Console

19:46:36 Started by user devspace
19:46:36 Running as SYSTEM
19:46:36 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
19:46:36 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11249969185620403318.sh
19:46:36 + source /home/settings.env
19:46:36 ++ OMERO_DB_HOST=pg
19:46:36 ++ OMERO_DB_USER=postgres
19:46:36 ++ OMERO_DB_PASS=
19:46:36 ++ OMERO_ROOT_PASS=omero
19:46:36 ++ OMERO_DATA_DIR=/OMERO
19:46:36 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
19:46:36 + OMERO_DB_NAME=OMERO-server
19:46:36 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
19:46:36 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
19:46:36 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
19:46:36 + OMERO_DATA_DIR=/home/omero/omero-server-data
19:46:36 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
19:46:36 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
19:46:36 ++ deactivate nondestructive
19:46:36 ++ '[' -n '' ']'
19:46:36 ++ '[' -n '' ']'
19:46:36 ++ hash -r
19:46:36 ++ '[' -n '' ']'
19:46:36 ++ unset VIRTUAL_ENV
19:46:36 ++ unset VIRTUAL_ENV_PROMPT
19:46:36 ++ '[' '!' nondestructive = nondestructive ']'
19:46:36 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
19:46:36 ++ export VIRTUAL_ENV
19:46:36 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
19:46:36 ++ 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
19:46:36 ++ export PATH
19:46:36 ++ '[' -n '' ']'
19:46:36 ++ '[' -z '' ']'
19:46:36 ++ _OLD_VIRTUAL_PS1=
19:46:36 ++ PS1='(.venv3) '
19:46:36 ++ export PS1
19:46:36 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
19:46:36 ++ export VIRTUAL_ENV_PROMPT
19:46:36 ++ hash -r
19:46:36 + omero admin stop
19:47:07 Server not running
19:47:08 + echo not running
19:47:08 not running
19:47:08 + sleep 5
19:47:13 + deactivate
19:47:13 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
19:47:13 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
19:47:13 + export PATH
19:47:13 + unset _OLD_VIRTUAL_PATH
19:47:13 + '[' -n '' ']'
19:47:13 + hash -r
19:47:13 + '[' -n '' ']'
19:47:13 + unset VIRTUAL_ENV
19:47:13 + unset VIRTUAL_ENV_PROMPT
19:47:13 + '[' '!' '' = nondestructive ']'
19:47:13 + unset -f deactivate
19:47:13 + rm -rf /home/omero/workspace/OMERO-server/.venv3
19:49:34 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
19:49:55 + '[' false = true ']'
19:49:55 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
19:49:55 Skipping PURGE_DATA:CleanDbAndRepo
19:49:55 + 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-5.23.1.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
19:50:01 Copied 1 artifact from "OMERO-build" build number 52
19:50:01 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 45
19:50:01 Copied 2 artifacts from "OMERO-build-build" build number 57
19:50:01 [OMERO-server] $ /bin/bash -xe /tmp/jenkins17615794239844922582.sh
19:50:01 + source /home/settings.env
19:50:01 ++ OMERO_DB_HOST=pg
19:50:01 ++ OMERO_DB_USER=postgres
19:50:01 ++ OMERO_DB_PASS=
19:50:01 ++ OMERO_ROOT_PASS=omero
19:50:01 ++ OMERO_DATA_DIR=/OMERO
19:50:01 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
19:50:01 + OMERO_DB_NAME=OMERO-server
19:50:01 + OMERO_DATA_DIR=/home/omero/omero-server-data
19:50:01 + mkdir -p /home/omero/omero-server-data
19:50:01 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
19:50:01 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
19:50:01 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
19:50:01 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
19:50:01 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
19:50:01 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
19:50:01 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
19:50:01 ++ ls OMERO.server-5.6.3-655-4199fa2d41-ice36-b52.zip
19:50:01 + ZIP=OMERO.server-5.6.3-655-4199fa2d41-ice36-b52.zip
19:50:01 + '[' '!' -z '' ']'
19:50:01 + DIST=OMERO.server-5.6.3-655-4199fa2d41-ice36-b52
19:50:01 + unzip OMERO.server-5.6.3-655-4199fa2d41-ice36-b52.zip
19:50:01 Archive:  OMERO.server-5.6.3-655-4199fa2d41-ice36-b52.zip
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/blitz/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/grid/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/profiles/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/error/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/grid/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/luts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/luts/janelia/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/luts/matplotlib/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/luts/ncsa_paledit/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/luts/seaborn/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/luts/wcif/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/analysis_scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/annotation_scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/export_scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/figure_scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/import_scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/scripts/omero/util_scripts/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/server/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/share/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/share/licenses/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/misc/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__1/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__10/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__11/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__2/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__3/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__4/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__5/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__6/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__7/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__8/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3A__9/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3__4/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3__5/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3__6/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO3__7/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.1__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.2__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.2__0/t/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.3__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.4__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.0__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.1__1/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.2__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4DEV__1/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4DEV__2/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4DEV__3/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/var/
19:50:01    creating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/var/tmp/
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/LICENSE.txt  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/backup.cfg  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/blitz/mail-senders.example  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/blitz/mail-server.example  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/build.properties  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/env.bat  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/env.sh  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/hibernate.properties  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/ice.config  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/logback-cli.xml  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/logback-indexing-cli.xml  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/logback-indexing.xml  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/logback.xml  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/mime.types  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/node1.cfg  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/node2.cfg  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/omero.properties  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/profiles/psql  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/rollover.cfg  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/Windows.cfg  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/error/maintainance.html  
19:50:01   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/grid/README  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/grid/default.xml  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/grid/templates.xml  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/grid/windefault.xml  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/ice.config  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/internal.cfg  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/master.cfg  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/templates/robot.template  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/etc/testdropbox.config  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/history.rst  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/OMEZarrReader.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/accessors-smart.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/activation.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/aggdesigner-algorithm.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/aircompressor.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/antlr.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/aopalliance.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/apiguardian-api.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/asm.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/avatica-core.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/avatica-metrics.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/aws-java-sdk-core.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/aws-java-sdk-kms.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/aws-java-sdk-s3.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/base.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-anim.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-awt-util.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-bridge.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-codec.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-constants.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-css.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-dom.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-ext.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-gvt.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-i18n.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-parser.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-script.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-shared-resources.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-svg-dom.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-svggen.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-transcoder.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-util.jar  
19:50:02   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/lib/client/batik-xml.jar  
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19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.3__0/OMERO4.2__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.4__0/OMERO4.1__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4.4__0/OMERO4.3__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO4__0/OMERO3A__11.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.0__0/OMERO4.4__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.1__1/OMERO5.0__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.1__1/OMERO5.1__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.2__0/OMERO5.1__1.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/OMERO5.2__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/delete-ns-orphans.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/OMERO5.3__0.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/OMERO5.3__1.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/psql-footer.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/psql-header.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/schema.sql  
19:50:15   inflating: OMERO.server-5.6.3-655-4199fa2d41-ice36-b52/sql/psql/OMERO5.4__0/views.sql  
19:50:16 + rm -f OMERO.server-5.6.3-655-4199fa2d41-ice36-b52.zip
19:50:16 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-655-4199fa2d41-ice36-b52 /home/omero/workspace/OMERO-server/OMERO.server
19:50:16 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
19:50:16 ++ deactivate nondestructive
19:50:16 ++ '[' -n '' ']'
19:50:16 ++ '[' -n '' ']'
19:50:16 ++ hash -r
19:50:16 ++ '[' -n '' ']'
19:50:16 ++ unset VIRTUAL_ENV
19:50:16 ++ unset VIRTUAL_ENV_PROMPT
19:50:16 ++ '[' '!' nondestructive = nondestructive ']'
19:50:16 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
19:50:16 ++ export VIRTUAL_ENV
19:50:16 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
19:50:16 ++ 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
19:50:16 ++ export PATH
19:50:16 ++ '[' -n '' ']'
19:50:16 ++ '[' -z '' ']'
19:50:16 ++ _OLD_VIRTUAL_PS1=
19:50:16 ++ PS1='(.venv3) '
19:50:16 ++ export PS1
19:50:16 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
19:50:16 ++ export VIRTUAL_ENV_PROMPT
19:50:16 ++ hash -r
19:50:16 + pip install -U pip
19:50:17 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
19:50:17 Collecting pip
19:50:17   Using cached pip-26.2.1-py3-none-any.whl (1.8 MB)
19:50:17 Installing collected packages: pip
19:50:17   Attempting uninstall: pip
19:50:17     Found existing installation: pip 22.3.1
19:50:18     Uninstalling pip-22.3.1:
19:50:18       Successfully uninstalled pip-22.3.1
19:50:31 Successfully installed pip-26.2.1
19:50:31 + 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
19:50:32 Collecting zeroc-ice==3.6.5
19:50:32   Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
19:50:35      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 15.6 MB/s  0:00:02
19:50:35 Installing collected packages: zeroc-ice
19:50:38 Successfully installed zeroc-ice-3.6.5
19:50:38 + pip install markdown
19:50:39 Collecting markdown
19:50:39   Using cached markdown-3.10.3-py3-none-any.whl.metadata (5.1 kB)
19:50:39 Using cached markdown-3.10.3-py3-none-any.whl (110 kB)
19:50:39 Installing collected packages: markdown
19:50:40 Successfully installed markdown-3.10.3
19:50:40 + pip install reportlab
19:50:41 Collecting reportlab
19:50:41   Using cached reportlab-5.0.0-py3-none-any.whl.metadata (1.6 kB)
19:50:41 Collecting pillow>=9.0.0 (from reportlab)
19:50:41   Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
19:50:41 Collecting charset-normalizer (from reportlab)
19:50:41   Using cached charset_normalizer-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (45 kB)
19:50:41 Using cached reportlab-5.0.0-py3-none-any.whl (2.0 MB)
19:50:41 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
19:50:41 Using cached charset_normalizer-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (262 kB)
19:50:41 Installing collected packages: pillow, charset-normalizer, reportlab
19:50:49 
19:50:49 Successfully installed charset-normalizer-3.5.1 pillow-12.3.0 reportlab-5.0.0
19:50:49 + pip install omego
19:50:50 Collecting omego
19:50:50   Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
19:50:50 Collecting future (from omego)
19:50:50   Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
19:50:51 Collecting yaclifw>=0.1.1 (from omego)
19:50:51   Using cached yaclifw-0.2.0-py3-none-any.whl
19:50:51 Collecting six (from yaclifw>=0.1.1->omego)
19:50:51   Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
19:50:51 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
19:50:51 Using cached future-1.0.0-py3-none-any.whl (491 kB)
19:50:51 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
19:50:51 Installing collected packages: six, future, yaclifw, omego
19:50:56 
19:50:56 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
19:50:56 + pip install tables
19:50:57 Collecting tables
19:50:57   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)
19:50:57 Collecting numpy>=1.20.0 (from tables)
19:50:57   Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
19:50:57 Collecting numexpr>=2.6.2 (from tables)
19:50:57   Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
19:50:57 Collecting packaging (from tables)
19:50:57   Using cached packaging-26.3-py3-none-any.whl.metadata (3.5 kB)
19:50:57 Collecting py-cpuinfo (from tables)
19:50:57   Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
19:50:58 Collecting blosc2>=2.3.0 (from tables)
19:50:58   Using cached blosc2-4.11.0-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (7.8 kB)
19:50:58 Collecting ndindex (from blosc2>=2.3.0->tables)
19:50:58   Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
19:50:58 Collecting msgpack (from blosc2>=2.3.0->tables)
19:50:58   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)
19:50:58 Collecting pydantic (from blosc2>=2.3.0->tables)
19:50:58   Using cached pydantic-2.13.4-py3-none-any.whl.metadata (109 kB)
19:50:58 Collecting httpx[http2] (from blosc2>=2.3.0->tables)
19:50:58   Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
19:50:58 Collecting rich (from blosc2>=2.3.0->tables)
19:50:58   Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
19:50:58 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
19:50:58   Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
19:50:59 Collecting anyio (from httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached anyio-4.14.2-py3-none-any.whl.metadata (4.6 kB)
19:50:59 Collecting certifi (from httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached certifi-2026.7.22-py3-none-any.whl.metadata (2.5 kB)
19:50:59 Collecting httpcore==1.* (from httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB)
19:50:59 Collecting idna (from httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached idna-3.19-py3-none-any.whl.metadata (9.2 kB)
19:50:59 Collecting h2<5,>=3 (from httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached h2-4.4.1-py3-none-any.whl.metadata (3.8 kB)
19:50:59 Collecting hyperframe<7,>=6.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached hyperframe-6.1.0-py3-none-any.whl.metadata (4.3 kB)
19:50:59 Collecting hpack<5,>=4.2 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached hpack-4.2.0-py3-none-any.whl.metadata (3.3 kB)
19:50:59 Collecting h11>=0.16 (from httpcore==1.*->httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB)
19:50:59 Collecting typing_extensions>=4.5 (from anyio->httpx[http2]->blosc2>=2.3.0->tables)
19:50:59   Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
19:50:59 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
19:50:59   Using cached annotated_types-0.8.0-py3-none-any.whl.metadata (15 kB)
19:51:00 Collecting pydantic-core==2.46.4 (from pydantic->blosc2>=2.3.0->tables)
19:51:00   Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
19:51:00 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
19:51:00   Using cached typing_inspection-0.4.4-py3-none-any.whl.metadata (2.6 kB)
19:51:00 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
19:51:00   Using cached markdown_it_py-4.2.0-py3-none-any.whl.metadata (7.4 kB)
19:51:01 Collecting pygments<3.0.0,>=2.13.0 (from rich->blosc2>=2.3.0->tables)
19:51:01   Using cached pygments-2.21.0-py3-none-any.whl.metadata (2.5 kB)
19:51:01 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
19:51:01   Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
19:51:01 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)
19:51:01 Using cached blosc2-4.11.0-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.5 MB)
19:51:01 Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (443 kB)
19:51:01 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
19:51:01 Using cached httpx-0.28.1-py3-none-any.whl (73 kB)
19:51:01 Using cached h2-4.4.1-py3-none-any.whl (62 kB)
19:51:01 Using cached hpack-4.2.0-py3-none-any.whl (34 kB)
19:51:01 Using cached httpcore-1.0.9-py3-none-any.whl (78 kB)
19:51:01 Using cached hyperframe-6.1.0-py3-none-any.whl (13 kB)
19:51:01 Using cached h11-0.16.0-py3-none-any.whl (37 kB)
19:51:01 Using cached anyio-4.14.2-py3-none-any.whl (125 kB)
19:51:01 Using cached idna-3.19-py3-none-any.whl (68 kB)
19:51:01 Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB)
19:51:01 Using cached certifi-2026.7.22-py3-none-any.whl (136 kB)
19:51:01 Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (423 kB)
19:51:01 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
19:51:01 Using cached packaging-26.3-py3-none-any.whl (129 kB)
19:51:01 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
19:51:02 Using cached pydantic-2.13.4-py3-none-any.whl (472 kB)
19:51:02 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
19:51:02 Using cached annotated_types-0.8.0-py3-none-any.whl (13 kB)
19:51:02 Using cached typing_inspection-0.4.4-py3-none-any.whl (14 kB)
19:51:02 Using cached rich-15.0.0-py3-none-any.whl (310 kB)
19:51:02 Using cached pygments-2.21.0-py3-none-any.whl (1.3 MB)
19:51:02 Using cached markdown_it_py-4.2.0-py3-none-any.whl (91 kB)
19:51:02 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
19:51:02 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
19:51:02 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
19:51:47 
19:51:47 Successfully installed annotated-types-0.8.0 anyio-4.14.2 blosc2-4.11.0 certifi-2026.7.22 h11-0.16.0 h2-4.4.1 hpack-4.2.0 httpcore-1.0.9 httpx-0.28.1 hyperframe-6.1.0 idna-3.19 markdown-it-py-4.2.0 mdurl-0.1.2 msgpack-1.2.1 ndindex-1.10.1 numexpr-2.14.2 numpy-2.4.6 packaging-26.3 py-cpuinfo-9.0.0 pydantic-2.13.4 pydantic-core-2.46.4 pygments-2.21.0 rich-15.0.0 tables-3.11.1 threadpoolctl-3.6.0 typing-inspection-0.4.4 typing_extensions-4.16.0
19:51:47 + pip install jinja2
19:51:48 Collecting jinja2
19:51:48   Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
19:51:49 Collecting MarkupSafe>=2.0 (from jinja2)
19:51:49   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)
19:51:49 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
19:51:49 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
19:51:49 Installing collected packages: MarkupSafe, jinja2
19:51:50 
19:51:50 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
19:51:50 + pip install omero-py
19:51:51 Collecting omero-py
19:51:51   Using cached omero_py-5.23.0-py3-none-any.whl.metadata (6.5 kB)
19:51:51 Collecting appdirs (from omero-py)
19:51:51   Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
19:51:51 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
19:51:51 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
19:51:51 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
19:51:51 Collecting PyYAML (from omero-py)
19:51:51   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)
19:51:51 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
19:51:51 Collecting requests (from omero-py)
19:51:51   Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
19:51:51 Collecting portalocker (from omero-py)
19:51:51   Using cached portalocker-4.1.0-py3-none-any.whl.metadata (11 kB)
19:51:51 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.5.1)
19:51:51 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.19)
19:51:52 Collecting urllib3<3,>=1.26 (from requests->omero-py)
19:51:52   Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
19:51:52 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.7.22)
19:51:52 Using cached omero_py-5.23.0-py3-none-any.whl (2.8 MB)
19:51:52 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
19:51:52 Using cached portalocker-4.1.0-py3-none-any.whl (65 kB)
19:51:52 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
19:51:52 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
19:51:52 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
19:51:52 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, requests, omero-py
19:52:09 
19:52:09 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.23.0 portalocker-4.1.0 requests-2.34.2 urllib3-2.7.0
19:52:09 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
19:52:10 Collecting omero-metadata
19:52:10   Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-nnubte3a/omero-metadata_b1aa574bde704ef28c52182ecf747f43
19:52:10   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-nnubte3a/omero-metadata_b1aa574bde704ef28c52182ecf747f43
19:52:11   Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit a292a4f14f3e6ffde1acc5ba08a7ca0ebf1a29b7
19:52:11   Installing build dependencies: started
19:52:13   Installing build dependencies: finished with status 'done'
19:52:13   Getting requirements to build wheel: started
19:52:13   Getting requirements to build wheel: finished with status 'done'
19:52:13   Preparing metadata (pyproject.toml): started
19:52:13   Preparing metadata (pyproject.toml): finished with status 'done'
19:52:13 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.23.0)
19:52:14 Collecting pandas<3,>=2 (from omero-metadata)
19:52:14   Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
19:52:14 Requirement already satisfied: numpy>=1.23.2 in ./.venv3/lib64/python3.11/site-packages (from pandas<3,>=2->omero-metadata) (2.4.6)
19:52:14 Collecting python-dateutil>=2.8.2 (from pandas<3,>=2->omero-metadata)
19:52:14   Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
19:52:14 Collecting pytz>=2020.1 (from pandas<3,>=2->omero-metadata)
19:52:14   Using cached pytz-2026.3.post1-py2.py3-none-any.whl.metadata (22 kB)
19:52:14 Collecting tzdata>=2022.7 (from pandas<3,>=2->omero-metadata)
19:52:14   Using cached tzdata-2026.3-py2.py3-none-any.whl.metadata (1.4 kB)
19:52:14 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
19:52:14 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
19:52:14 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)
19:52:14 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (6.0.3)
19:52:14 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
19:52:14 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
19:52:14 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (4.1.0)
19:52:14 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil>=2.8.2->pandas<3,>=2->omero-metadata) (1.17.0)
19:52:14 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.5.1)
19:52:14 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.19)
19:52:14 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)
19:52:14 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.7.22)
19:52:14 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB)
19:52:14 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
19:52:14 Using cached pytz-2026.3.post1-py2.py3-none-any.whl (508 kB)
19:52:14 Using cached tzdata-2026.3-py2.py3-none-any.whl (348 kB)
19:52:14 Building wheels for collected packages: omero-metadata
19:52:14   Building wheel for omero-metadata (pyproject.toml): started
19:52:15   Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
19:52:15   Created wheel for omero-metadata: filename=omero_metadata-0.14.1.dev0-py3-none-any.whl size=39360 sha256=5d9e2796a90b365dc5618d5c6527fe3059d4bc524c643e70f80f386fd903a9c6
19:52:15   Stored in directory: /tmp/pip-ephem-wheel-cache-znysnl6y/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
19:52:15 Successfully built omero-metadata
19:52:15 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
19:53:02 
19:53:02 Successfully installed omero-metadata-0.14.1.dev0 pandas-2.3.3 python-dateutil-2.9.0.post0 pytz-2026.3.post1 tzdata-2026.3
19:53:02 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
19:53:03 Collecting omero-cli-render
19:53:03   Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-yzcl3vxz/omero-cli-render_be642b582a48443eb465a81f98e8ec5c
19:53:03   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-yzcl3vxz/omero-cli-render_be642b582a48443eb465a81f98e8ec5c
19:53:04   Running command git checkout -b merge_ci --track origin/merge_ci
19:53:05   Switched to a new branch 'merge_ci'
19:53:05   branch 'merge_ci' set up to track 'origin/merge_ci'.
19:53:05   Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit d65945971b5d4b35fa8f78301dd96724e1b66b49
19:53:05   Installing build dependencies: started
19:53:06   Installing build dependencies: finished with status 'done'
19:53:06   Getting requirements to build wheel: started
19:53:06   Getting requirements to build wheel: finished with status 'done'
19:53:06   Preparing metadata (pyproject.toml): started
19:53:06   Preparing metadata (pyproject.toml): finished with status 'done'
19:53:06 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
19:53:06 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.23.0)
19:53:06 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
19:53:06 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
19:53:06 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)
19:53:06 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)
19:53:06 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)
19:53:06 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
19:53:06 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (4.1.0)
19:53:06 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.5.1)
19:53:06 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.19)
19:53:06 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)
19:53:06 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.7.22)
19:53:06 Building wheels for collected packages: omero-cli-render
19:53:06   Building wheel for omero-cli-render (pyproject.toml): started
19:53:07   Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
19:53:07   Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19841 sha256=c5f76a17ba6a2401b54497944bc479483e64ffaaeff7df9bf05e4f3b2bd2c0d8
19:53:07   Stored in directory: /tmp/pip-ephem-wheel-cache-3l_5_tec/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
19:53:07 Successfully built omero-cli-render
19:53:07 Installing collected packages: omero-cli-render
19:53:07 Successfully installed omero-cli-render-0.8.2.dev0
19:53:07 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
19:53:08 Collecting omero-cli-duplicate
19:53:08   Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-asxh7dr7/omero-cli-duplicate_1c12c3789877484b86621acf528d5bce
19:53:08   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-asxh7dr7/omero-cli-duplicate_1c12c3789877484b86621acf528d5bce
19:53:09   Running command git checkout -b merge_ci --track origin/merge_ci
19:53:09   Switched to a new branch 'merge_ci'
19:53:09   branch 'merge_ci' set up to track 'origin/merge_ci'.
19:53:09   Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit c68dc6a63687f99875baad0ba06e6bfd68a599fb
19:53:09   Installing build dependencies: started
19:53:11   Installing build dependencies: finished with status 'done'
19:53:11   Getting requirements to build wheel: started
19:53:11   Getting requirements to build wheel: finished with status 'done'
19:53:11   Preparing metadata (pyproject.toml): started
19:53:11   Preparing metadata (pyproject.toml): finished with status 'done'
19:53:11 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.23.0)
19:53:11 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
19:53:11 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
19:53:11 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
19:53:11 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)
19:53:11 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
19:53:11 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)
19:53:11 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.34.2)
19:53:11 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (4.1.0)
19:53:11 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.5.1)
19:53:11 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.19)
19:53:11 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)
19:53:11 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.7.22)
19:53:11 Building wheels for collected packages: omero-cli-duplicate
19:53:11   Building wheel for omero-cli-duplicate (pyproject.toml): started
19:53:12   Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
19:53:12   Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11540 sha256=e5f5463abbbb8badb5568775c54e92ef424e61c30014f24b9aca7ccae023a308
19:53:12   Stored in directory: /tmp/pip-ephem-wheel-cache-8spwc8i9/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
19:53:12 Successfully built omero-cli-duplicate
19:53:12 Installing collected packages: omero-cli-duplicate
19:53:12 Successfully installed omero-cli-duplicate-0.4.1.dev0
19:53:12 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
19:53:13 Collecting omero-cli-zarr
19:53:13   Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-ua3gnu16/omero-cli-zarr_f8a1ff54e01640ebab63930067ee1432
19:53:13   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-ua3gnu16/omero-cli-zarr_f8a1ff54e01640ebab63930067ee1432
19:53:14   Running command git checkout -b merge_ci --track origin/merge_ci
19:53:15   Switched to a new branch 'merge_ci'
19:53:15   branch 'merge_ci' set up to track 'origin/merge_ci'.
19:53:15   Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit 6649bcd9287445302763e27e8c7a06e5a1976f8c
19:53:15   Installing build dependencies: started
19:53:16   Installing build dependencies: finished with status 'done'
19:53:16   Getting requirements to build wheel: started
19:53:16   Getting requirements to build wheel: finished with status 'done'
19:53:16   Installing backend dependencies: started
19:53:18   Installing backend dependencies: finished with status 'done'
19:53:18   Preparing metadata (pyproject.toml): started
19:53:18   Preparing metadata (pyproject.toml): finished with status 'done'
19:53:18 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.23.0)
19:53:18 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
19:53:18   Using cached ome_zarr-0.18.0-py3-none-any.whl.metadata (2.9 kB)
19:53:18 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.6)
19:53:18 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:18   Using cached dask-2026.7.1-py3-none-any.whl.metadata (3.8 kB)
19:53:18 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:18   Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
19:53:19 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)
19:53:19   Using cached fsspec-2026.7.0-py3-none-any.whl.metadata (10 kB)
19:53:19 Collecting aiohttp (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:19   Using cached aiohttp-3.14.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
19:53:19 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.34.2)
19:53:19 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
19:53:20 Collecting toolz (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB)
19:53:20 Collecting rangehttpserver (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl.metadata (769 bytes)
19:53:20 Collecting ome-zarr-models>=1.6 (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached ome_zarr_models-1.7-py3-none-any.whl.metadata (3.0 kB)
19:53:20 Collecting Deprecated (from ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB)
19:53:20 Collecting click>=8.1 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached click-8.4.2-py3-none-any.whl.metadata (2.6 kB)
19:53:20 Collecting cloudpickle>=3.0.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
19:53:20   Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB)
19:53:20 Requirement already satisfied: packaging>=20.0 in ./.venv3/lib64/python3.11/site-packages (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr) (26.3)
19:53:20 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:20 Collecting importlib_metadata>=4.13.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:22 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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19:53:23   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)
19:53:23 Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in ./.venv3/lib64/python3.11/site-packages (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr) (2.9.0.post0)
19:53:23 Collecting wrapt<3.0.0,>=1.10.10 (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:24 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:24 Collecting aiosignal>=1.4.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:24 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:24 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:24 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:24 Collecting yarl<2.0,>=1.17.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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19:53:25 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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19:53:26 Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB)
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19:53:26 Using cached wrapt-2.3.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (161 kB)
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19:53:27 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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19:53:27 Using cached zipp-4.1.0-py3-none-any.whl (10 kB)
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19:53:27 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
19:53:27 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
19:53:28 Building wheels for collected packages: omero-cli-zarr
19:53:28   Building wheel for omero-cli-zarr (pyproject.toml): started
19:53:28   Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
19:53:28   Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev168+g6649bcd-py3-none-any.whl size=38399 sha256=e8372bf41c912b6fff853322d769a32a35b5edd27b56483714f45888ef78e9d0
19:53:28   Stored in directory: /tmp/pip-ephem-wheel-cache-8ckp28mv/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
19:53:28 Successfully built omero-cli-zarr
19:53:28 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
19:54:03   Attempting uninstall: pydantic-core
19:54:03     Found existing installation: pydantic_core 2.46.4
19:54:03     Uninstalling pydantic_core-2.46.4:
19:54:03       Successfully uninstalled pydantic_core-2.46.4
19:54:36   Attempting uninstall: pydantic
19:54:36     Found existing installation: pydantic 2.13.4
19:54:36     Uninstalling pydantic-2.13.4:
19:54:36       Successfully uninstalled pydantic-2.13.4
19:55:16 
19:55:16 Successfully installed Deprecated-1.3.1 aiobotocore-3.9.0 aiohappyeyeballs-2.7.1 aiohttp-3.14.3 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.56 click-8.4.2 cloudpickle-3.1.2 dask-2026.7.1 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.7.0 google-crc32c-1.8.0 imageio-2.37.4 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.dev168+g6649bcd 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-2026.7.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 wrapt-2.3.0 yarl-1.24.5 zarr-3.1.6 zipp-4.1.0
19:55:16 + pip install omero-certificates
19:55:18 Collecting omero-certificates
19:55:18   Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
19:55:18 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.23.0)
19:55:18 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
19:55:18 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
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19:55:18 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.34.2)
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19:55:18 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.19)
19:55:18 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)
19:55:18 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.7.22)
19:55:18 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
19:55:19 Installing collected packages: omero-certificates
19:55:19 Successfully installed omero-certificates-0.4.0
19:55:19 + for x in *.tar.gz
19:55:19 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
19:55:20 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
19:55:20   Installing build dependencies: started
19:55:22   Installing build dependencies: finished with status 'done'
19:55:22   Getting requirements to build wheel: started
19:55:22   Getting requirements to build wheel: finished with status 'done'
19:55:22   Preparing metadata (pyproject.toml): started
19:55:23   Preparing metadata (pyproject.toml): finished with status 'done'
19:55:23 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.23.0)
19:55:23 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
19:55:23 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
19:55:23 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)
19:55:23 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)
19:55:23 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
19:55:23 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)
19:55:23 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
19:55:23 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (4.1.0)
19:55:23 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.5.1)
19:55:23 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.19)
19:55:23 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)
19:55:23 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.7.22)
19:55:23 Building wheels for collected packages: omero-dropbox
19:55:23   Building wheel for omero-dropbox (pyproject.toml): started
19:55:23   Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
19:55:23   Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49155 sha256=40a05ff29add108c0a0af24b234e30f54e4fed7b19bb58762ac45afd8f0c63e9
19:55:23   Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
19:55:23 Successfully built omero-dropbox
19:55:23 Installing collected packages: omero-dropbox
19:55:24 Successfully installed omero-dropbox-5.7.1.dev0
19:55:24 + for x in *.tar.gz
19:55:24 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
19:55:25 Processing ./omero_marshal-0.9.2.dev0.tar.gz
19:55:25   Installing build dependencies: started
19:55:27   Installing build dependencies: finished with status 'done'
19:55:27   Getting requirements to build wheel: started
19:55:27   Getting requirements to build wheel: finished with status 'done'
19:55:27   Preparing metadata (pyproject.toml): started
19:55:27   Preparing metadata (pyproject.toml): finished with status 'done'
19:55:27 Building wheels for collected packages: omero_marshal
19:55:27   Building wheel for omero_marshal (pyproject.toml): started
19:55:28   Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
19:55:28   Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88121 sha256=7f4f00114b0a774f7a332da286cce2b7a828d59ab75226a3037885c2a82f3450
19:55:28   Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
19:55:28 Successfully built omero_marshal
19:55:28 Installing collected packages: omero_marshal
19:55:30 Successfully installed omero_marshal-0.9.2.dev0
19:55:30 + for x in *.tar.gz
19:55:30 + pip install -U omero_py-5.23.1.dev0.tar.gz
19:55:32 Processing ./omero_py-5.23.1.dev0.tar.gz
19:55:32   Installing build dependencies: started
19:55:33   Installing build dependencies: finished with status 'done'
19:55:33   Getting requirements to build wheel: started
19:55:34   Getting requirements to build wheel: finished with status 'done'
19:55:34   Preparing metadata (pyproject.toml): started
19:55:34   Preparing metadata (pyproject.toml): finished with status 'done'
19:55:34 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (1.4.4)
19:55:34 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (1.0.0)
19:55:34 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (2.4.6)
19:55:34 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (12.3.0)
19:55:34 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (6.0.3)
19:55:34 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (3.6.5)
19:55:34 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (2.34.2)
19:55:34 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (4.1.0)
19:55:34 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (3.5.1)
19:55:34 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (3.19)
19:55:34 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (2.7.0)
19:55:34 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (2026.7.22)
19:55:34 Building wheels for collected packages: omero-py
19:55:34   Building wheel for omero-py (pyproject.toml): started
19:55:35   Building wheel for omero-py (pyproject.toml): finished with status 'done'
19:55:35   Created wheel for omero-py: filename=omero_py-5.23.1.dev0-py3-none-any.whl size=2786959 sha256=d0bda51c6070e6745a5b0d2d91e72511b1593e6c03336cae7d37b97ee8ab3acf
19:55:35   Stored in directory: /home/omero/.cache/pip/wheels/99/0a/38/75d301c3c2feff37b61c572a590c9d07ab2e52df205857b74d
19:55:35 Successfully built omero-py
19:55:36 Installing collected packages: omero-py
19:55:36   Attempting uninstall: omero-py
19:55:36     Found existing installation: omero-py 5.23.0
19:55:37     Uninstalling omero-py-5.23.0:
19:55:50       Successfully uninstalled omero-py-5.23.0
19:56:05 Successfully installed omero-py-5.23.1.dev0
19:56:05 + for x in *.tar.gz
19:56:05 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
19:56:06 Processing ./omero_scripts-5.10.1.dev0.tar.gz
19:56:06   Installing build dependencies: started
19:56:08   Installing build dependencies: finished with status 'done'
19:56:08   Getting requirements to build wheel: started
19:56:08   Getting requirements to build wheel: finished with status 'done'
19:56:08   Preparing metadata (pyproject.toml): started
19:56:08   Preparing metadata (pyproject.toml): finished with status 'done'
19:56:08 Building wheels for collected packages: omero-scripts
19:56:08   Building wheel for omero-scripts (pyproject.toml): started
19:56:09   Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
19:56:09   Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137217 sha256=156e79cf58df84ac052611d4d6f86cfc0ea03af723b70f167e3bf61317acf56f
19:56:09   Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
19:56:09 Successfully built omero-scripts
19:56:09 Installing collected packages: omero-scripts
19:56:10 Successfully installed omero-scripts-5.10.1.dev0
19:56:10 + for x in *.tar.gz
19:56:10 + pip install -U omero_web-5.32.1.dev0.tar.gz
19:56:11 Processing ./omero_web-5.32.1.dev0.tar.gz
19:56:11   Installing build dependencies: started
19:56:13   Installing build dependencies: finished with status 'done'
19:56:13   Getting requirements to build wheel: started
19:56:13   Getting requirements to build wheel: finished with status 'done'
19:56:13   Preparing metadata (pyproject.toml): started
19:56:13   Preparing metadata (pyproject.toml): finished with status 'done'
19:56:13 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (5.23.1.dev0)
19:56:14 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.32.1.dev0)
19:56:14   Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
19:56:14 Collecting Django<5.3,>=5.2.9 (from omero-web==5.32.1.dev0)
19:56:14   Using cached django-5.2.17-py3-none-any.whl.metadata (4.1 kB)
19:56:14 Collecting django-pipeline>=4.1.0 (from omero-web==5.32.1.dev0)
19:56:14   Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
19:56:14 Collecting django-cors-headers==3.7.0 (from omero-web==5.32.1.dev0)
19:56:14   Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
19:56:14 Collecting whitenoise>=5.3.0 (from omero-web==5.32.1.dev0)
19:56:14   Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
19:56:14 Collecting gunicorn>=19.3 (from omero-web==5.32.1.dev0)
19:56:14   Using cached gunicorn-26.1.0-py3-none-any.whl.metadata (5.5 kB)
19:56:14 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)
19:56:14 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (12.3.0)
19:56:14 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (2026.3.post1)
19:56:14 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (4.1.0)
19:56:14 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (26.3)
19:56:14 Collecting importlib-resources (from omero-web==5.32.1.dev0)
19:56:15   Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
19:56:15 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
19:56:15   Using cached asgiref-3.12.1-py3-none-any.whl.metadata (9.4 kB)
19:56:15 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
19:56:15   Using cached sqlparse-0.6.0-py3-none-any.whl.metadata (6.0 kB)
19:56:15 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)
19:56:15 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0)
19:56:15   Using cached wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB)
19:56:15 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)
19:56:15 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)
19:56:15 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)
19:56:15 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)
19:56:15 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)
19:56:15 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)
19:56:15 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) (3.5.1)
19:56:15 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) (3.19)
19:56:15 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)
19:56:15 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) (2026.7.22)
19:56:15 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
19:56:15 Using cached django-5.2.17-py3-none-any.whl (8.3 MB)
19:56:15 Using cached asgiref-3.12.1-py3-none-any.whl (25 kB)
19:56:15 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
19:56:15 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
19:56:15 Using cached gunicorn-26.1.0-py3-none-any.whl (216 kB)
19:56:15 Using cached sqlparse-0.6.0-py3-none-any.whl (50 kB)
19:56:15 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
19:56:15 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
19:56:15 Using cached wheel-0.48.0-py3-none-any.whl (33 kB)
19:56:15 Building wheels for collected packages: omero-web
19:56:15   Building wheel for omero-web (pyproject.toml): started
19:56:17   Building wheel for omero-web (pyproject.toml): finished with status 'done'
19:56:17   Created wheel for omero-web: filename=omero_web-5.32.1.dev0-py3-none-any.whl size=2820717 sha256=7228c6bae68a24b4a7f67580241e502a1e30d74d3ddb74d3151f9f88a4ab4d1d
19:56:17   Stored in directory: /home/omero/.cache/pip/wheels/e6/f6/6f/ec36dda9edad720aabd7330edafa8a6a62d6ebfa4c7467248f
19:56:17 Successfully built omero-web
19:56:17 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
19:57:26 
19:57:26 Successfully installed Django-5.2.17 asgiref-3.12.1 concurrent-log-handler-0.9.29 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-26.1.0 importlib-resources-7.1.0 omero-web-5.32.1.dev0 sqlparse-0.6.0 wheel-0.48.0 whitenoise-6.12.0
19:57:26 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
19:57:26 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
19:57:26 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
19:57:26 --2026-08-19 19:57:26--  https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
19:57:26 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.109.133, ...
19:57:26 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
19:57:26 HTTP request sent, awaiting response... 200 OK
19:57:27 Length: 133663 (131K) [text/plain]
19:57:27 Saving to: ‘Figure_To_Pdf.py’
19:57:27 
19:57:27      0K .......... .......... .......... .......... .......... 38% 2.89M 0s
19:57:27     50K .......... .......... .......... .......... .......... 76% 10.2M 0s
19:57:27    100K .......... .......... ..........                      100% 2.95M=0.03s
19:57:27 
19:57:27 2026-08-19 19:57:27 (4.01 MB/s) - ‘Figure_To_Pdf.py’ saved [133663/133663]
19:57:27 
19:57:27 + chmod 755 Figure_To_Pdf.py
19:57:27 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
19:57:27 + omero config set omero.db.name OMERO-server
19:57:34 + omero config set omero.db.host pg
19:57:39 + omero config set omero.db.user postgres
19:57:44 + omero config set omero.data.dir /home/omero/omero-server-data
19:57:50 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
19:57:55 + omero config set omero.db.poolsize 25
19:58:00 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
19:58:05 + omero config set omero.security.trustStorePassword changeit
19:58:10 + omero config set omero.mail.config true
19:58:16 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
19:58:21 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
19:58:26 + omero certificates
19:58:31 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
19:58:31 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
19:58:31 + '[' false = true ']'
19:58:31 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
19:58:31 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
19:58:31 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG            dbcommand => upgrade
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG               dbhost => localhost
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG               dbname => OMERO-server
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG               dbpass => omero
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG               dbuser => omero
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG             rootpass => omero
19:58:31 2026-08-19 19:58:31,663 [    omego.db] DEBUG            serverdir => /home/omero/workspace/OMERO-server/OMERO.server
19:58:31 2026-08-19 19:58:31,664 [omego.extern] INFO  Executing : omero version
19:58:36 OMERO.py version:
19:58:36 OMERO.server version:
19:58:36 5.6.3-655-4199fa2d41-ice36-b52
19:58:36 5.23.1.dev0
19:58:36 2026-08-19 19:58:36,590 [omego.extern] INFO  Completed [4.926 s]
19:58:36 2026-08-19 19:58:36,590 [omego.extern] DEBUG Using omero CLI from omero
19:58:36 2026-08-19 19:58:36,590 [    omego.db] INFO  DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
19:58:36 2026-08-19 19:58:36,591 [omego.extern] INFO  Running [current environment]: omero config get --show-password
19:58:36 2026-08-19 19:58:36,591 [omego.extern] INFO  Executing : omero config get --show-password
19:58:42 2026-08-19 19:58:42,348 [omego.extern] INFO  Completed [5.758 s]
19:58:42 2026-08-19 19:58:42,349 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
19:58:42 2026-08-19 19:58:42,349 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
19:58:42 2026-08-19 19:58:42,355 [omego.extern] INFO  Completed [0.006 s]
19:58:42 2026-08-19 19:58:42,355 [    omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.15\n'
19:58:42 2026-08-19 19:58:42,356 [    omego.db] INFO  psql version: psql (PostgreSQL) 16.15
19:58:42 
19:58:42 2026-08-19 19:58:42,356 [omego.extern] INFO  Running [current environment]: omero config get --show-password
19:58:42 2026-08-19 19:58:42,356 [omego.extern] INFO  Executing : omero config get --show-password
19:58:47 2026-08-19 19:58:47,592 [omego.extern] INFO  Completed [5.237 s]
19:58:47 2026-08-19 19:58:47,593 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
19:58:47 2026-08-19 19:58:47,593 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
19:58:47 2026-08-19 19:58:47,617 [omego.extern] INFO  Completed [0.024 s]
19:58:47 2026-08-19 19:58:47,617 [    omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.2") at port "5432".\n'
19:58:47 2026-08-19 19:58:47,617 [    omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
19:58:47 2026-08-19 19:58:47,617 [omego.extern] INFO  Running [current environment]: omero config get --show-password
19:58:47 2026-08-19 19:58:47,617 [omego.extern] INFO  Executing : omero config get --show-password
19:58:52 2026-08-19 19:58:52,736 [omego.extern] INFO  Completed [5.118 s]
19:58:52 2026-08-19 19:58:52,736 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
19:58:52 2026-08-19 19:58:52,736 [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
19:58:52 2026-08-19 19:58:52,866 [omego.extern] INFO  Completed [0.130 s]
19:58:52 2026-08-19 19:58:52,866 [    omego.db] DEBUG stdout: b'OMERO5.4|0\n'
19:58:52 2026-08-19 19:58:52,866 [    omego.db] INFO  Current omero db version: ('OMERO5.4', '0')
19:58:52 2026-08-19 19:58:52,922 [    omego.db] INFO  Database is already at OMERO5.4__0
19:58:52 + export LANG=en_US.UTF-8
19:58:52 + LANG=en_US.UTF-8
19:58:52 + export LANGUAGE=en_US:en
19:58:52 + LANGUAGE=en_US:en
19:58:52 + export LC_ALL=en_US.UTF-8
19:58:52 + LC_ALL=en_US.UTF-8
19:58:52 + BUILD_ID=DONT_KILL_ME
19:58:52 + omero admin start
19:59:04 WARNING: lock files in /home/omero/omero-server-data
19:59:04 ----------------------------------------
19:59:04 /home/omero/omero-server-data/.omero/repository/a3d421b1-9991-42f6-9eb8-867f8e8779af/.lock
19:59:04 ----------------------------------------
19:59:04 
19:59:04 You may want to stop all server processes and remove
19:59:04 these files manually. Lock files can remain after an
19:59:04 abrupt server outage and are especially frequent on
19:59:04 remotely mounted filesystems like NFS.
19:59:04 
19:59:04 No descriptor given. Using etc/grid/default.xml
19:59:16 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
19:59:16 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
19:59:16 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
19:59:16 Waiting on startup. Use CTRL-C to exit
19:59:16 + omero admin waitup
19:59:22 Waiting on startup. Use CTRL-C to exit
19:59:23 + omero admin diagnostics
19:59:28 
19:59:28 ================================================================================
19:59:28 OMERO Diagnostics (admin)
19:59:28 ================================================================================
19:59:28         
19:59:28 Commands:   java -version                  21.0.12   (/usr/bin/java)
19:59:28 Commands:   python -V                      3.11.13   (/home/omero/workspace/OMERO-server/.venv3/bin/python)
19:59:28 Commands:   icegridnode --version          3.6.5     (/opt/ice-3.6.5/bin/icegridnode)
19:59:28 Commands:   icegridadmin --version         3.6.5     (/opt/ice-3.6.5/bin/icegridadmin)
19:59:28 Commands:   psql --version                 16.15     (/usr/bin/psql)
19:59:28 Commands:   openssl version                3.5.527   (/usr/bin/openssl)
19:59:28 
19:59:28 Component:  OMERO.py                       5.23.1.dev0
19:59:28 Component:  OMERO.server                   5.6.3-655-4199fa2d41-ice36-b52
19:59:28 
19:59:28 Server:     icegridnode                    running
19:59:28 Server:     Blitz-0                        active (pid = 3345, enabled)
19:59:28 Server:     Indexer-0                      active (pid = 3367, enabled)
19:59:28 Server:     OMERO.Glacier2                 active (pid = 3371, enabled)
19:59:28 Server:     OMERO.IceStorm                 active (pid = 3397, enabled)
19:59:28 Server:     Processor-0                    activating (enabled)
19:59:28 Server:     Tables-0                       activating (enabled)
19:59:28 
19:59:28 Log dir:    /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
19:59:28 Log files:  Blitz-0.log                    22.7 KB       errors=0    warnings=1   
19:59:28 Log files:  DropBox.log                    n/a
19:59:28 Log files:  FileServer.log                 n/a
19:59:28 Log files:  Indexer-0.log                  2.6 KB       
19:59:28 Log files:  MonitorServer.log              n/a
19:59:28 Log files:  Processor-0.log                592 B        
19:59:28 Log files:  Tables-0.log                   841 B        
19:59:28 Log files:  TestDropBox.log                n/a
19:59:28 Log files:  master.err                     empty
19:59:28 Log files:  master.out                     30.5 KB      
19:59:28 Log files:  Total size                     0.06 MB
19:59:28 
19:59:28 
19:59:28 Environment:OMERO_HOME=(unset)             
19:59:28 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 
19:59:28 Environment:OMERO_NODE=(unset)             
19:59:28 Environment:OMERO_MASTER=(unset)           
19:59:28 Environment:OMERO_USERDIR=(unset)          
19:59:28 Environment:OMERO_TMPDIR=(unset)           
19:59:28 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 
19:59:28 Environment:PYTHONPATH=(unset)             
19:59:28 Environment:ICE_HOME=/opt/ice-3.6.5        
19:59:28 Environment:LD_LIBRARY_PATH=(unset)        
19:59:28 Environment:DYLD_LIBRARY_PATH=(unset)      
19:59:28 
19:59:28 OMERO SSL port:4064                           
19:59:28 OMERO TCP port:4063                           
19:59:28 OMERO data dir:'/home/omero/omero-server-data' Exists? True	Is writable? True
19:59:28 OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)
19:59:28 
19:59:28 JVM settings: Blitz-${index}                -Xmx7200m
19:59:28 JVM settings: Indexer-${index}              -Xmx4800m
19:59:28 JVM settings: PixelData-${index}            -Xmx7200m
19:59:28 JVM settings: Repository-${index}           -Xmx4800m
19:59:28 
19:59:28 Jar:        lib/server/formats-api.jar     Bio-Formats API	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
19:59:28 Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
19:59:28 Jar:        lib/server/formats-gpl.jar     Bio-Formats library	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
19:59:28 Jar:        lib/server/ome-codecs.jar      OME Codecs	1.1.3	26 February 2026	70fd9b72a9834f1af4852c1e5b5676c57a2c360e
19:59:28 Jar:        lib/server/ome-common.jar      OME Common Java	6.2.1	27 February 2026	a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
19:59:28 Jar:        lib/server/ome-jai.jar         OME JAI	0.1.5	30 June 2025	257a1c1410c0103485248d05752a5174262a38b6
19:59:28 Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)	5.3.4	25 June 2025	57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
19:59:28 Jar:        lib/server/ome-poi.jar         OME POI	5.3.11	11 November 2025	a2f3944ac71db9e7e51a6f64ec46beeb60613afb
19:59:28 Jar:        lib/server/ome-xml.jar         OME XML library	6.5.3	22 January 2026	21d1362abd9ce26e13888d2b2d028753d21ac96e
19:59:28 Jar:        lib/server/omero-blitz.jar     jar	5.8.6-SNAPSHOT		
19:59:28 Jar:        lib/server/omero-common.jar    jar	5.7.6-SNAPSHOT		
19:59:28 Jar:        lib/server/omero-gateway.jar   jar	5.11.1-SNAPSHOT		
19:59:28 Jar:        lib/server/omero-model.jar     jar	5.7.6-SNAPSHOT		
19:59:28 Jar:        lib/server/omero-renderer.jar  jar	5.6.6-SNAPSHOT		
19:59:28 Jar:        lib/server/omero-romio.jar     jar	5.8.6-SNAPSHOT		
19:59:28 Jar:        lib/server/omero-server.jar    jar	5.7.6-SNAPSHOT		
19:59:29 + deactivate
19:59:29 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
19:59:29 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
19:59:29 + export PATH
19:59:29 + unset _OLD_VIRTUAL_PATH
19:59:29 + '[' -n '' ']'
19:59:29 + hash -r
19:59:29 + '[' -n '' ']'
19:59:29 + unset VIRTUAL_ENV
19:59:29 + unset VIRTUAL_ENV_PROMPT
19:59:29 + '[' '!' '' = nondestructive ']'
19:59:29 + unset -f deactivate
19:59:29 Finished: SUCCESS