Console

01:39:59 Started by upstream project "Trigger" build number 20
01:39:59 originally caused by:
01:39:59  Started by timer
01:39:59 Running as SYSTEM
01:39:59 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
01:39:59 [OMERO-server] $ /bin/bash -xe /tmp/jenkins757465615987284578.sh
01:39:59 + source /home/settings.env
01:39:59 ++ OMERO_DB_HOST=pg
01:39:59 ++ OMERO_DB_USER=postgres
01:39:59 ++ OMERO_DB_PASS=
01:39:59 ++ OMERO_ROOT_PASS=omero
01:39:59 ++ OMERO_DATA_DIR=/OMERO
01:39:59 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
01:39:59 + OMERO_DB_NAME=OMERO-server
01:39:59 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
01:39:59 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:39:59 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:39:59 + OMERO_DATA_DIR=/home/omero/omero-server-data
01:39:59 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
01:39:59 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
01:40:00 ++ deactivate nondestructive
01:40:00 ++ '[' -n '' ']'
01:40:00 ++ '[' -n '' ']'
01:40:00 ++ hash -r
01:40:00 ++ '[' -n '' ']'
01:40:00 ++ unset VIRTUAL_ENV
01:40:00 ++ unset VIRTUAL_ENV_PROMPT
01:40:00 ++ '[' '!' nondestructive = nondestructive ']'
01:40:00 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
01:40:00 ++ export VIRTUAL_ENV
01:40:00 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:40:00 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:40:00 ++ export PATH
01:40:00 ++ '[' -n '' ']'
01:40:00 ++ '[' -z '' ']'
01:40:00 ++ _OLD_VIRTUAL_PS1=
01:40:00 ++ PS1='(.venv3) '
01:40:00 ++ export PS1
01:40:00 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
01:40:00 ++ export VIRTUAL_ENV_PROMPT
01:40:00 ++ hash -r
01:40:00 + omero admin stop
01:40:20 Waiting on shutdown. Use CTRL-C to exit
01:40:20 .+ sleep 5
01:40:35 + deactivate
01:40:35 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
01:40:35 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:40:35 + export PATH
01:40:35 + unset _OLD_VIRTUAL_PATH
01:40:35 + '[' -n '' ']'
01:40:35 + hash -r
01:40:35 + '[' -n '' ']'
01:40:35 + unset VIRTUAL_ENV
01:40:35 + unset VIRTUAL_ENV_PROMPT
01:40:35 + '[' '!' '' = nondestructive ']'
01:40:35 + unset -f deactivate
01:40:35 + rm -rf /home/omero/workspace/OMERO-server/.venv3
01:43:39 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
01:43:58 + '[' false = true ']'
01:43:58 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
01:43:58 Skipping PURGE_DATA:CleanDbAndRepo
01:43:58 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.6-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.22.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.10.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.32.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
01:44:04 Copied 1 artifact from "OMERO-build" build number 12
01:44:04 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 11
01:44:04 Copied 2 artifacts from "OMERO-build-build" build number 22
01:44:04 [OMERO-server] $ /bin/bash -xe /tmp/jenkins12876372673723071291.sh
01:44:04 + source /home/settings.env
01:44:04 ++ OMERO_DB_HOST=pg
01:44:04 ++ OMERO_DB_USER=postgres
01:44:04 ++ OMERO_DB_PASS=
01:44:04 ++ OMERO_ROOT_PASS=omero
01:44:04 ++ OMERO_DATA_DIR=/OMERO
01:44:04 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
01:44:04 + OMERO_DB_NAME=OMERO-server
01:44:04 + OMERO_DATA_DIR=/home/omero/omero-server-data
01:44:04 + mkdir -p /home/omero/omero-server-data
01:44:04 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
01:44:04 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:44:04 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
01:44:04 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
01:44:04 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
01:44:04 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
01:44:04 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
01:44:04 ++ ls OMERO.server-5.6.3-627-c9427e48f4-ice36-b12.zip
01:44:04 + ZIP=OMERO.server-5.6.3-627-c9427e48f4-ice36-b12.zip
01:44:04 + '[' '!' -z '' ']'
01:44:04 + DIST=OMERO.server-5.6.3-627-c9427e48f4-ice36-b12
01:44:04 + unzip OMERO.server-5.6.3-627-c9427e48f4-ice36-b12.zip
01:44:04 Archive:  OMERO.server-5.6.3-627-c9427e48f4-ice36-b12.zip
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/blitz/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/grid/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/profiles/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/error/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/grid/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/luts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/luts/janelia/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/luts/matplotlib/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/luts/ncsa_paledit/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/luts/seaborn/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/luts/wcif/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/analysis_scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/annotation_scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/export_scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/figure_scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/import_scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/scripts/omero/util_scripts/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/server/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/share/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/share/licenses/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/misc/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__1/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__10/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__11/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__2/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__3/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__4/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__5/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__6/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__7/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__8/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__9/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__4/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__5/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__6/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__7/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.1__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.2__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.2__0/t/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.3__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.4__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.0__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.1__1/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.2__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4DEV__1/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4DEV__2/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4DEV__3/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/var/
01:44:04    creating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/var/tmp/
01:44:04   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/LICENSE.txt  
01:44:04   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/backup.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/blitz/mail-senders.example  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/blitz/mail-server.example  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/build.properties  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/env.bat  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/env.sh  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/hibernate.properties  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/ice.config  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/logback-cli.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/logback-indexing-cli.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/logback-indexing.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/logback.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/mime.types  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/node1.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/node2.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/omero.properties  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/profiles/psql  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/rollover.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/Windows.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/error/maintainance.html  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/grid/README  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/grid/default.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/grid/templates.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/grid/windefault.xml  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/ice.config  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/internal.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/master.cfg  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/templates/robot.template  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/etc/testdropbox.config  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/history.rst  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/OMEZarrReader.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/accessors-smart.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/activation.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/aggdesigner-algorithm.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/aircompressor.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/antlr.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/aopalliance.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/apiguardian-api.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/asm.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/avatica-core.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/avatica-metrics.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/aws-java-sdk-core.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/aws-java-sdk-kms.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/aws-java-sdk-s3.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/base.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-anim.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-awt-util.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-bridge.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-codec.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-constants.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-css.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-dom.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-ext.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-gvt.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-i18n.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-parser.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-script.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-shared-resources.jar  
01:44:05   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-svg-dom.jar  
01:44:06   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/lib/client/batik-svggen.jar  
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01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__6/OMERO3A__5.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__7/OMERO3A__6.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__8/OMERO3A__6.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3A__9/OMERO3A__8.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__4/OMERO3__1.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__5/OMERO3__4.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__6/OMERO3__5.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO3__7/OMERO3__6.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.1__0/OMERO4__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.2__0/OMERO4.1__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.3__0/OMERO4.2__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.4__0/OMERO4.1__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4.4__0/OMERO4.3__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO4__0/OMERO3A__11.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.0__0/OMERO4.4__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.1__1/OMERO5.0__0.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql  
01:44:17   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.1__1/OMERO5.1__0.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.2__0/OMERO5.1__1.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/OMERO5.2__0.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/delete-ns-orphans.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/OMERO5.3__0.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/OMERO5.3__1.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/psql-footer.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/psql-header.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/schema.sql  
01:44:18   inflating: OMERO.server-5.6.3-627-c9427e48f4-ice36-b12/sql/psql/OMERO5.4__0/views.sql  
01:44:18 + rm -f OMERO.server-5.6.3-627-c9427e48f4-ice36-b12.zip
01:44:18 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-627-c9427e48f4-ice36-b12 /home/omero/workspace/OMERO-server/OMERO.server
01:44:18 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
01:44:18 ++ deactivate nondestructive
01:44:18 ++ '[' -n '' ']'
01:44:18 ++ '[' -n '' ']'
01:44:18 ++ hash -r
01:44:18 ++ '[' -n '' ']'
01:44:18 ++ unset VIRTUAL_ENV
01:44:18 ++ unset VIRTUAL_ENV_PROMPT
01:44:18 ++ '[' '!' nondestructive = nondestructive ']'
01:44:18 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
01:44:18 ++ export VIRTUAL_ENV
01:44:18 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:44:18 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:44:18 ++ export PATH
01:44:18 ++ '[' -n '' ']'
01:44:18 ++ '[' -z '' ']'
01:44:18 ++ _OLD_VIRTUAL_PS1=
01:44:18 ++ PS1='(.venv3) '
01:44:18 ++ export PS1
01:44:18 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
01:44:18 ++ export VIRTUAL_ENV_PROMPT
01:44:18 ++ hash -r
01:44:18 + pip install -U pip
01:44:19 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
01:44:19 Collecting pip
01:44:19   Using cached pip-26.1.2-py3-none-any.whl (1.8 MB)
01:44:19 Installing collected packages: pip
01:44:19   Attempting uninstall: pip
01:44:19     Found existing installation: pip 22.3.1
01:44:20     Uninstalling pip-22.3.1:
01:44:20       Successfully uninstalled pip-22.3.1
01:44:33 Successfully installed pip-26.1.2
01:44:33 + pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
01:44:34 Collecting zeroc-ice==3.6.5
01:44:34   Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
01:44:37      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 13.7 MB/s  0:00:02
01:44:37 Installing collected packages: zeroc-ice
01:44:40 Successfully installed zeroc-ice-3.6.5
01:44:40 + pip install markdown
01:44:41 Collecting markdown
01:44:41   Using cached markdown-3.10.2-py3-none-any.whl.metadata (5.1 kB)
01:44:41 Using cached markdown-3.10.2-py3-none-any.whl (108 kB)
01:44:41 Installing collected packages: markdown
01:44:42 Successfully installed markdown-3.10.2
01:44:42 + pip install reportlab
01:44:43 Collecting reportlab
01:44:43   Using cached reportlab-5.0.0-py3-none-any.whl.metadata (1.6 kB)
01:44:43 Collecting pillow>=9.0.0 (from reportlab)
01:44:43   Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
01:44:44 Collecting charset-normalizer (from reportlab)
01:44:44   Using cached charset_normalizer-3.4.9-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (41 kB)
01:44:44 Using cached reportlab-5.0.0-py3-none-any.whl (2.0 MB)
01:44:44 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
01:44:44 Using cached charset_normalizer-3.4.9-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (221 kB)
01:44:44 Installing collected packages: pillow, charset-normalizer, reportlab
01:44:52 
01:44:52 Successfully installed charset-normalizer-3.4.9 pillow-12.3.0 reportlab-5.0.0
01:44:52 + pip install omego
01:44:53 Collecting omego
01:44:53   Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
01:44:53 Collecting future (from omego)
01:44:53   Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
01:44:54 Collecting yaclifw>=0.1.1 (from omego)
01:44:54   Using cached yaclifw-0.2.0-py3-none-any.whl
01:44:54 Collecting six (from yaclifw>=0.1.1->omego)
01:44:54   Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
01:44:54 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
01:44:54 Using cached future-1.0.0-py3-none-any.whl (491 kB)
01:44:54 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
01:44:54 Installing collected packages: six, future, yaclifw, omego
01:44:58 
01:44:58 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
01:44:58 + pip install tables
01:44:59 Collecting tables
01:44:59   Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.1 kB)
01:45:00 Collecting numpy>=1.20.0 (from tables)
01:45:00   Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
01:45:00 Collecting numexpr>=2.6.2 (from tables)
01:45:00   Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
01:45:00 Collecting packaging (from tables)
01:45:00   Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
01:45:00 Collecting py-cpuinfo (from tables)
01:45:00   Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
01:45:00 Collecting blosc2>=2.3.0 (from tables)
01:45:01   Downloading blosc2-4.9.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (7.8 kB)
01:45:01 Collecting ndindex (from blosc2>=2.3.0->tables)
01:45:01   Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
01:45:01 Collecting msgpack (from blosc2>=2.3.0->tables)
01:45:01   Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
01:45:01 Collecting pydantic (from blosc2>=2.3.0->tables)
01:45:01   Using cached pydantic-2.13.4-py3-none-any.whl.metadata (109 kB)
01:45:01 Collecting httpx[http2] (from blosc2>=2.3.0->tables)
01:45:01   Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
01:45:02 Collecting rich (from blosc2>=2.3.0->tables)
01:45:02   Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
01:45:02 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
01:45:02   Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
01:45:02 Collecting anyio (from httpx[http2]->blosc2>=2.3.0->tables)
01:45:02   Using cached anyio-4.14.2-py3-none-any.whl.metadata (4.6 kB)
01:45:02 Collecting certifi (from httpx[http2]->blosc2>=2.3.0->tables)
01:45:02   Using cached certifi-2026.6.17-py3-none-any.whl.metadata (2.5 kB)
01:45:02 Collecting httpcore==1.* (from httpx[http2]->blosc2>=2.3.0->tables)
01:45:02   Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB)
01:45:02 Collecting idna (from httpx[http2]->blosc2>=2.3.0->tables)
01:45:02   Using cached idna-3.18-py3-none-any.whl.metadata (6.1 kB)
01:45:02 Collecting h2<5,>=3 (from httpx[http2]->blosc2>=2.3.0->tables)
01:45:02   Using cached h2-4.3.0-py3-none-any.whl.metadata (5.1 kB)
01:45:03 Collecting hyperframe<7,>=6.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
01:45:03   Using cached hyperframe-6.1.0-py3-none-any.whl.metadata (4.3 kB)
01:45:03 Collecting hpack<5,>=4.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
01:45:03   Using cached hpack-4.2.0-py3-none-any.whl.metadata (3.3 kB)
01:45:03 Collecting h11>=0.16 (from httpcore==1.*->httpx[http2]->blosc2>=2.3.0->tables)
01:45:03   Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB)
01:45:03 Collecting typing_extensions>=4.5 (from anyio->httpx[http2]->blosc2>=2.3.0->tables)
01:45:03   Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
01:45:03 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
01:45:03   Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)
01:45:04 Collecting pydantic-core==2.46.4 (from pydantic->blosc2>=2.3.0->tables)
01:45:04   Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
01:45:04 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
01:45:04   Using cached typing_inspection-0.4.2-py3-none-any.whl.metadata (2.6 kB)
01:45:04 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
01:45:04   Using cached markdown_it_py-4.2.0-py3-none-any.whl.metadata (7.4 kB)
01:45:04 Collecting pygments<3.0.0,>=2.13.0 (from rich->blosc2>=2.3.0->tables)
01:45:04   Using cached pygments-2.20.0-py3-none-any.whl.metadata (2.5 kB)
01:45:04 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
01:45:04   Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
01:45:04 Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (7.2 MB)
01:45:04 Downloading blosc2-4.9.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.3 MB)
01:45:05    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 7.3/7.3 MB 12.1 MB/s  0:00:00
01:45:05 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
01:45:05 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
01:45:05 Using cached httpx-0.28.1-py3-none-any.whl (73 kB)
01:45:05 Using cached h2-4.3.0-py3-none-any.whl (61 kB)
01:45:05 Using cached hpack-4.2.0-py3-none-any.whl (34 kB)
01:45:05 Using cached httpcore-1.0.9-py3-none-any.whl (78 kB)
01:45:05 Using cached hyperframe-6.1.0-py3-none-any.whl (13 kB)
01:45:05 Using cached h11-0.16.0-py3-none-any.whl (37 kB)
01:45:05 Using cached anyio-4.14.2-py3-none-any.whl (125 kB)
01:45:05 Using cached idna-3.18-py3-none-any.whl (65 kB)
01:45:06 Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB)
01:45:06 Using cached certifi-2026.6.17-py3-none-any.whl (133 kB)
01:45:06 Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (423 kB)
01:45:06 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
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01:45:06 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
01:45:06 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
01:45:06 Installing collected packages: py-cpuinfo, typing_extensions, threadpoolctl, pygments, packaging, numpy, ndindex, msgpack, mdurl, idna, hyperframe, hpack, h11, certifi, annotated-types, typing-inspection, pydantic-core, numexpr, markdown-it-py, httpcore, h2, anyio, rich, pydantic, httpx, blosc2, tables
01:45:51 
01:45:51 Successfully installed annotated-types-0.7.0 anyio-4.14.2 blosc2-4.9.1 certifi-2026.6.17 h11-0.16.0 h2-4.3.0 hpack-4.2.0 httpcore-1.0.9 httpx-0.28.1 hyperframe-6.1.0 idna-3.18 markdown-it-py-4.2.0 mdurl-0.1.2 msgpack-1.2.1 ndindex-1.10.1 numexpr-2.14.1 numpy-2.4.6 packaging-26.2 py-cpuinfo-9.0.0 pydantic-2.13.4 pydantic-core-2.46.4 pygments-2.20.0 rich-15.0.0 tables-3.11.1 threadpoolctl-3.6.0 typing-inspection-0.4.2 typing_extensions-4.16.0
01:45:51 + pip install jinja2
01:45:53 Collecting jinja2
01:45:53   Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
01:45:53 Collecting MarkupSafe>=2.0 (from jinja2)
01:45:53   Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
01:45:53 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
01:45:53 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
01:45:53 Installing collected packages: MarkupSafe, jinja2
01:45:54 
01:45:54 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
01:45:54 + pip install omero-py
01:45:55 Collecting omero-py
01:45:55   Using cached omero_py-5.22.1-py3-none-any.whl.metadata (6.5 kB)
01:45:55 Collecting appdirs (from omero-py)
01:45:55   Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
01:45:55 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
01:45:55 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
01:45:55 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
01:45:55 Collecting PyYAML (from omero-py)
01:45:55   Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
01:45:55 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
01:45:55 Collecting requests (from omero-py)
01:45:55   Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
01:45:55 Collecting portalocker (from omero-py)
01:45:55   Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
01:45:55 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.9)
01:45:55 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.18)
01:45:56 Collecting urllib3<3,>=1.26 (from requests->omero-py)
01:45:56   Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
01:45:56 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.6.17)
01:45:56 Using cached omero_py-5.22.1-py3-none-any.whl (2.8 MB)
01:45:56 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
01:45:56 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
01:45:56 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
01:45:56 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
01:45:56 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
01:45:56 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, requests, omero-py
01:46:12 
01:46:12 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.22.1 portalocker-3.2.0 requests-2.34.2 urllib3-2.7.0
01:46:12 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
01:46:13 Collecting omero-metadata
01:46:13   Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-52_7uldx/omero-metadata_220c0c48d24a4ad5b3cac009cdada49b
01:46:13   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-52_7uldx/omero-metadata_220c0c48d24a4ad5b3cac009cdada49b
01:46:14   Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 8797f73216a282cf049ab3cd0b86e4570f477ed5
01:46:14   Installing build dependencies: started
01:46:15   Installing build dependencies: finished with status 'done'
01:46:15   Getting requirements to build wheel: started
01:46:16   Getting requirements to build wheel: finished with status 'done'
01:46:16   Preparing metadata (pyproject.toml): started
01:46:16   Preparing metadata (pyproject.toml): finished with status 'done'
01:46:16 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.22.1)
01:46:16 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
01:46:16 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
01:46:16 Collecting pandas (from omero-metadata)
01:46:16   Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
01:46:16 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
01:46:16 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
01:46:16 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.6)
01:46:16 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (12.3.0)
01:46:16 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
01:46:16 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
01:46:16 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
01:46:16 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
01:46:16 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
01:46:16   Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
01:46:16 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil>=2.8.2->pandas->omero-metadata) (1.17.0)
01:46:17 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.9)
01:46:17 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.18)
01:46:17 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.7.0)
01:46:17 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.6.17)
01:46:17 Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.3 MB)
01:46:17 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
01:46:17 Building wheels for collected packages: omero-metadata
01:46:17   Building wheel for omero-metadata (pyproject.toml): started
01:46:17   Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
01:46:17   Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=6b50e60f376ad7d815f1999517ab6c8d5b8232f4d12ed4af5c39e040bc1a1ed5
01:46:17   Stored in directory: /tmp/pip-ephem-wheel-cache-24b8m5_s/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
01:46:17 Successfully built omero-metadata
01:46:17 Installing collected packages: python-dateutil, pandas, omero-metadata
01:46:54 
01:46:54 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.3 python-dateutil-2.9.0.post0
01:46:54 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
01:46:55 Collecting omero-cli-render
01:46:55   Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-q25ztecr/omero-cli-render_6971e4b91b3142e0bbca63b33f60fcc4
01:46:55   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-q25ztecr/omero-cli-render_6971e4b91b3142e0bbca63b33f60fcc4
01:46:56   Running command git checkout -b merge_ci --track origin/merge_ci
01:46:57   Switched to a new branch 'merge_ci'
01:46:57   branch 'merge_ci' set up to track 'origin/merge_ci'.
01:46:57   Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 9f6f3b33eede130028f619bcc4955aca4d1ea4e8
01:46:57   Installing build dependencies: started
01:46:58   Installing build dependencies: finished with status 'done'
01:46:58   Getting requirements to build wheel: started
01:46:58   Getting requirements to build wheel: finished with status 'done'
01:46:58   Preparing metadata (pyproject.toml): started
01:46:58   Preparing metadata (pyproject.toml): finished with status 'done'
01:46:58 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
01:46:58 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.22.1)
01:46:58 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
01:46:58 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
01:46:58 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.6)
01:46:58 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (12.3.0)
01:46:58 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
01:46:58 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
01:46:58 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
01:46:58 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.9)
01:46:58 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.18)
01:46:58 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.7.0)
01:46:58 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.6.17)
01:46:58 Building wheels for collected packages: omero-cli-render
01:46:58   Building wheel for omero-cli-render (pyproject.toml): started
01:46:59   Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
01:46:59   Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19838 sha256=3903839c86c5a728239c49ef3fe7eb7c7aa109999780810994b46ebbb01ad6d9
01:46:59   Stored in directory: /tmp/pip-ephem-wheel-cache-tl_45lbr/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
01:46:59 Successfully built omero-cli-render
01:46:59 Installing collected packages: omero-cli-render
01:46:59 Successfully installed omero-cli-render-0.8.2.dev0
01:46:59 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
01:47:00 Collecting omero-cli-duplicate
01:47:00   Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-lgz8o0qn/omero-cli-duplicate_cb6cf9d7548f4600a217efd289f0a84d
01:47:00   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-lgz8o0qn/omero-cli-duplicate_cb6cf9d7548f4600a217efd289f0a84d
01:47:01   Running command git checkout -b merge_ci --track origin/merge_ci
01:47:01   Switched to a new branch 'merge_ci'
01:47:01   branch 'merge_ci' set up to track 'origin/merge_ci'.
01:47:01   Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit ad42f379577b077f8b1047d873d8d4b9c2a9783d
01:47:01   Installing build dependencies: started
01:47:03   Installing build dependencies: finished with status 'done'
01:47:03   Getting requirements to build wheel: started
01:47:03   Getting requirements to build wheel: finished with status 'done'
01:47:03   Preparing metadata (pyproject.toml): started
01:47:03   Preparing metadata (pyproject.toml): finished with status 'done'
01:47:03 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.22.1)
01:47:03 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
01:47:03 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
01:47:03 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
01:47:03 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.3.0)
01:47:03 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
01:47:03 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5)
01:47:03 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.34.2)
01:47:03 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
01:47:03 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.9)
01:47:03 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.18)
01:47:03 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.7.0)
01:47:03 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.6.17)
01:47:03 Building wheels for collected packages: omero-cli-duplicate
01:47:03   Building wheel for omero-cli-duplicate (pyproject.toml): started
01:47:03   Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
01:47:03   Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=b91918917ce0a068dca2deb84e6f410d901ad367038814c563655c1acc96efa2
01:47:03   Stored in directory: /tmp/pip-ephem-wheel-cache-woxqwuao/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
01:47:03 Successfully built omero-cli-duplicate
01:47:03 Installing collected packages: omero-cli-duplicate
01:47:04 Successfully installed omero-cli-duplicate-0.4.1.dev0
01:47:04 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
01:47:05 Collecting omero-cli-zarr
01:47:05   Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-wdqcvxbl/omero-cli-zarr_344d27fb56ff46ff88266ae3b59f3a10
01:47:05   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-wdqcvxbl/omero-cli-zarr_344d27fb56ff46ff88266ae3b59f3a10
01:47:06   Running command git checkout -b merge_ci --track origin/merge_ci
01:47:06   Switched to a new branch 'merge_ci'
01:47:06   branch 'merge_ci' set up to track 'origin/merge_ci'.
01:47:06   Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit d0e400a012de76e7e325f87489d2ba027a6d755e
01:47:06   Installing build dependencies: started
01:47:07   Installing build dependencies: finished with status 'done'
01:47:07   Getting requirements to build wheel: started
01:47:07   Getting requirements to build wheel: finished with status 'done'
01:47:07   Installing backend dependencies: started
01:47:09   Installing backend dependencies: finished with status 'done'
01:47:09   Preparing metadata (pyproject.toml): started
01:47:09   Preparing metadata (pyproject.toml): finished with status 'done'
01:47:09 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.22.1)
01:47:10 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
01:47:10   Using cached ome_zarr-0.18.0-py3-none-any.whl.metadata (2.9 kB)
01:47:10 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.6)
01:47:10 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
01:47:10   Using cached dask-2026.7.1-py3-none-any.whl.metadata (3.8 kB)
01:47:10 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
01:47:10   Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
01:47:10 Collecting fsspec!=2021.07.0,!=2023.9.0,>=0.8 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
01:47:10   Using cached fsspec-2026.6.0-py3-none-any.whl.metadata (10 kB)
01:47:11 Collecting aiohttp (from ome-zarr>=0.13.0->omero-cli-zarr)
01:47:11   Using cached aiohttp-3.14.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
01:47:11 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.34.2)
01:47:11 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
01:47:11   Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
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01:47:13 Collecting pydantic-core==2.41.5 (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:13 Collecting locket (from partd>=1.4.0->dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:13 Collecting aiobotocore<4.0.0,>=2.19.0 (from s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:13 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:14 Collecting botocore<1.43.47,>=1.43.3 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:14 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:14 Collecting multidict<7.0.0,>=6.0.0 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
01:47:14   Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
01:47:15 Collecting wrapt<3.0.0,>=1.10.10 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:15 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:15 Collecting aiosignal>=1.4.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:15 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:15 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:15 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:16 Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
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01:47:17 Using cached partd-1.4.2-py3-none-any.whl (18 kB)
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01:47:17 Using cached s3fs-2026.6.0-py3-none-any.whl (32 kB)
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01:47:17 Using cached aiohttp-3.14.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.8 MB)
01:47:17 Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB)
01:47:17 Downloading botocore-1.43.46-py3-none-any.whl (15.4 MB)
01:47:18    ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.4/15.4 MB 12.9 MB/s  0:00:01
01:47:18 Using cached jmespath-1.1.0-py3-none-any.whl (20 kB)
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01:47:18 Using cached wrapt-2.2.2-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (159 kB)
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01:47:18 Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl (15 kB)
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01:47:18 Using cached google_crc32c-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (33 kB)
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01:47:18 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
01:47:18 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
01:47:19 Building wheels for collected packages: omero-cli-zarr
01:47:19   Building wheel for omero-cli-zarr (pyproject.toml): started
01:47:19   Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
01:47:19   Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev162+gd0e400a-py3-none-any.whl size=38285 sha256=211d409c29097896c6a937e1c89b5449a9b57b5d35babaa350373e437bf8f5fd
01:47:19   Stored in directory: /tmp/pip-ephem-wheel-cache-g18yvqj1/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
01:47:19 Successfully built omero-cli-zarr
01:47:19 Installing collected packages: rangehttpserver, zipp, wrapt, toolz, tifffile, scipy, pydantic-core, propcache, numcodecs, networkx, multidict, locket, lazy-loader, jmespath, imageio, google-crc32c, fsspec, frozenlist, donfig, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, zarr, yarl, scikit-image, pydantic, partd, importlib_metadata, Deprecated, botocore, aiosignal, pydantic-zarr, dask, aiohttp, ome-zarr-models, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
01:47:53   Attempting uninstall: pydantic-core
01:47:53     Found existing installation: pydantic_core 2.46.4
01:47:53     Uninstalling pydantic_core-2.46.4:
01:47:53       Successfully uninstalled pydantic_core-2.46.4
01:48:25   Attempting uninstall: pydantic
01:48:26     Found existing installation: pydantic 2.13.4
01:48:26     Uninstalling pydantic-2.13.4:
01:48:26       Successfully uninstalled pydantic-2.13.4
01:49:03 
01:49:03 Successfully installed Deprecated-1.3.1 aiobotocore-3.8.0 aiohappyeyeballs-2.7.1 aiohttp-3.14.1 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.46 click-8.4.2 cloudpickle-3.1.2 dask-2026.7.1 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.6.0 google-crc32c-1.8.0 imageio-2.37.3 importlib_metadata-9.0.0 jmespath-1.1.0 lazy-loader-0.5 locket-1.0.0 multidict-6.7.1 networkx-3.6.1 numcodecs-0.16.5 ome-zarr-0.18.0 ome-zarr-models-1.7 omero-cli-zarr-0.5.5.dev162+gd0e400a partd-1.4.2 propcache-0.5.2 pydantic-2.12.5 pydantic-core-2.41.5 pydantic-zarr-0.9.2 rangehttpserver-1.4.0 s3fs-2026.6.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 wrapt-2.2.2 yarl-1.24.2 zarr-3.1.6 zipp-4.1.0
01:49:03 + pip install omero-certificates
01:49:05 Collecting omero-certificates
01:49:05   Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
01:49:05 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.22.1)
01:49:05 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
01:49:05 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
01:49:05 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.6)
01:49:05 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.3.0)
01:49:05 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
01:49:05 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
01:49:05 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.34.2)
01:49:05 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
01:49:05 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.9)
01:49:05 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.18)
01:49:05 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.7.0)
01:49:05 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.6.17)
01:49:05 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
01:49:05 Installing collected packages: omero-certificates
01:49:05 Successfully installed omero-certificates-0.4.0
01:49:05 + for x in *.tar.gz
01:49:05 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
01:49:06 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
01:49:06   Installing build dependencies: started
01:49:07   Installing build dependencies: finished with status 'done'
01:49:07   Getting requirements to build wheel: started
01:49:08   Getting requirements to build wheel: finished with status 'done'
01:49:08   Preparing metadata (pyproject.toml): started
01:49:08   Preparing metadata (pyproject.toml): finished with status 'done'
01:49:08 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.22.1)
01:49:08 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
01:49:08 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
01:49:08 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.6)
01:49:08 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.3.0)
01:49:08 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
01:49:08 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5)
01:49:08 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
01:49:08 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
01:49:08 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.9)
01:49:08 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.18)
01:49:08 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.7.0)
01:49:08 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.6.17)
01:49:08 Building wheels for collected packages: omero-dropbox
01:49:08   Building wheel for omero-dropbox (pyproject.toml): started
01:49:08   Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
01:49:08   Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49153 sha256=2dee54ab82dcd70767ffe716d83d958503a115b195c86089a22bfaabacd15b30
01:49:08   Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
01:49:08 Successfully built omero-dropbox
01:49:08 Installing collected packages: omero-dropbox
01:49:09 Successfully installed omero-dropbox-5.7.1.dev0
01:49:09 + for x in *.tar.gz
01:49:09 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
01:49:10 Processing ./omero_marshal-0.9.2.dev0.tar.gz
01:49:10   Installing build dependencies: started
01:49:11   Installing build dependencies: finished with status 'done'
01:49:11   Getting requirements to build wheel: started
01:49:12   Getting requirements to build wheel: finished with status 'done'
01:49:12   Preparing metadata (pyproject.toml): started
01:49:12   Preparing metadata (pyproject.toml): finished with status 'done'
01:49:12 Building wheels for collected packages: omero_marshal
01:49:12   Building wheel for omero_marshal (pyproject.toml): started
01:49:12   Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
01:49:12   Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88129 sha256=066509d877845e55d74894517a84965e0f1b91258976bb63418dd9284b0d31d0
01:49:12   Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
01:49:12 Successfully built omero_marshal
01:49:13 Installing collected packages: omero_marshal
01:49:15 Successfully installed omero_marshal-0.9.2.dev0
01:49:15 + for x in *.tar.gz
01:49:15 + pip install -U omero_py-5.22.2.dev0.tar.gz
01:49:15 Processing ./omero_py-5.22.2.dev0.tar.gz
01:49:16   Installing build dependencies: started
01:49:17   Installing build dependencies: finished with status 'done'
01:49:17   Getting requirements to build wheel: started
01:49:17   Getting requirements to build wheel: finished with status 'done'
01:49:17   Preparing metadata (pyproject.toml): started
01:49:18   Preparing metadata (pyproject.toml): finished with status 'done'
01:49:18 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.4.4)
01:49:18 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.0.0)
01:49:18 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.4.6)
01:49:18 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (12.3.0)
01:49:18 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (6.0.3)
01:49:18 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.6.5)
01:49:18 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.34.2)
01:49:18 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.2.0)
01:49:18 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.4.9)
01:49:18 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.18)
01:49:18 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2.7.0)
01:49:18 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2026.6.17)
01:49:18 Building wheels for collected packages: omero-py
01:49:18   Building wheel for omero-py (pyproject.toml): started
01:49:19   Building wheel for omero-py (pyproject.toml): finished with status 'done'
01:49:19   Created wheel for omero-py: filename=omero_py-5.22.2.dev0-py3-none-any.whl size=2787060 sha256=d1095d184e3ccbb88d46a4f9cf9302c4950293319aa67e4c41ed10f998cdc3fb
01:49:19   Stored in directory: /home/omero/.cache/pip/wheels/ec/3f/72/4027ca0a7faf1f66d4577cc07619b0497ac8e99396d43dd8fa
01:49:19 Successfully built omero-py
01:49:19 Installing collected packages: omero-py
01:49:19   Attempting uninstall: omero-py
01:49:19     Found existing installation: omero-py 5.22.1
01:49:20     Uninstalling omero-py-5.22.1:
01:49:30       Successfully uninstalled omero-py-5.22.1
01:49:44 Successfully installed omero-py-5.22.2.dev0
01:49:44 + for x in *.tar.gz
01:49:44 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
01:49:45 Processing ./omero_scripts-5.10.1.dev0.tar.gz
01:49:45   Installing build dependencies: started
01:49:47   Installing build dependencies: finished with status 'done'
01:49:47   Getting requirements to build wheel: started
01:49:47   Getting requirements to build wheel: finished with status 'done'
01:49:47   Preparing metadata (pyproject.toml): started
01:49:47   Preparing metadata (pyproject.toml): finished with status 'done'
01:49:47 Building wheels for collected packages: omero-scripts
01:49:47   Building wheel for omero-scripts (pyproject.toml): started
01:49:47   Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
01:49:47   Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137216 sha256=2ad9a39525c5f9f66fc0407053f39841d5d7cc85fe9cabe71ec62cdcbcf608cd
01:49:47   Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
01:49:48 Successfully built omero-scripts
01:49:48 Installing collected packages: omero-scripts
01:49:49 Successfully installed omero-scripts-5.10.1.dev0
01:49:49 + for x in *.tar.gz
01:49:49 + pip install -U omero_web-5.32.1.dev0.tar.gz
01:49:49 Processing ./omero_web-5.32.1.dev0.tar.gz
01:49:50   Installing build dependencies: started
01:49:51   Installing build dependencies: finished with status 'done'
01:49:51   Getting requirements to build wheel: started
01:49:52   Getting requirements to build wheel: finished with status 'done'
01:49:52   Preparing metadata (pyproject.toml): started
01:49:52   Preparing metadata (pyproject.toml): finished with status 'done'
01:49:52 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (5.22.2.dev0)
01:49:52 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.32.1.dev0)
01:49:52   Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
01:49:52 Collecting Django<5.3,>=5.2.9 (from omero-web==5.32.1.dev0)
01:49:52   Using cached django-5.2.16-py3-none-any.whl.metadata (4.1 kB)
01:49:52 Collecting django-pipeline>=4.1.0 (from omero-web==5.32.1.dev0)
01:49:52   Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
01:49:53 Collecting django-cors-headers==3.7.0 (from omero-web==5.32.1.dev0)
01:49:53   Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
01:49:53 Collecting whitenoise>=5.3.0 (from omero-web==5.32.1.dev0)
01:49:53   Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
01:49:53 Collecting gunicorn>=19.3 (from omero-web==5.32.1.dev0)
01:49:53   Using cached gunicorn-26.0.0-py3-none-any.whl.metadata (5.4 kB)
01:49:53 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (0.9.2.dev0)
01:49:53 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (12.3.0)
01:49:53 Collecting pytz (from omero-web==5.32.1.dev0)
01:49:53   Using cached pytz-2026.2-py2.py3-none-any.whl.metadata (22 kB)
01:49:53 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (3.2.0)
01:49:53 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (26.2)
01:49:53 Collecting importlib-resources (from omero-web==5.32.1.dev0)
01:49:53   Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
01:49:53 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
01:49:53   Using cached asgiref-3.12.1-py3-none-any.whl.metadata (9.4 kB)
01:49:53 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
01:49:53   Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
01:49:53 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0) (65.5.1)
01:49:53 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0)
01:49:53   Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
01:49:53 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (1.4.4)
01:49:53 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (1.0.0)
01:49:53 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (2.4.6)
01:49:53 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (6.0.3)
01:49:53 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==5.32.1.dev0) (3.6.5)
01:49:53 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.32.1.dev0) (2.34.2)
01:49:53 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (3.4.9)
01:49:53 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (3.18)
01:49:53 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (2.7.0)
01:49:53 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (2026.6.17)
01:49:53 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
01:49:53 Using cached django-5.2.16-py3-none-any.whl (8.3 MB)
01:49:54 Using cached asgiref-3.12.1-py3-none-any.whl (25 kB)
01:49:54 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
01:49:54 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
01:49:54 Using cached gunicorn-26.0.0-py3-none-any.whl (212 kB)
01:49:54 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
01:49:54 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
01:49:54 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
01:49:54 Using cached pytz-2026.2-py2.py3-none-any.whl (510 kB)
01:49:54 Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
01:49:54 Building wheels for collected packages: omero-web
01:49:54   Building wheel for omero-web (pyproject.toml): started
01:49:55   Building wheel for omero-web (pyproject.toml): finished with status 'done'
01:49:55   Created wheel for omero-web: filename=omero_web-5.32.1.dev0-py3-none-any.whl size=2820645 sha256=b5543cc618502dfdfc7387e400fb2fdcb2392fe9e494c065024e2bd2871e3426
01:49:55   Stored in directory: /home/omero/.cache/pip/wheels/e6/f6/6f/ec36dda9edad720aabd7330edafa8a6a62d6ebfa4c7467248f
01:49:55 Successfully built omero-web
01:49:55 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
01:51:01 
01:51:01 Successfully installed Django-5.2.16 asgiref-3.12.1 concurrent-log-handler-0.9.29 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-26.0.0 importlib-resources-7.1.0 omero-web-5.32.1.dev0 pytz-2026.2 sqlparse-0.5.5 wheel-0.47.0 whitenoise-6.12.0
01:51:01 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
01:51:01 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
01:51:01 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
01:51:01 --2026-07-18 01:51:01--  https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
01:51:01 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.108.133, ...
01:51:01 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
01:51:01 HTTP request sent, awaiting response... 200 OK
01:51:01 Length: 139337 (136K) [text/plain]
01:51:01 Saving to: ‘Figure_To_Pdf.py’
01:51:01 
01:51:01      0K .......... .......... .......... .......... .......... 36% 2.77M 0s
01:51:01     50K .......... .......... .......... .......... .......... 73% 5.01M 0s
01:51:01    100K .......... .......... .......... ......               100% 7.05M=0.03s
01:51:01 
01:51:01 2026-07-18 01:51:01 (4.11 MB/s) - ‘Figure_To_Pdf.py’ saved [139337/139337]
01:51:01 
01:51:01 + chmod 755 Figure_To_Pdf.py
01:51:01 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
01:51:01 + omero config set omero.db.name OMERO-server
01:51:07 + omero config set omero.db.host pg
01:51:12 + omero config set omero.db.user postgres
01:51:16 + omero config set omero.data.dir /home/omero/omero-server-data
01:51:21 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
01:51:25 + omero config set omero.db.poolsize 25
01:51:30 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
01:51:34 + omero config set omero.security.trustStorePassword changeit
01:51:39 + omero config set omero.mail.config true
01:51:43 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
01:51:48 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
01:51:52 + omero certificates
01:51:56 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
01:51:56 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
01:51:57 + '[' false = true ']'
01:51:57 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
01:51:57 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
01:51:57 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
01:51:57 2026-07-18 01:51:57,325 [    omego.db] DEBUG            dbcommand => upgrade
01:51:57 2026-07-18 01:51:57,325 [    omego.db] DEBUG               dbhost => localhost
01:51:57 2026-07-18 01:51:57,325 [    omego.db] DEBUG               dbname => OMERO-server
01:51:57 2026-07-18 01:51:57,325 [    omego.db] DEBUG               dbpass => omero
01:51:57 2026-07-18 01:51:57,326 [    omego.db] DEBUG               dbuser => omero
01:51:57 2026-07-18 01:51:57,326 [    omego.db] DEBUG             rootpass => omero
01:51:57 2026-07-18 01:51:57,326 [    omego.db] DEBUG            serverdir => /home/omero/workspace/OMERO-server/OMERO.server
01:51:57 2026-07-18 01:51:57,326 [omego.extern] INFO  Executing : omero version
01:52:01 OMERO.py version:
01:52:01 OMERO.server version:
01:52:01 5.6.3-627-c9427e48f4-ice36-b12
01:52:01 5.22.2.dev0
01:52:01 2026-07-18 01:52:01,957 [omego.extern] INFO  Completed [4.631 s]
01:52:01 2026-07-18 01:52:01,957 [omego.extern] DEBUG Using omero CLI from omero
01:52:01 2026-07-18 01:52:01,957 [    omego.db] INFO  DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
01:52:01 2026-07-18 01:52:01,958 [omego.extern] INFO  Running [current environment]: omero config get --show-password
01:52:01 2026-07-18 01:52:01,958 [omego.extern] INFO  Executing : omero config get --show-password
01:52:06 2026-07-18 01:52:06,508 [omego.extern] INFO  Completed [4.550 s]
01:52:06 2026-07-18 01:52:06,508 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
01:52:06 2026-07-18 01:52:06,508 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
01:52:06 2026-07-18 01:52:06,514 [omego.extern] INFO  Completed [0.006 s]
01:52:06 2026-07-18 01:52:06,514 [    omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.14\n'
01:52:06 2026-07-18 01:52:06,514 [    omego.db] INFO  psql version: psql (PostgreSQL) 16.14
01:52:06 
01:52:06 2026-07-18 01:52:06,514 [omego.extern] INFO  Running [current environment]: omero config get --show-password
01:52:06 2026-07-18 01:52:06,514 [omego.extern] INFO  Executing : omero config get --show-password
01:52:11 2026-07-18 01:52:11,355 [omego.extern] INFO  Completed [4.841 s]
01:52:11 2026-07-18 01:52:11,355 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
01:52:11 2026-07-18 01:52:11,356 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
01:52:11 2026-07-18 01:52:11,372 [omego.extern] INFO  Completed [0.017 s]
01:52:11 2026-07-18 01:52:11,372 [    omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.5") at port "5432".\n'
01:52:11 2026-07-18 01:52:11,372 [    omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
01:52:11 2026-07-18 01:52:11,372 [omego.extern] INFO  Running [current environment]: omero config get --show-password
01:52:11 2026-07-18 01:52:11,372 [omego.extern] INFO  Executing : omero config get --show-password
01:52:15 2026-07-18 01:52:15,996 [omego.extern] INFO  Completed [4.623 s]
01:52:15 2026-07-18 01:52:15,996 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
01:52:15 2026-07-18 01:52:15,996 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
01:52:16 2026-07-18 01:52:16,037 [omego.extern] INFO  Completed [0.041 s]
01:52:16 2026-07-18 01:52:16,037 [    omego.db] DEBUG stdout: b'OMERO5.4|0\n'
01:52:16 2026-07-18 01:52:16,037 [    omego.db] INFO  Current omero db version: ('OMERO5.4', '0')
01:52:16 2026-07-18 01:52:16,135 [    omego.db] INFO  Database is already at OMERO5.4__0
01:52:16 + export LANG=en_US.UTF-8
01:52:16 + LANG=en_US.UTF-8
01:52:16 + export LANGUAGE=en_US:en
01:52:16 + LANGUAGE=en_US:en
01:52:16 + export LC_ALL=en_US.UTF-8
01:52:16 + LC_ALL=en_US.UTF-8
01:52:16 + BUILD_ID=DONT_KILL_ME
01:52:16 + omero admin start
01:52:26 No descriptor given. Using etc/grid/default.xml
01:52:36 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
01:52:36 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
01:52:36 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
01:52:36 Waiting on startup. Use CTRL-C to exit
01:52:36 + omero admin waitup
01:52:41 Waiting on startup. Use CTRL-C to exit
01:52:41 + omero admin diagnostics
01:52:46 
01:52:46 ================================================================================
01:52:46 OMERO Diagnostics (admin)
01:52:46 ================================================================================
01:52:46         
01:52:46 Commands:   java -version                  21.0.11   (/usr/bin/java)
01:52:46 Commands:   python -V                      3.11.13   (/home/omero/workspace/OMERO-server/.venv3/bin/python)
01:52:46 Commands:   icegridnode --version          3.6.5     (/opt/ice-3.6.5/bin/icegridnode)
01:52:46 Commands:   icegridadmin --version         3.6.5     (/opt/ice-3.6.5/bin/icegridadmin)
01:52:46 Commands:   psql --version                 16.14     (/usr/bin/psql)
01:52:46 Commands:   openssl version                3.5.527   (/usr/bin/openssl)
01:52:46 
01:52:46 Component:  OMERO.py                       5.22.2.dev0
01:52:46 Component:  OMERO.server                   5.6.3-627-c9427e48f4-ice36-b12
01:52:46 
01:52:46 Server:     icegridnode                    running
01:52:46 Server:     Blitz-0                        active (pid = 20178, enabled)
01:52:46 Server:     Indexer-0                      active (pid = 20203, enabled)
01:52:46 Server:     OMERO.Glacier2                 active (pid = 20223, enabled)
01:52:46 Server:     OMERO.IceStorm                 active (pid = 20227, enabled)
01:52:46 Server:     Processor-0                    active (pid = 20236, enabled)
01:52:46 Server:     Tables-0                       active (pid = 20207, enabled)
01:52:46 
01:52:46 Log dir:    /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
01:52:46 Log files:  Blitz-0.log                    32.5 KB       errors=0    warnings=1   
01:52:46 Log files:  DropBox.log                    n/a
01:52:46 Log files:  FileServer.log                 n/a
01:52:46 Log files:  Indexer-0.log                  2.6 KB       
01:52:46 Log files:  MonitorServer.log              n/a
01:52:46 Log files:  Processor-0.log                735 B        
01:52:46 Log files:  Tables-0.log                   961 B        
01:52:46 Log files:  TestDropBox.log                n/a
01:52:46 Log files:  master.err                     empty
01:52:46 Log files:  master.out                     30.5 KB      
01:52:46 Log files:  Total size                     0.07 MB
01:52:46 
01:52:46 
01:52:46 Environment:OMERO_HOME=(unset)             
01:52:46 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 
01:52:46 Environment:OMERO_NODE=(unset)             
01:52:46 Environment:OMERO_MASTER=(unset)           
01:52:46 Environment:OMERO_USERDIR=(unset)          
01:52:46 Environment:OMERO_TMPDIR=(unset)           
01:52:46 Environment:PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 
01:52:46 Environment:PYTHONPATH=(unset)             
01:52:46 Environment:ICE_HOME=/opt/ice-3.6.5        
01:52:46 Environment:LD_LIBRARY_PATH=(unset)        
01:52:46 Environment:DYLD_LIBRARY_PATH=(unset)      
01:52:46 
01:52:46 OMERO SSL port:4064                           
01:52:46 OMERO TCP port:4063                           
01:52:46 OMERO data dir:'/home/omero/omero-server-data' Exists? True	Is writable? True
01:52:46 OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)
01:52:46 
01:52:46 JVM settings: Blitz-${index}                -Xmx7200m
01:52:46 JVM settings: Indexer-${index}              -Xmx4800m
01:52:46 JVM settings: PixelData-${index}            -Xmx7200m
01:52:46 JVM settings: Repository-${index}           -Xmx4800m
01:52:46 
01:52:46 Jar:        lib/server/formats-api.jar     Bio-Formats API	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
01:52:46 Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
01:52:46 Jar:        lib/server/formats-gpl.jar     Bio-Formats library	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
01:52:46 Jar:        lib/server/ome-codecs.jar      OME Codecs	1.1.3	26 February 2026	70fd9b72a9834f1af4852c1e5b5676c57a2c360e
01:52:46 Jar:        lib/server/ome-common.jar      OME Common Java	6.2.1	27 February 2026	a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
01:52:46 Jar:        lib/server/ome-jai.jar         OME JAI	0.1.5	30 June 2025	257a1c1410c0103485248d05752a5174262a38b6
01:52:46 Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)	5.3.4	25 June 2025	57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
01:52:46 Jar:        lib/server/ome-poi.jar         OME POI	5.3.11	11 November 2025	a2f3944ac71db9e7e51a6f64ec46beeb60613afb
01:52:46 Jar:        lib/server/ome-xml.jar         OME XML library	6.5.3	22 January 2026	21d1362abd9ce26e13888d2b2d028753d21ac96e
01:52:46 Jar:        lib/server/omero-blitz.jar     jar	5.8.6-SNAPSHOT		
01:52:46 Jar:        lib/server/omero-common.jar    jar	5.7.6-SNAPSHOT		
01:52:46 Jar:        lib/server/omero-gateway.jar   jar	5.11.1-SNAPSHOT		
01:52:46 Jar:        lib/server/omero-model.jar     jar	5.7.6-SNAPSHOT		
01:52:46 Jar:        lib/server/omero-renderer.jar  jar	5.6.6-SNAPSHOT		
01:52:46 Jar:        lib/server/omero-romio.jar     jar	5.8.6-SNAPSHOT		
01:52:46 Jar:        lib/server/omero-server.jar    jar	5.7.6-SNAPSHOT		
01:52:47 + deactivate
01:52:47 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
01:52:47 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
01:52:47 + export PATH
01:52:47 + unset _OLD_VIRTUAL_PATH
01:52:47 + '[' -n '' ']'
01:52:47 + hash -r
01:52:47 + '[' -n '' ']'
01:52:47 + unset VIRTUAL_ENV
01:52:47 + unset VIRTUAL_ENV_PROMPT
01:52:47 + '[' '!' '' = nondestructive ']'
01:52:47 + unset -f deactivate
01:52:47 Finished: SUCCESS