .......... .......... .......... .......... .......... 16% 21.0M 0s
09:31:40 200K .......... .......... .......... .......... .......... 20% 7.76M 0s
09:31:40 250K .......... .......... .......... .......... .......... 24% 27.9M 0s
09:31:40 300K .......... .......... .......... .......... .......... 28% 104M 0s
09:31:40 350K .......... .......... .......... .......... .......... 32% 28.9M 0s
09:31:40 400K .......... .......... .......... .......... .......... 36% 41.8M 0s
09:31:40 450K .......... .......... .......... .......... .......... 40% 8.14M 0s
09:31:40 500K .......... .......... .......... .......... .......... 44% 30.9M 0s
09:31:40 550K .......... .......... .......... .......... .......... 48% 31.6M 0s
09:31:40 600K .......... .......... .......... .......... .......... 52% 151M 0s
09:31:40 650K .......... .......... .......... .......... .......... 56% 31.1M 0s
09:31:40 700K .......... .......... .......... .......... .......... 60% 8.64M 0s
09:31:40 750K .......... .......... .......... .......... .......... 64% 33.6M 0s
09:31:40 800K .......... .......... .......... .......... .......... 68% 32.3M 0s
09:31:40 850K .......... .......... .......... .......... .......... 72% 87.8M 0s
09:31:40 900K .......... .......... .......... .......... .......... 76% 28.4M 0s
09:31:40 950K .......... .......... .......... .......... .......... 80% 9.25M 0s
09:31:40 1000K .......... .......... .......... .......... .......... 84% 35.5M 0s
09:31:40 1050K .......... .......... .......... .......... .......... 88% 94.9M 0s
09:31:40 1100K .......... .......... .......... .......... .......... 92% 30.5M 0s
09:31:40 1150K .......... .......... .......... .......... .......... 96% 28.1M 0s
09:31:40 1200K .......... .......... .......... .......... . 100% 10.4M=0.07s
09:31:40
09:31:40 2025-06-26 09:31:40 (16.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
09:31:40
09:31:40 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:31:40 ++ deactivate nondestructive
09:31:40 ++ '[' -n '' ']'
09:31:40 ++ '[' -n '' ']'
09:31:40 ++ hash -r
09:31:40 ++ '[' -n '' ']'
09:31:40 ++ unset VIRTUAL_ENV
09:31:40 ++ unset VIRTUAL_ENV_PROMPT
09:31:40 ++ '[' '!' nondestructive = nondestructive ']'
09:31:40 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:31:40 ++ export VIRTUAL_ENV
09:31:40 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:31:40 ++ 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
09:31:40 ++ export PATH
09:31:40 ++ '[' -n '' ']'
09:31:40 ++ '[' -z '' ']'
09:31:40 ++ _OLD_VIRTUAL_PS1=
09:31:40 ++ PS1='(.venv3) '
09:31:40 ++ export PS1
09:31:40 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
09:31:40 ++ export VIRTUAL_ENV_PROMPT
09:31:40 ++ hash -r
09:31:40 + pip install -U pip
09:31:40 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
09:31:40 Collecting pip
09:31:40 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
09:31:40 Installing collected packages: pip
09:31:40 Attempting uninstall: pip
09:31:40 Found existing installation: pip 22.3.1
09:31:40 Uninstalling pip-22.3.1:
09:31:40 Successfully uninstalled pip-22.3.1
09:31:41 Successfully installed pip-25.1.1
09:31:41 WARNING: There was an error checking the latest version of pip.
09:31:41 + 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
09:31:42 Collecting zeroc-ice==3.6.5
09:31:43 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)
09:31:46 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 12.7 MB/s eta 0:00:00
09:31:46 Installing collected packages: zeroc-ice
09:31:46 Successfully installed zeroc-ice-3.6.5
09:31:47 + pip install markdown
09:31:47 Collecting markdown
09:31:47 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB)
09:31:47 Using cached markdown-3.8.2-py3-none-any.whl (106 kB)
09:31:47 Installing collected packages: markdown
09:31:47 Successfully installed markdown-3.8.2
09:31:47 + pip install reportlab
09:31:48 Collecting reportlab
09:31:48 Using cached reportlab-4.4.2-py3-none-any.whl.metadata (1.8 kB)
09:31:48 Collecting pillow>=9.0.0 (from reportlab)
09:31:48 Using cached pillow-11.2.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (8.9 kB)
09:31:48 Collecting charset-normalizer (from reportlab)
09:31:48 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
09:31:49 Using cached reportlab-4.4.2-py3-none-any.whl (2.0 MB)
09:31:49 Using cached pillow-11.2.1-cp311-cp311-manylinux_2_28_x86_64.whl (4.6 MB)
09:31:49 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
09:31:49 Installing collected packages: pillow, charset-normalizer, reportlab
09:31:50
09:31:50 Successfully installed charset-normalizer-3.4.2 pillow-11.2.1 reportlab-4.4.2
09:31:50 + pip install pyarrow
09:31:51 Collecting pyarrow
09:31:51 Using cached pyarrow-20.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
09:31:51 Using cached pyarrow-20.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.3 MB)
09:31:51 Installing collected packages: pyarrow
09:31:52 Successfully installed pyarrow-20.0.0
09:31:52 + pip install omego
09:31:53 Collecting omego
09:31:53 Using cached omego-0.7.0-py3-none-any.whl
09:31:53 Collecting future (from omego)
09:31:53 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
09:31:53 Collecting yaclifw>=0.1.1 (from omego)
09:31:53 Using cached yaclifw-0.2.0-py3-none-any.whl
09:31:53 Collecting six (from yaclifw>=0.1.1->omego)
09:31:53 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
09:31:53 Using cached future-1.0.0-py3-none-any.whl (491 kB)
09:31:53 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
09:31:53 Installing collected packages: six, future, yaclifw, omego
09:31:54
09:31:54 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
09:31:54 + pip install tables
09:31:54 Collecting tables
09:31:54 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
09:31:55 Collecting numpy>=1.20.0 (from tables)
09:31:55 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (62 kB)
09:31:55 Collecting numexpr>=2.6.2 (from tables)
09:31:55 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
09:31:55 Collecting packaging (from tables)
09:31:55 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
09:31:55 Collecting py-cpuinfo (from tables)
09:31:55 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
09:31:55 Collecting blosc2>=2.3.0 (from tables)
09:31:55 Downloading blosc2-3.5.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.9 kB)
09:31:56 Collecting typing-extensions>=4.4.0 (from tables)
09:31:56 Using cached typing_extensions-4.14.0-py3-none-any.whl.metadata (3.0 kB)
09:31:56 Collecting ndindex (from blosc2>=2.3.0->tables)
09:31:56 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
09:31:56 Collecting msgpack (from blosc2>=2.3.0->tables)
09:31:56 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
09:31:56 Collecting platformdirs (from blosc2>=2.3.0->tables)
09:31:56 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
09:31:56 Collecting requests (from blosc2>=2.3.0->tables)
09:31:56 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)
09:31:56 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2)
09:31:56 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
09:31:56 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
09:31:56 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
09:31:56 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
09:31:56 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
09:31:56 Using cached certifi-2025.6.15-py3-none-any.whl.metadata (2.4 kB)
09:31:56 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
09:31:56 Downloading blosc2-3.5.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB)
09:32:01 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.4/4.4 MB 1.0 MB/s eta 0:00:00
09:32:01 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB)
09:32:01 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl (16.9 MB)
09:32:01 Using cached typing_extensions-4.14.0-py3-none-any.whl (43 kB)
09:32:01 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
09:32:01 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
09:32:01 Using cached packaging-25.0-py3-none-any.whl (66 kB)
09:32:01 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
09:32:01 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
09:32:01 Using cached requests-2.32.4-py3-none-any.whl (64 kB)
09:32:01 Using cached idna-3.10-py3-none-any.whl (70 kB)
09:32:02 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
09:32:02 Using cached certifi-2025.6.15-py3-none-any.whl (157 kB)
09:32:02 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
09:32:05
09:32:05 Successfully installed blosc2-3.5.0 certifi-2025.6.15 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-4.14.0 urllib3-2.5.0
09:32:05 + pip install jinja2
09:32:06 Collecting jinja2
09:32:06 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
09:32:06 Collecting MarkupSafe>=2.0 (from jinja2)
09:32:06 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
09:32:06 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
09:32:06 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
09:32:06 Installing collected packages: MarkupSafe, jinja2
09:32:06
09:32:06 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
09:32:06 + pip install omero-py
09:32:07 Collecting omero-py
09:32:07 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB)
09:32:07 Collecting urllib3<2 (from omero-py)
09:32:07 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
09:32:07 Collecting appdirs (from omero-py)
09:32:07 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
09:32:07 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
09:32:07 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.1)
09:32:07 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.2.1)
09:32:07 Collecting PyYAML (from omero-py)
09:32:07 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
09:32:07 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
09:32:07 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4)
09:32:07 Collecting portalocker (from omero-py)
09:32:07 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
09:32:07 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
09:32:07 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
09:32:07 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.6.15)
09:32:07 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB)
09:32:07 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
09:32:07 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
09:32:07 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
09:32:07 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
09:32:07 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, omero-py
09:32:07 Attempting uninstall: urllib3
09:32:07 Found existing installation: urllib3 2.5.0
09:32:07 Uninstalling urllib3-2.5.0:
09:32:07 Successfully uninstalled urllib3-2.5.0
09:32:10
09:32:10 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20
09:32:10 + pip install git+https://github.com/dominikl/omero-cli-zarr.git@extinfo#egg=omero-cli-zarr
09:32:11 Collecting omero-cli-zarr
09:32:11 Cloning https://github.com/dominikl/omero-cli-zarr.git (to revision extinfo) to /tmp/pip-install-52ea8we4/omero-cli-zarr_8d290d2994f64bff96307295e5d92d43
09:32:11 Running command git clone --filter=blob:none --quiet https://github.com/dominikl/omero-cli-zarr.git /tmp/pip-install-52ea8we4/omero-cli-zarr_8d290d2994f64bff96307295e5d92d43
09:32:12 Running command git checkout -b extinfo --track origin/extinfo
09:32:12 Switched to a new branch 'extinfo'
09:32:12 branch 'extinfo' set up to track 'origin/extinfo'.
09:32:12 Resolved https://github.com/dominikl/omero-cli-zarr.git to commit 38b38f9e1ebaab0a72ed370fc9378d86f2d9b2e8
09:32:12 Installing build dependencies: started
09:32:13 Installing build dependencies: finished with status 'done'
09:32:13 Getting requirements to build wheel: started
09:32:14 Getting requirements to build wheel: finished with status 'done'
09:32:14 Installing backend dependencies: started
09:32:15 Installing backend dependencies: finished with status 'done'
09:32:15 Preparing metadata (pyproject.toml): started
09:32:15 Preparing metadata (pyproject.toml): finished with status 'done'
09:32:15 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.21.0)
09:32:15 Collecting ome-zarr>=0.5.0 (from omero-cli-zarr)
09:32:15 Using cached ome_zarr-0.11.1-py3-none-any.whl.metadata (2.9 kB)
09:32:15 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.5.0->omero-cli-zarr) (2.3.1)
09:32:15 Collecting dask (from ome-zarr>=0.5.0->omero-cli-zarr)
09:32:15 Using cached dask-2025.5.1-py3-none-any.whl.metadata (3.8 kB)
09:32:15 Collecting zarr<3,>=2.8.1 (from ome-zarr>=0.5.0->omero-cli-zarr)
09:32:15 Using cached zarr-2.18.7-py3-none-any.whl.metadata (5.8 kB)
09:32:15 Collecting fsspec!=2021.07.0,!=2023.9.0,>=0.8 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:15 Using cached fsspec-2025.5.1-py3-none-any.whl.metadata (11 kB)
09:32:16 Collecting aiohttp<4 (from ome-zarr>=0.5.0->omero-cli-zarr)
09:32:16 Using cached aiohttp-3.12.13-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.6 kB)
09:32:16 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.5.0->omero-cli-zarr) (2.32.4)
09:32:16 Collecting scikit-image (from ome-zarr>=0.5.0->omero-cli-zarr)
09:32:16 Using cached scikit_image-0.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
09:32:16 Collecting toolz (from ome-zarr>=0.5.0->omero-cli-zarr)
09:32:16 Using cached toolz-1.0.0-py3-none-any.whl.metadata (5.1 kB)
09:32:16 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:16 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
09:32:17 Collecting aiosignal>=1.1.2 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:17 Using cached aiosignal-1.3.2-py2.py3-none-any.whl.metadata (3.8 kB)
09:32:17 Collecting attrs>=17.3.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:17 Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)
09:32:17 Collecting frozenlist>=1.1.1 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:17 Using cached frozenlist-1.7.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
09:32:17 Collecting multidict<7.0,>=4.5 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:17 Downloading multidict-6.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
09:32:18 Collecting propcache>=0.2.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
09:32:18 Collecting yarl<2.0,>=1.17.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB)
09:32:18 Requirement already satisfied: idna>=2.0 in ./.venv3/lib64/python3.11/site-packages (from yarl<2.0,>=1.17.0->aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr) (3.10)
09:32:18 Collecting asciitree (from zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached asciitree-0.3.3-py3-none-any.whl
09:32:18 Collecting fasteners (from zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached fasteners-0.19-py3-none-any.whl.metadata (4.9 kB)
09:32:18 Collecting numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0 (from zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached numcodecs-0.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB)
09:32:18 Collecting deprecated (from numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0->zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB)
09:32:18 Collecting s3fs (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached s3fs-2025.5.1-py3-none-any.whl.metadata (1.9 kB)
09:32:18 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.26.20)
09:32:18 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
09:32:18 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.0.0)
09:32:18 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (11.2.1)
09:32:18 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (6.0.2)
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09:32:18 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (3.2.0)
09:32:18 Collecting click>=8.1 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:18 Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB)
09:32:19 Collecting cloudpickle>=3.0.0 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached cloudpickle-3.1.1-py3-none-any.whl.metadata (7.1 kB)
09:32:19 Requirement already satisfied: packaging>=20.0 in ./.venv3/lib64/python3.11/site-packages (from dask->ome-zarr>=0.5.0->omero-cli-zarr) (25.0)
09:32:19 Collecting partd>=1.4.0 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
09:32:19 Collecting importlib_metadata>=4.13.0 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached importlib_metadata-8.7.0-py3-none-any.whl.metadata (4.8 kB)
09:32:19 Collecting zipp>=3.20 (from importlib_metadata>=4.13.0->dask->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached zipp-3.23.0-py3-none-any.whl.metadata (3.6 kB)
09:32:19 Collecting locket (from partd>=1.4.0->dask->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
09:32:19 Collecting wrapt<2,>=1.10 (from deprecated->numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0->zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 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)
09:32:19 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.5.0->omero-cli-zarr) (3.4.2)
09:32:19 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.5.0->omero-cli-zarr) (2025.6.15)
09:32:19 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached aiobotocore-2.23.0-py3-none-any.whl.metadata (24 kB)
09:32:19 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:19 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
09:32:19 Collecting botocore<1.38.28,>=1.38.23 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:20 Using cached botocore-1.38.27-py3-none-any.whl.metadata (5.7 kB)
09:32:20 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:20 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
09:32:20 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:20 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
09:32:20 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr) (1.17.0)
09:32:20 Collecting scipy>=1.11.4 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:20 Using cached scipy-1.16.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (61 kB)
09:32:20 Collecting networkx>=3.0 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:20 Using cached networkx-3.5-py3-none-any.whl.metadata (6.3 kB)
09:32:20 Collecting imageio!=2.35.0,>=2.33 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
09:32:20 Using cached imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB)
09:32:20 Collecting tifffile>=2022.8.12 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
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09:32:20 Collecting lazy-loader>=0.4 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
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09:32:21 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (348 kB)
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09:32:22 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
09:32:22 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
09:32:22 Using cached scikit_image-0.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.8 MB)
09:32:22 Using cached imageio-2.37.0-py3-none-any.whl (315 kB)
09:32:22 Using cached lazy_loader-0.4-py3-none-any.whl (12 kB)
09:32:22 Using cached networkx-3.5-py3-none-any.whl (2.0 MB)
09:32:22 Using cached scipy-1.16.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (35.3 MB)
09:32:23 Using cached tifffile-2025.6.11-py3-none-any.whl (230 kB)
09:32:23 Building wheels for collected packages: omero-cli-zarr
09:32:23 Building wheel for omero-cli-zarr (pyproject.toml): started
09:32:23 Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
09:32:23 Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.0.2.dev452+g38b38f9-py3-none-any.whl size=31066 sha256=a79a35f4c0f4450a075327a4536f17a04afcde59c264f77ef0428acb71aac244
09:32:23 Stored in directory: /tmp/pip-ephem-wheel-cache-we08czun/wheels/dd/b9/0c/0415f7fe907b9498563db54fc83efe934b62c0a5e710ef7b23
09:32:23 Successfully built omero-cli-zarr
09:32:23 Installing collected packages: asciitree, zipp, wrapt, toolz, tifffile, scipy, python-dateutil, propcache, networkx, multidict, locket, lazy-loader, jmespath, imageio, fsspec, frozenlist, fasteners, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, yarl, scikit-image, partd, importlib_metadata, deprecated, botocore, aiosignal, numcodecs, dask, aiohttp, zarr, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
09:32:35
09:32:35 Successfully installed aiobotocore-2.23.0 aiohappyeyeballs-2.6.1 aiohttp-3.12.13 aioitertools-0.12.0 aiosignal-1.3.2 asciitree-0.3.3 attrs-25.3.0 botocore-1.38.27 click-8.2.1 cloudpickle-3.1.1 dask-2025.5.1 deprecated-1.2.18 fasteners-0.19 frozenlist-1.7.0 fsspec-2025.5.1 imageio-2.37.0 importlib_metadata-8.7.0 jmespath-1.0.1 lazy-loader-0.4 locket-1.0.0 multidict-6.5.1 networkx-3.5 numcodecs-0.15.1 ome-zarr-0.11.1 omero-cli-zarr-0.0.2.dev452+g38b38f9 partd-1.4.2 propcache-0.3.2 python-dateutil-2.9.0.post0 s3fs-2025.5.1 scikit-image-0.25.2 scipy-1.16.0 tifffile-2025.6.11 toolz-1.0.0 wrapt-1.17.2 yarl-1.20.1 zarr-2.18.7 zipp-3.23.0
09:32:35 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
09:32:36 Collecting omero-metadata
09:32:36 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-fklgbl8n/omero-metadata_74365dde60074d0780dab6b12f8b44e4
09:32:36 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-fklgbl8n/omero-metadata_74365dde60074d0780dab6b12f8b44e4
09:32:37 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 0ddde71ff2818e06ad511cb63b9d0b1059ebce68
09:32:37 Installing build dependencies: started
09:32:38 Installing build dependencies: finished with status 'done'
09:32:38 Getting requirements to build wheel: started
09:32:38 Getting requirements to build wheel: finished with status 'done'
09:32:38 Preparing metadata (pyproject.toml): started
09:32:38 Preparing metadata (pyproject.toml): finished with status 'done'
09:32:38 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0)
09:32:38 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
09:32:38 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
09:32:38 Collecting pandas (from omero-metadata)
09:32:38 Using cached pandas-2.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
09:32:38 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
09:32:38 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
09:32:38 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
09:32:38 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.1)
09:32:38 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (11.2.1)
09:32:38 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)
09:32:38 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4)
09:32:38 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
09:32:38 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
09:32:38 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
09:32:38 Collecting pytz>=2020.1 (from pandas->omero-metadata)
09:32:38 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
09:32:39 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
09:32:39 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
09:32:39 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)
09:32:39 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)
09:32:39 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)
09:32:39 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.6.15)
09:32:39 Using cached pandas-2.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
09:32:39 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
09:32:39 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
09:32:39 Building wheels for collected packages: omero-metadata
09:32:39 Building wheel for omero-metadata (pyproject.toml): started
09:32:39 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
09:32:39 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=f724e521995f8a853f5f1c7ac8fecbd49fdd10055936842e4369a922dbed5a57
09:32:39 Stored in directory: /tmp/pip-ephem-wheel-cache-qmcd5ykb/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
09:32:39 Successfully built omero-metadata
09:32:39 Installing collected packages: pytz, tzdata, pandas, omero-metadata
09:32:45
09:32:45 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.0 pytz-2025.2 tzdata-2025.2
09:32:45 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
09:32:45 Collecting omero-cli-render
09:32:45 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-yq4q8ys2/omero-cli-render_866938dae17c4838b11cb6bb08e4ed94
09:32:45 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-yq4q8ys2/omero-cli-render_866938dae17c4838b11cb6bb08e4ed94
09:32:46 Running command git checkout -b merge_ci --track origin/merge_ci
09:32:46 Switched to a new branch 'merge_ci'
09:32:46 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:32:46 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 91963d51fe538f97773d9d7422cb8001e2da8706
09:32:46 Installing build dependencies: started
09:32:47 Installing build dependencies: finished with status 'done'
09:32:47 Getting requirements to build wheel: started
09:32:47 Getting requirements to build wheel: finished with status 'done'
09:32:47 Preparing metadata (pyproject.toml): started
09:32:48 Preparing metadata (pyproject.toml): finished with status 'done'
09:32:48 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
09:32:48 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0)
09:32:48 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
09:32:48 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
09:32:48 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
09:32:48 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.1)
09:32:48 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.2.1)
09:32:48 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)
09:32:48 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4)
09:32:48 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
09:32:48 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)
09:32:48 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)
09:32:48 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.6.15)
09:32:48 Building wheels for collected packages: omero-cli-render
09:32:48 Building wheel for omero-cli-render (pyproject.toml): started
09:32:48 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
09:32:48 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=6e79fc2a59cb9e98956a96f6f4afed9cd30b9d1de6d282277c595a18adb30379
09:32:48 Stored in directory: /tmp/pip-ephem-wheel-cache-6t7cny8w/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
09:32:48 Successfully built omero-cli-render
09:32:48 Installing collected packages: omero-cli-render
09:32:48 Successfully installed omero-cli-render-0.8.2.dev0
09:32:48 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
09:32:49 Collecting omero-cli-duplicate
09:32:49 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-01msjlaz/omero-cli-duplicate_9688d1aebfe6412fb2779dfef6d7c888
09:32:49 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-01msjlaz/omero-cli-duplicate_9688d1aebfe6412fb2779dfef6d7c888
09:32:49 Running command git checkout -b merge_ci --track origin/merge_ci
09:32:50 Switched to a new branch 'merge_ci'
09:32:50 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:32:50 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 6149ec18cbf85a2e89d336a49ad9d971c345112a
09:32:50 Installing build dependencies: started
09:32:51 Installing build dependencies: finished with status 'done'
09:32:51 Getting requirements to build wheel: started
09:32:51 Getting requirements to build wheel: finished with status 'done'
09:32:51 Preparing metadata (pyproject.toml): started
09:32:51 Preparing metadata (pyproject.toml): finished with status 'done'
09:32:51 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0)
09:32:51 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
09:32:51 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
09:32:51 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
09:32:51 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.1)
09:32:51 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.2.1)
09:32:51 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
09:32:51 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)
09:32:51 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4)
09:32:51 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
09:32:51 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)
09:32:51 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)
09:32:51 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.6.15)
09:32:51 Building wheels for collected packages: omero-cli-duplicate
09:32:51 Building wheel for omero-cli-duplicate (pyproject.toml): started
09:32:51 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
09:32:51 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=8b48774228d7bb1993084beb2e5cb6bc830ab9cb0758ffc8cc7a9a2e140e7f78
09:32:51 Stored in directory: /tmp/pip-ephem-wheel-cache-w1ydkl1n/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
09:32:51 Successfully built omero-cli-duplicate
09:32:52 Installing collected packages: omero-cli-duplicate
09:32:52 Successfully installed omero-cli-duplicate-0.4.1.dev0
09:32:52 + pip install omero-certificates
09:32:52 Collecting omero-certificates
09:32:52 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
09:32:52 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0)
09:32:52 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
09:32:52 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
09:32:52 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
09:32:52 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.1)
09:32:52 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (11.2.1)
09:32:52 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
09:32:52 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)
09:32:52 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4)
09:32:52 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
09:32:52 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)
09:32:52 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)
09:32:52 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.6.15)
09:32:52 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
09:32:52 Installing collected packages: omero-certificates
09:32:52 Successfully installed omero-certificates-0.4.0
09:32:53 + for x in *.tar.gz
09:32:53 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
09:32:53 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
09:32:53 Installing build dependencies: started
09:32:54 Installing build dependencies: finished with status 'done'
09:32:54 Getting requirements to build wheel: started
09:32:54 Getting requirements to build wheel: finished with status 'done'
09:32:54 Preparing metadata (pyproject.toml): started
09:32:54 Preparing metadata (pyproject.toml): finished with status 'done'
09:32:54 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0)
09:32:54 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
09:32:54 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
09:32:54 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
09:32:54 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.1)
09:32:54 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.2.1)
09:32:54 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
09:32:54 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)
09:32:54 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4)
09:32:54 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
09:32:54 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)
09:32:54 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)
09:32:54 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.6.15)
09:32:54 Building wheels for collected packages: omero-dropbox
09:32:54 Building wheel for omero-dropbox (pyproject.toml): started
09:32:55 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
09:32:55 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=a44d3fd9343542373b75e153f0d11416d592c198bd029b53fecfeedf0e63163a
09:32:55 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
09:32:55 Successfully built omero-dropbox
09:32:55 Installing collected packages: omero-dropbox
09:32:55 Successfully installed omero-dropbox-5.7.1.dev0
09:32:55 + for x in *.tar.gz
09:32:55 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
09:32:55 Processing ./omero_marshal-0.9.1.dev0.tar.gz
09:32:55 Installing build dependencies: started
09:32:56 Installing build dependencies: finished with status 'done'
09:32:56 Getting requirements to build wheel: started
09:32:57 Getting requirements to build wheel: finished with status 'done'
09:32:57 Preparing metadata (pyproject.toml): started
09:32:57 Preparing metadata (pyproject.toml): finished with status 'done'
09:32:57 Building wheels for collected packages: omero_marshal
09:32:57 Building wheel for omero_marshal (pyproject.toml): started
09:32:57 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
09:32:57 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=9574f45849077d9ff27a30c5c36cbbaca4fd5bc001aa21a9e8a8515439fa3e8b
09:32:57 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
09:32:57 Successfully built omero_marshal
09:32:57 Installing collected packages: omero_marshal
09:32:58 Successfully installed omero_marshal-0.9.1.dev0
09:32:58 + for x in *.tar.gz
09:32:58 + pip install -U omero_py-5.21.1.dev0.tar.gz
09:32:58 Processing ./omero_py-5.21.1.dev0.tar.gz
09:32:58 Installing build dependencies: started
09:32:59 Installing build dependencies: finished with status 'done'
09:32:59 Getting requirements to build wheel: started
09:33:00 Getting requirements to build wheel: finished with status 'done'
09:33:00 Preparing metadata (pyproject.toml): started
09:33:00 Preparing metadata (pyproject.toml): finished with status 'done'
09:33:00 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20)
09:33:00 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4)
09:33:00 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0)
09:33:00 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.1)
09:33:00 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.2.1)
09:33:00 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2)
09:33:00 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)
09:33:00 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4)
09:33:00 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0)
09:33:00 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)
09:33:00 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10)
09:33:00 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.6.15)
09:33:00 Building wheels for collected packages: omero-py
09:33:00 Building wheel for omero-py (pyproject.toml): started
09:33:01 Building wheel for omero-py (pyproject.toml): finished with status 'done'
09:33:01 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783499 sha256=2e4557c27bc7dc56463def85163797c8ad97c6c766c1605e317deecc2d0761b8
09:33:01 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d
09:33:01 Successfully built omero-py
09:33:01 Installing collected packages: omero-py
09:33:01 Attempting uninstall: omero-py
09:33:01 Found existing installation: omero-py 5.21.0
09:33:01 Uninstalling omero-py-5.21.0:
09:33:02 Successfully uninstalled omero-py-5.21.0
09:33:04 Successfully installed omero-py-5.21.1.dev0
09:33:04 + for x in *.tar.gz
09:33:04 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
09:33:04 Processing ./omero_scripts-5.9.2.dev0.tar.gz
09:33:04 Installing build dependencies: started
09:33:05 Installing build dependencies: finished with status 'done'
09:33:05 Getting requirements to build wheel: started
09:33:06 Getting requirements to build wheel: finished with status 'done'
09:33:06 Preparing metadata (pyproject.toml): started
09:33:06 Preparing metadata (pyproject.toml): finished with status 'done'
09:33:06 Building wheels for collected packages: omero-scripts
09:33:06 Building wheel for omero-scripts (pyproject.toml): started
09:33:06 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
09:33:06 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=decaa6fde178990fe4b5ac996f5928129b6870601c16c6bed75746ea1b74634a
09:33:06 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
09:33:06 Successfully built omero-scripts
09:33:06 Installing collected packages: omero-scripts
09:33:06 Successfully installed omero-scripts-5.9.2.dev0
09:33:06 + for x in *.tar.gz
09:33:06 + pip install -U omero_web-5.29.2.dev0.tar.gz
09:33:07 Processing ./omero_web-5.29.2.dev0.tar.gz
09:33:07 Installing build dependencies: started
09:33:08 Installing build dependencies: finished with status 'done'
09:33:08 Getting requirements to build wheel: started
09:33:08 Getting requirements to build wheel: finished with status 'done'
09:33:08 Preparing metadata (pyproject.toml): started
09:33:09 Preparing metadata (pyproject.toml): finished with status 'done'
09:33:09 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)
09:33:09 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0)
09:33:09 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
09:33:09 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0)
09:33:09 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB)
09:33:09 Collecting django-pipeline (from omero-web==5.29.2.dev0)
09:33:09 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
09:33:09 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0)
09:33:09 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
09:33:09 Collecting django-csp (from omero-web==5.29.2.dev0)
09:33:09 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
09:33:09 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0)
09:33:09 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
09:33:09 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0)
09:33:09 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
09:33:09 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)
09:33:09 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.2.1)
09:33:09 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2)
09:33:09 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0)
09:33:09 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0)
09:33:09 Collecting importlib-resources (from omero-web==5.29.2.dev0)
09:33:09 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
09:33:09 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
09:33:09 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
09:33:09 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
09:33:09 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
09:33:09 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)
09:33:09 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)
09:33:09 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)
09:33:09 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)
09:33:09 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)
09:33:09 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)
09:33:09 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)
09:33:09 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1)
09:33:09 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0)
09:33:09 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
09:33:09 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)
09:33:09 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)
09:33:09 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) (2025.6.15)
09:33:09 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
09:33:10 Using cached django-4.2.23-py3-none-any.whl (8.0 MB)
09:33:10 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
09:33:10 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
09:33:10 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
09:33:10 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
09:33:10 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
09:33:10 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
09:33:10 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
09:33:10 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
09:33:10 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
09:33:10 Building wheels for collected packages: omero-web
09:33:10 Building wheel for omero-web (pyproject.toml): started
09:33:11 Building wheel for omero-web (pyproject.toml): finished with status 'done'
09:33:11 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=08fbbb12701391895297cf201a52f2c6c4c8c60e1f7b28b4c4df2f9592246056
09:33:11 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c
09:33:11 Successfully built omero-web
09:33:11 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
09:33:14
09:33:14 Successfully installed Django-4.2.23 asgiref-3.8.1 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
09:33:14 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
09:33:14 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
09:33:14 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
09:33:14 --2025-06-26 09:33:14-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
09:33:14 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.111.133, ...
09:33:14 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
09:33:15 HTTP request sent, awaiting response... 200 OK
09:33:15 Length: 125072 (122K) [text/plain]
09:33:15 Saving to: ‘Figure_To_Pdf.py’
09:33:15
09:33:15 0K .......... .......... .......... .......... .......... 40% 3.83M 0s
09:33:15 50K .......... .......... .......... .......... .......... 81% 16.2M 0s
09:33:15 100K .......... .......... .. 100% 4.09M=0.02s
09:33:15
09:33:15 2025-06-26 09:33:15 (5.67 MB/s) - ‘Figure_To_Pdf.py’ saved [125072/125072]
09:33:15
09:33:15 + chmod 755 Figure_To_Pdf.py
09:33:15 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
09:33:15 + omero config set omero.db.name OMERO-server
09:33:17 + omero config set omero.db.host pg
09:33:18 + omero config set omero.db.user postgres
09:33:20 + omero config set omero.data.dir /home/omero/omero-server-data
09:33:22 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
09:33:23 + omero config set omero.db.poolsize 25
09:33:25 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
09:33:27 + omero config set omero.security.trustStorePassword changeit
09:33:29 + omero config set omero.mail.config true
09:33:30 + omero config set omero.mail.from qa@openmicroscopy.org.uk
09:33:32 + omero config set omero.mail.host smtp.dundee.ac.uk
09:33:34 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
09:33:36 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
09:33:37 + omero certificates
09:33:39 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
09:33:39 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
09:33:39 + '[' false = true ']'
09:33:39 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
09:33:39 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
09:33:39 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG dbcommand => upgrade
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG dbhost => localhost
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG dbname => OMERO-server
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG dbpass => omero
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG dbuser => omero
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG rootpass => omero
09:33:39 2025-06-26 09:33:39,934 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
09:33:39 2025-06-26 09:33:39,934 [omego.extern] INFO Executing : omero version
09:33:41 OMERO.py version:
09:33:41 OMERO.server version:
09:33:41 5.6.3-569-4523d266fe-ice36-b451
09:33:41 5.21.1.dev0
09:33:41 2025-06-26 09:33:41,736 [omego.extern] INFO Completed [1.801 s]
09:33:41 2025-06-26 09:33:41,736 [omego.extern] DEBUG Using omero CLI from omero
09:33:41 2025-06-26 09:33:41,736 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
09:33:41 2025-06-26 09:33:41,736 [omego.extern] INFO Running [current environment]: omero config get --show-password
09:33:41 2025-06-26 09:33:41,736 [omego.extern] INFO Executing : omero config get --show-password
09:33:43 2025-06-26 09:33:43,471 [omego.extern] INFO Completed [1.735 s]
09:33:43 2025-06-26 09:33:43,471 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
09:33:43 2025-06-26 09:33:43,471 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
09:33:43 2025-06-26 09:33:43,806 [omego.extern] INFO Completed [0.335 s]
09:33:43 2025-06-26 09:33:43,806 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
09:33:43 2025-06-26 09:33:43,806 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
09:33:43
09:33:43 2025-06-26 09:33:43,806 [omego.extern] INFO Running [current environment]: omero config get --show-password
09:33:43 2025-06-26 09:33:43,807 [omego.extern] INFO Executing : omero config get --show-password
09:33:45 2025-06-26 09:33:45,510 [omego.extern] INFO Completed [1.703 s]
09:33:45 2025-06-26 09:33:45,510 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
09:33:45 2025-06-26 09:33:45,510 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
09:33:45 2025-06-26 09:33:45,657 [omego.extern] INFO Completed [0.147 s]
09:33:45 2025-06-26 09:33:45,657 [ 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'
09:33:45 2025-06-26 09:33:45,657 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
09:33:45 2025-06-26 09:33:45,657 [omego.extern] INFO Running [current environment]: omero config get --show-password
09:33:45 2025-06-26 09:33:45,657 [omego.extern] INFO Executing : omero config get --show-password
09:33:47 2025-06-26 09:33:47,378 [omego.extern] INFO Completed [1.721 s]
09:33:47 2025-06-26 09:33:47,378 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
09:33:47 2025-06-26 09:33:47,378 [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
09:33:47 2025-06-26 09:33:47,388 [omego.extern] INFO Completed [0.010 s]
09:33:47 2025-06-26 09:33:47,389 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
09:33:47 2025-06-26 09:33:47,389 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
09:33:47 2025-06-26 09:33:47,390 [ omego.db] INFO Database is already at OMERO5.4__0
09:33:47 + export LANG=en_US.UTF-8
09:33:47 + LANG=en_US.UTF-8
09:33:47 + export LANGUAGE=en_US:en
09:33:47 + LANGUAGE=en_US:en
09:33:47 + export LC_ALL=en_US.UTF-8
09:33:47 + LC_ALL=en_US.UTF-8
09:33:47 + BUILD_ID=DONT_KILL_ME
09:33:47 + omero admin start
09:33:52 No descriptor given. Using etc/grid/default.xml
09:34:01 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
09:34:01 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
09:34:01 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
09:34:01 Waiting on startup. Use CTRL-C to exit
09:34:01 + omero admin waitup
09:34:02 Waiting on startup. Use CTRL-C to exit
09:34:03 + omero admin diagnostics
09:34:05
09:34:05 ================================================================================
09:34:05 OMERO Diagnostics (admin)
09:34:05 ================================================================================
09:34:05
09:34:05 Commands: java -version 11.0.25 (/usr/bin/java)
09:34:05 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
09:34:05 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
09:34:05 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
09:34:05 Commands: psql --version 16.9 (/usr/bin/psql)
09:34:05 Commands: openssl version 3.2.24 (/usr/bin/openssl)
09:34:05
09:34:05 Component: OMERO.py 5.21.1.dev0
09:34:05 Component: OMERO.server 5.6.3-569-4523d266fe-ice36-b451
09:34:05
09:34:05 Server: icegridnode running
09:34:05 Server: Blitz-0 active (pid = 18513, enabled)
09:34:05 Server: Indexer-0 activating (enabled)
09:34:05 Server: OMERO.Glacier2 active (pid = 18544, enabled)
09:34:05 Server: OMERO.IceStorm active (pid = 18568, enabled)
09:34:05 Server: Processor-0 active (pid = 18551, enabled)
09:34:05 Server: Tables-0 active (pid = 18571, enabled)
09:34:05
09:34:05 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
09:34:05 Log files: Blitz-0.log 33.1 KB errors=0 warnings=1
09:34:05 Log files: DropBox.log n/a
09:34:05 Log files: FileServer.log n/a
09:34:05 Log files: Indexer-0.log 483 B
09:34:05 Log files: MonitorServer.log n/a
09:34:05 Log files: Processor-0.log 735 B
09:34:05 Log files: Tables-0.log 961 B
09:34:05 Log files: TestDropBox.log n/a
09:34:05 Log files: master.err empty
09:34:05 Log files: master.out 30.5 KB
09:34:05 Log files: Total size 0.07 MB
09:34:05
09:34:05
09:34:05 Environment:OMERO_HOME=(unset)
09:34:05 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:34:05 Environment:OMERO_NODE=(unset)
09:34:05 Environment:OMERO_MASTER=(unset)
09:34:05 Environment:OMERO_USERDIR=(unset)
09:34:05 Environment:OMERO_TMPDIR=(unset)
09:34:05 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
09:34:05 Environment:PYTHONPATH=(unset)
09:34:05 Environment:ICE_HOME=/opt/ice-3.6.5
09:34:05 Environment:LD_LIBRARY_PATH=(unset)
09:34:05 Environment:DYLD_LIBRARY_PATH=(unset)
09:34:05
09:34:05 OMERO SSL port:4064
09:34:05 OMERO TCP port:4063
09:34:05 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
09:34:05 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
09:34:05
09:34:05 JVM settings: Blitz-${index} -Xmx7200m
09:34:05 JVM settings: Indexer-${index} -Xmx4800m
09:34:05 JVM settings: PixelData-${index} -Xmx7200m
09:34:05 JVM settings: Repository-${index} -Xmx4800m
09:34:05
09:34:05 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 26 June 2025 07357216dd1a7e214b156c0b92c581c3280edd65
09:34:05 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 26 June 2025 07357216dd1a7e214b156c0b92c581c3280edd65
09:34:05 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 26 June 2025 07357216dd1a7e214b156c0b92c581c3280edd65
09:34:05 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.1-SNAPSHOT 26 June 2025 75f8620db9caa0ec1b9db9dd0c139623ad68f14a
09:34:05 Jar: lib/server/ome-common.jar OME Common Java 6.0.27-SNAPSHOT 26 June 2025 75f8620db9caa0ec1b9db9dd0c139623ad68f14a
09:34:05 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 26 June 2025 75f8620db9caa0ec1b9db9dd0c139623ad68f14a
09:34:05 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 26 June 2025 75f8620db9caa0ec1b9db9dd0c139623ad68f14a
09:34:05 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 26 June 2025 75f8620db9caa0ec1b9db9dd0c139623ad68f14a
09:34:05 Jar: lib/server/ome-xml.jar OME XML library 6.5.0-SNAPSHOT 26 June 2025 75f8620db9caa0ec1b9db9dd0c139623ad68f14a
09:34:05 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
09:34:05 Jar: lib/server/omero-zarr-pixel-buffer-0.4.1.jar OMERO Zarr Pixel Buffer 0.4.1 7c2d45bab0b51137dada7abda144282d6dcc76e1
09:34:05 + deactivate
09:34:05 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:34:05 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:34:05 + export PATH
09:34:05 + unset _OLD_VIRTUAL_PATH
09:34:05 + '[' -n '' ']'
09:34:05 + hash -r
09:34:05 + '[' -n '' ']'
09:34:05 + unset VIRTUAL_ENV
09:34:05 + unset VIRTUAL_ENV_PROMPT
09:34:05 + '[' '!' '' = nondestructive ']'
09:34:05 + unset -f deactivate
09:34:06 Finished: SUCCESS
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