Console

12:33:13 Started by upstream project "Trigger" build number 26
12:33:13 originally caused by:
12:33:13  Started by user devspace
12:33:13 Running as SYSTEM
12:33:14 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
12:33:14 [OMERO-server] $ /bin/bash -xe /tmp/jenkins5800350202277575869.sh
12:33:14 + source /home/settings.env
12:33:14 ++ OMERO_DB_HOST=pg
12:33:14 ++ OMERO_DB_USER=postgres
12:33:14 ++ OMERO_DB_PASS=
12:33:14 ++ OMERO_ROOT_PASS=omero
12:33:14 ++ OMERO_DATA_DIR=/OMERO
12:33:14 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
12:33:14 + OMERO_DB_NAME=OMERO-server
12:33:14 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
12:33:14 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:33:14 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:33:14 + OMERO_DATA_DIR=/home/omero/omero-server-data
12:33:14 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
12:33:14 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
12:33:14 ++ deactivate nondestructive
12:33:14 ++ '[' -n '' ']'
12:33:14 ++ '[' -n '' ']'
12:33:14 ++ hash -r
12:33:14 ++ '[' -n '' ']'
12:33:14 ++ unset VIRTUAL_ENV
12:33:14 ++ unset VIRTUAL_ENV_PROMPT
12:33:14 ++ '[' '!' nondestructive = nondestructive ']'
12:33:14 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
12:33:14 ++ export VIRTUAL_ENV
12:33:14 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:33:14 ++ 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
12:33:14 ++ export PATH
12:33:14 ++ '[' -n '' ']'
12:33:14 ++ '[' -z '' ']'
12:33:14 ++ _OLD_VIRTUAL_PS1=
12:33:14 ++ PS1='(.venv3) '
12:33:14 ++ export PS1
12:33:14 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
12:33:14 ++ export VIRTUAL_ENV_PROMPT
12:33:14 ++ hash -r
12:33:14 + omero admin stop
12:33:50 Server not running
12:33:51 + echo not running
12:33:51 not running
12:33:51 + sleep 5
12:33:56 + deactivate
12:33:56 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
12:33:56 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:33:56 + export PATH
12:33:56 + unset _OLD_VIRTUAL_PATH
12:33:56 + '[' -n '' ']'
12:33:56 + hash -r
12:33:56 + '[' -n '' ']'
12:33:56 + unset VIRTUAL_ENV
12:33:56 + unset VIRTUAL_ENV_PROMPT
12:33:56 + '[' '!' '' = nondestructive ']'
12:33:56 + unset -f deactivate
12:33:56 + rm -rf /home/omero/workspace/OMERO-server/.venv3
12:36:50 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
12:37:11 + '[' false = true ']'
12:37:11 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
12:37:11 Skipping PURGE_DATA:CleanDbAndRepo
12:37:11 + 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
12:37:18 Copied 1 artifact from "OMERO-build" build number 17
12:37:18 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 15
12:37:19 Copied 2 artifacts from "OMERO-build-build" build number 27
12:37:19 [OMERO-server] $ /bin/bash -xe /tmp/jenkins12179738232349380802.sh
12:37:19 + source /home/settings.env
12:37:19 ++ OMERO_DB_HOST=pg
12:37:19 ++ OMERO_DB_USER=postgres
12:37:19 ++ OMERO_DB_PASS=
12:37:19 ++ OMERO_ROOT_PASS=omero
12:37:19 ++ OMERO_DATA_DIR=/OMERO
12:37:19 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
12:37:19 + OMERO_DB_NAME=OMERO-server
12:37:19 + OMERO_DATA_DIR=/home/omero/omero-server-data
12:37:19 + mkdir -p /home/omero/omero-server-data
12:37:19 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
12:37:19 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:37:19 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
12:37:19 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
12:37:19 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
12:37:19 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
12:37:19 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
12:37:19 ++ ls OMERO.server-5.6.3-637-6181d3b055-ice36-b17.zip
12:37:19 + ZIP=OMERO.server-5.6.3-637-6181d3b055-ice36-b17.zip
12:37:19 + '[' '!' -z '' ']'
12:37:19 + DIST=OMERO.server-5.6.3-637-6181d3b055-ice36-b17
12:37:19 + unzip OMERO.server-5.6.3-637-6181d3b055-ice36-b17.zip
12:37:19 Archive:  OMERO.server-5.6.3-637-6181d3b055-ice36-b17.zip
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/blitz/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/grid/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/profiles/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/error/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/grid/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/luts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/luts/janelia/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/luts/matplotlib/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/luts/ncsa_paledit/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/luts/seaborn/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/luts/wcif/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/analysis_scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/annotation_scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/export_scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/figure_scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/import_scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/scripts/omero/util_scripts/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/server/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/share/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/share/licenses/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/misc/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__1/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__10/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__11/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__2/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__3/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__4/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__5/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__6/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__7/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__8/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3A__9/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3__4/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3__5/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3__6/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO3__7/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.1__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.2__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.2__0/t/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.3__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.4__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.0__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.1__1/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.2__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4DEV__1/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4DEV__2/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4DEV__3/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/var/
12:37:19    creating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/var/tmp/
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/LICENSE.txt  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/backup.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/blitz/mail-senders.example  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/blitz/mail-server.example  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/build.properties  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/env.bat  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/env.sh  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/hibernate.properties  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/ice.config  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/logback-cli.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/logback-indexing-cli.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/logback-indexing.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/logback.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/mime.types  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/node1.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/node2.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/omero.properties  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/profiles/psql  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/rollover.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/Windows.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/error/maintainance.html  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/grid/README  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/grid/default.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/grid/templates.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/grid/windefault.xml  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/ice.config  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/internal.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/master.cfg  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/templates/robot.template  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/etc/testdropbox.config  
12:37:19   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/history.rst  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/OMEZarrReader.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/accessors-smart.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/activation.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/aggdesigner-algorithm.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/aircompressor.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/antlr.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/aopalliance.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/apiguardian-api.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/asm.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/avatica-core.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/avatica-metrics.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/aws-java-sdk-core.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/aws-java-sdk-kms.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/aws-java-sdk-s3.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/base.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-anim.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-awt-util.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-bridge.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-codec.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-constants.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-css.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-dom.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-ext.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-gvt.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-i18n.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-parser.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-script.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-shared-resources.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-svg-dom.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-svggen.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-transcoder.jar  
12:37:20   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/lib/client/batik-util.jar  
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12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.3__0/OMERO4.2__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.4__0/OMERO4.1__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4.4__0/OMERO4.3__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO4__0/OMERO3A__11.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.0__0/OMERO4.4__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.1__1/OMERO5.0__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.1__1/OMERO5.1__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.2__0/OMERO5.1__1.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/OMERO5.2__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/delete-ns-orphans.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/OMERO5.3__0.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/OMERO5.3__1.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/psql-footer.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/psql-header.sql  
12:37:34   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/schema.sql  
12:37:35   inflating: OMERO.server-5.6.3-637-6181d3b055-ice36-b17/sql/psql/OMERO5.4__0/views.sql  
12:37:35 + rm -f OMERO.server-5.6.3-637-6181d3b055-ice36-b17.zip
12:37:35 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-637-6181d3b055-ice36-b17 /home/omero/workspace/OMERO-server/OMERO.server
12:37:35 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
12:37:35 ++ deactivate nondestructive
12:37:35 ++ '[' -n '' ']'
12:37:35 ++ '[' -n '' ']'
12:37:35 ++ hash -r
12:37:35 ++ '[' -n '' ']'
12:37:35 ++ unset VIRTUAL_ENV
12:37:35 ++ unset VIRTUAL_ENV_PROMPT
12:37:35 ++ '[' '!' nondestructive = nondestructive ']'
12:37:35 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
12:37:35 ++ export VIRTUAL_ENV
12:37:35 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:37:35 ++ 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
12:37:35 ++ export PATH
12:37:35 ++ '[' -n '' ']'
12:37:35 ++ '[' -z '' ']'
12:37:35 ++ _OLD_VIRTUAL_PS1=
12:37:35 ++ PS1='(.venv3) '
12:37:35 ++ export PS1
12:37:35 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
12:37:35 ++ export VIRTUAL_ENV_PROMPT
12:37:35 ++ hash -r
12:37:35 + pip install -U pip
12:37:36 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
12:37:36 Collecting pip
12:37:36   Using cached pip-26.1.2-py3-none-any.whl (1.8 MB)
12:37:36 Installing collected packages: pip
12:37:36   Attempting uninstall: pip
12:37:36     Found existing installation: pip 22.3.1
12:37:37     Uninstalling pip-22.3.1:
12:37:37       Successfully uninstalled pip-22.3.1
12:37:51 Successfully installed pip-26.1.2
12:37:52 + 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
12:37:53 Collecting zeroc-ice==3.6.5
12:37:53   Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
12:37:56      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 13.8 MB/s  0:00:02
12:37:56 Installing collected packages: zeroc-ice
12:37:59 Successfully installed zeroc-ice-3.6.5
12:37:59 + pip install markdown
12:38:00 Collecting markdown
12:38:00   Using cached markdown-3.10.2-py3-none-any.whl.metadata (5.1 kB)
12:38:00 Using cached markdown-3.10.2-py3-none-any.whl (108 kB)
12:38:00 Installing collected packages: markdown
12:38:01 Successfully installed markdown-3.10.2
12:38:01 + pip install reportlab
12:38:02 Collecting reportlab
12:38:02   Using cached reportlab-5.0.0-py3-none-any.whl.metadata (1.6 kB)
12:38:02 Collecting pillow>=9.0.0 (from reportlab)
12:38:02   Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
12:38:03 Collecting charset-normalizer (from reportlab)
12:38:03   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)
12:38:03 Using cached reportlab-5.0.0-py3-none-any.whl (2.0 MB)
12:38:03 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
12:38:03 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)
12:38:03 Installing collected packages: pillow, charset-normalizer, reportlab
12:38:12 
12:38:12 Successfully installed charset-normalizer-3.4.9 pillow-12.3.0 reportlab-5.0.0
12:38:12 + pip install omego
12:38:13 Collecting omego
12:38:13   Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
12:38:13 Collecting future (from omego)
12:38:13   Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
12:38:13 Collecting yaclifw>=0.1.1 (from omego)
12:38:13   Using cached yaclifw-0.2.0-py3-none-any.whl
12:38:14 Collecting six (from yaclifw>=0.1.1->omego)
12:38:14   Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
12:38:14 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
12:38:14 Using cached future-1.0.0-py3-none-any.whl (491 kB)
12:38:14 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
12:38:14 Installing collected packages: six, future, yaclifw, omego
12:38:19 
12:38:19 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
12:38:19 + pip install tables
12:38:20 Collecting tables
12:38:20   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)
12:38:21 Collecting numpy>=1.20.0 (from tables)
12:38:21   Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
12:38:21 Collecting numexpr>=2.6.2 (from tables)
12:38:21   Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
12:38:21 Collecting packaging (from tables)
12:38:21   Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
12:38:21 Collecting py-cpuinfo (from tables)
12:38:21   Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
12:38:21 Collecting blosc2>=2.3.0 (from tables)
12:38:21   Using cached blosc2-4.9.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (7.8 kB)
12:38:21 Collecting ndindex (from blosc2>=2.3.0->tables)
12:38:21   Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
12:38:22 Collecting msgpack (from blosc2>=2.3.0->tables)
12:38:22   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)
12:38:22 Collecting pydantic (from blosc2>=2.3.0->tables)
12:38:22   Using cached pydantic-2.13.4-py3-none-any.whl.metadata (109 kB)
12:38:22 Collecting httpx[http2] (from blosc2>=2.3.0->tables)
12:38:22   Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
12:38:22 Collecting rich (from blosc2>=2.3.0->tables)
12:38:22   Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
12:38:22 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
12:38:22   Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
12:38:22 Collecting anyio (from httpx[http2]->blosc2>=2.3.0->tables)
12:38:23   Using cached anyio-4.14.2-py3-none-any.whl.metadata (4.6 kB)
12:38:23 Collecting certifi (from httpx[http2]->blosc2>=2.3.0->tables)
12:38:23   Downloading certifi-2026.7.22-py3-none-any.whl.metadata (2.5 kB)
12:38:23 Collecting httpcore==1.* (from httpx[http2]->blosc2>=2.3.0->tables)
12:38:23   Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB)
12:38:23 Collecting idna (from httpx[http2]->blosc2>=2.3.0->tables)
12:38:23   Using cached idna-3.18-py3-none-any.whl.metadata (6.1 kB)
12:38:23 Collecting h2<5,>=3 (from httpx[http2]->blosc2>=2.3.0->tables)
12:38:23   Using cached h2-4.3.0-py3-none-any.whl.metadata (5.1 kB)
12:38:23 Collecting hyperframe<7,>=6.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
12:38:23   Using cached hyperframe-6.1.0-py3-none-any.whl.metadata (4.3 kB)
12:38:24 Collecting hpack<5,>=4.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
12:38:24   Using cached hpack-4.2.0-py3-none-any.whl.metadata (3.3 kB)
12:38:24 Collecting h11>=0.16 (from httpcore==1.*->httpx[http2]->blosc2>=2.3.0->tables)
12:38:24   Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB)
12:38:24 Collecting typing_extensions>=4.5 (from anyio->httpx[http2]->blosc2>=2.3.0->tables)
12:38:24   Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
12:38:24 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
12:38:24   Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)
12:38:25 Collecting pydantic-core==2.46.4 (from pydantic->blosc2>=2.3.0->tables)
12:38:25   Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
12:38:25 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
12:38:25   Using cached typing_inspection-0.4.2-py3-none-any.whl.metadata (2.6 kB)
12:38:25 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
12:38:25   Using cached markdown_it_py-4.2.0-py3-none-any.whl.metadata (7.4 kB)
12:38:25 Collecting pygments<3.0.0,>=2.13.0 (from rich->blosc2>=2.3.0->tables)
12:38:25   Using cached pygments-2.20.0-py3-none-any.whl.metadata (2.5 kB)
12:38:25 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
12:38:25   Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
12:38:25 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)
12:38:25 Using cached blosc2-4.9.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.3 MB)
12:38:26 Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (443 kB)
12:38:26 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
12:38:26 Using cached httpx-0.28.1-py3-none-any.whl (73 kB)
12:38:26 Using cached h2-4.3.0-py3-none-any.whl (61 kB)
12:38:26 Using cached hpack-4.2.0-py3-none-any.whl (34 kB)
12:38:26 Using cached httpcore-1.0.9-py3-none-any.whl (78 kB)
12:38:26 Using cached hyperframe-6.1.0-py3-none-any.whl (13 kB)
12:38:26 Using cached h11-0.16.0-py3-none-any.whl (37 kB)
12:38:26 Using cached anyio-4.14.2-py3-none-any.whl (125 kB)
12:38:26 Using cached idna-3.18-py3-none-any.whl (65 kB)
12:38:26 Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB)
12:38:26 Downloading certifi-2026.7.22-py3-none-any.whl (136 kB)
12:38:26 Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (423 kB)
12:38:26 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
12:38:26 Using cached packaging-26.2-py3-none-any.whl (100 kB)
12:38:27 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
12:38:27 Using cached pydantic-2.13.4-py3-none-any.whl (472 kB)
12:38:27 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
12:38:27 Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB)
12:38:27 Using cached typing_inspection-0.4.2-py3-none-any.whl (14 kB)
12:38:27 Using cached rich-15.0.0-py3-none-any.whl (310 kB)
12:38:27 Using cached pygments-2.20.0-py3-none-any.whl (1.2 MB)
12:38:27 Using cached markdown_it_py-4.2.0-py3-none-any.whl (91 kB)
12:38:27 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
12:38:27 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
12:38:27 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
12:39:17 
12:39:17 Successfully installed annotated-types-0.7.0 anyio-4.14.2 blosc2-4.9.1 certifi-2026.7.22 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-2.14.2 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
12:39:17 + pip install jinja2
12:39:18 Collecting jinja2
12:39:18   Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
12:39:18 Collecting MarkupSafe>=2.0 (from jinja2)
12:39:18   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)
12:39:18 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
12:39:18 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
12:39:19 Installing collected packages: MarkupSafe, jinja2
12:39:20 
12:39:20 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
12:39:20 + pip install omero-py
12:39:21 Collecting omero-py
12:39:21   Using cached omero_py-5.22.1-py3-none-any.whl.metadata (6.5 kB)
12:39:21 Collecting appdirs (from omero-py)
12:39:21   Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
12:39:21 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
12:39:21 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
12:39:21 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
12:39:21 Collecting PyYAML (from omero-py)
12:39:21   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)
12:39:21 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
12:39:21 Collecting requests (from omero-py)
12:39:21   Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
12:39:21 Collecting portalocker (from omero-py)
12:39:21   Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
12:39:21 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.9)
12:39:21 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.18)
12:39:21 Collecting urllib3<3,>=1.26 (from requests->omero-py)
12:39:21   Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
12:39:21 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.7.22)
12:39:21 Using cached omero_py-5.22.1-py3-none-any.whl (2.8 MB)
12:39:21 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
12:39:21 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
12:39:21 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
12:39:22 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
12:39:22 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
12:39:22 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, requests, omero-py
12:39:41 
12:39:41 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
12:39:41 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
12:39:42 Collecting omero-metadata
12:39:42   Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-xhamhhqc/omero-metadata_f2f90a249f494f74b5cac140d59abb1a
12:39:42   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-xhamhhqc/omero-metadata_f2f90a249f494f74b5cac140d59abb1a
12:39:43   Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit dee7d5befc8e9063214b4939d4dbcc632ae7f539
12:39:43   Installing build dependencies: started
12:39:45   Installing build dependencies: finished with status 'done'
12:39:45   Getting requirements to build wheel: started
12:39:45   Getting requirements to build wheel: finished with status 'done'
12:39:45   Preparing metadata (pyproject.toml): started
12:39:45   Preparing metadata (pyproject.toml): finished with status 'done'
12:39:45 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.22.1)
12:39:45 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
12:39:45 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
12:39:46 Collecting pandas (from omero-metadata)
12:39:46   Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
12:39:46 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
12:39:46 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
12:39:46 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.6)
12:39:46 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)
12:39:46 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)
12:39:46 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
12:39:46 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
12:39:46 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
12:39:46 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
12:39:46   Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
12:39:46 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)
12:39:46 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)
12:39:46 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)
12:39:46 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)
12:39:46 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)
12:39:46 Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.3 MB)
12:39:46 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
12:39:46 Building wheels for collected packages: omero-metadata
12:39:46   Building wheel for omero-metadata (pyproject.toml): started
12:39:46   Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
12:39:46   Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=b4dc7ee4b0890d475d42e5c673a5e223030fd389209e4e9691ff03760300e3a1
12:39:46   Stored in directory: /tmp/pip-ephem-wheel-cache-ytqbmak4/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
12:39:46 Successfully built omero-metadata
12:39:46 Installing collected packages: python-dateutil, pandas, omero-metadata
12:40:28 
12:40:28 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.3 python-dateutil-2.9.0.post0
12:40:28 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
12:40:29 Collecting omero-cli-render
12:40:29   Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-xvjiy_83/omero-cli-render_90c0893293544c32ab7f28662f8457f9
12:40:29   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-xvjiy_83/omero-cli-render_90c0893293544c32ab7f28662f8457f9
12:40:30   Running command git checkout -b merge_ci --track origin/merge_ci
12:40:30   Switched to a new branch 'merge_ci'
12:40:30   branch 'merge_ci' set up to track 'origin/merge_ci'.
12:40:30   Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 72e42a76a4117a0c3d7f4ef264883bb874b34d21
12:40:30   Installing build dependencies: started
12:40:31   Installing build dependencies: finished with status 'done'
12:40:31   Getting requirements to build wheel: started
12:40:32   Getting requirements to build wheel: finished with status 'done'
12:40:32   Preparing metadata (pyproject.toml): started
12:40:32   Preparing metadata (pyproject.toml): finished with status 'done'
12:40:32 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
12:40:32 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.22.1)
12:40:32 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
12:40:32 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
12:40:32 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)
12:40:32 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)
12:40:32 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)
12:40:32 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
12:40:32 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
12:40:32 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)
12:40:32 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)
12:40:32 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)
12:40:32 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)
12:40:32 Building wheels for collected packages: omero-cli-render
12:40:32   Building wheel for omero-cli-render (pyproject.toml): started
12:40:32   Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
12:40:32   Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19838 sha256=34748a3ea1fc9716e556307973b8fdd4464f964e55873481f7f0bd3f9b849a16
12:40:32   Stored in directory: /tmp/pip-ephem-wheel-cache-o8isw0zs/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
12:40:32 Successfully built omero-cli-render
12:40:32 Installing collected packages: omero-cli-render
12:40:33 Successfully installed omero-cli-render-0.8.2.dev0
12:40:33 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
12:40:33 Collecting omero-cli-duplicate
12:40:33   Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-nodx6rxf/omero-cli-duplicate_24c0ff7534a14c1b9639a0841f1dba60
12:40:33   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-nodx6rxf/omero-cli-duplicate_24c0ff7534a14c1b9639a0841f1dba60
12:40:34   Running command git checkout -b merge_ci --track origin/merge_ci
12:40:35   Switched to a new branch 'merge_ci'
12:40:35   branch 'merge_ci' set up to track 'origin/merge_ci'.
12:40:35   Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 85008b90d699750527c67c4f45b5c076f5ccda26
12:40:35   Installing build dependencies: started
12:40:36   Installing build dependencies: finished with status 'done'
12:40:36   Getting requirements to build wheel: started
12:40:36   Getting requirements to build wheel: finished with status 'done'
12:40:36   Preparing metadata (pyproject.toml): started
12:40:37   Preparing metadata (pyproject.toml): finished with status 'done'
12:40:37 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.22.1)
12:40:37 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
12:40:37 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
12:40:37 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
12:40:37 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)
12:40:37 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
12:40:37 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)
12:40:37 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.34.2)
12:40:37 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
12:40:37 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)
12:40:37 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)
12:40:37 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)
12:40:37 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)
12:40:37 Building wheels for collected packages: omero-cli-duplicate
12:40:37   Building wheel for omero-cli-duplicate (pyproject.toml): started
12:40:37   Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
12:40:37   Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=24832be8ba95da820494fbfbedd76e2e0acfc218a9f96754284ecbb211d78d3b
12:40:37   Stored in directory: /tmp/pip-ephem-wheel-cache-ouskswit/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
12:40:37 Successfully built omero-cli-duplicate
12:40:37 Installing collected packages: omero-cli-duplicate
12:40:37 Successfully installed omero-cli-duplicate-0.4.1.dev0
12:40:37 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
12:40:38 Collecting omero-cli-zarr
12:40:38   Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-4ws6ikme/omero-cli-zarr_d04e70d288764986ae9de6897c7f06ab
12:40:38   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-4ws6ikme/omero-cli-zarr_d04e70d288764986ae9de6897c7f06ab
12:40:39   Running command git checkout -b merge_ci --track origin/merge_ci
12:40:39   Switched to a new branch 'merge_ci'
12:40:39   branch 'merge_ci' set up to track 'origin/merge_ci'.
12:40:39   Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit 23736d7fd7ce415add4e923fcab48e05d147e3ee
12:40:39   Installing build dependencies: started
12:40:41   Installing build dependencies: finished with status 'done'
12:40:41   Getting requirements to build wheel: started
12:40:41   Getting requirements to build wheel: finished with status 'done'
12:40:41   Installing backend dependencies: started
12:40:42   Installing backend dependencies: finished with status 'done'
12:40:42   Preparing metadata (pyproject.toml): started
12:40:43   Preparing metadata (pyproject.toml): finished with status 'done'
12:40:43 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.22.1)
12:40:43 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
12:40:43   Using cached ome_zarr-0.18.0-py3-none-any.whl.metadata (2.9 kB)
12:40:43 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.6)
12:40:43 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:43   Using cached dask-2026.7.1-py3-none-any.whl.metadata (3.8 kB)
12:40:43 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:43   Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
12:40:44 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)
12:40:44   Using cached fsspec-2026.6.0-py3-none-any.whl.metadata (10 kB)
12:40:44 Collecting aiohttp (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:44   Using cached aiohttp-3.14.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
12:40:44 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.34.2)
12:40:44 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:44   Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
12:40:45 Collecting toolz (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB)
12:40:45 Collecting rangehttpserver (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl.metadata (769 bytes)
12:40:45 Collecting ome-zarr-models>=1.6 (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached ome_zarr_models-1.7-py3-none-any.whl.metadata (3.0 kB)
12:40:45 Collecting Deprecated (from ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB)
12:40:45 Collecting click>=8.1 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached click-8.4.2-py3-none-any.whl.metadata (2.6 kB)
12:40:45 Collecting cloudpickle>=3.0.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB)
12:40:45 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) (26.2)
12:40:45 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:45   Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
12:40:45 Requirement already satisfied: pyyaml>=5.4.1 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) (6.0.3)
12:40:45 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)
12:40:45   Using cached importlib_metadata-9.0.0-py3-none-any.whl.metadata (4.5 kB)
12:40:46 Collecting s3fs>2024.2.0 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:46   Using cached s3fs-2026.6.0-py3-none-any.whl.metadata (1.2 kB)
12:40:46 Collecting zipp>=3.20 (from importlib_metadata>=4.13.0->dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:46   Using cached zipp-4.1.0-py3-none-any.whl.metadata (3.6 kB)
12:40:46 Collecting pydantic-zarr>=0.8.2 (from ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
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12:40:46 Collecting pydantic<2.13,>=2.11.5 (from ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
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12:40:47 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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12:40:47 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
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12:40:47 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (3.2.0)
12:40:47 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)
12:40:47   Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
12:40:47 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)
12:40:47   Using cached aiobotocore-3.8.0-py3-none-any.whl.metadata (29 kB)
12:40:47 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)
12:40:47   Using cached aioitertools-0.13.0-py3-none-any.whl.metadata (3.3 kB)
12:40:48 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)
12:40:48   Using cached botocore-1.43.46-py3-none-any.whl.metadata (5.6 kB)
12:40:48 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>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr) (2.9.0.post0)
12:40:48 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)
12:40:48   Using cached jmespath-1.1.0-py3-none-any.whl.metadata (7.6 kB)
12:40:48 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)
12:40:48   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)
12:40:48 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)
12:40:48   Using cached wrapt-2.2.2-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (7.4 kB)
12:40:49 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:49   Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl.metadata (5.9 kB)
12:40:49 Collecting aiosignal>=1.4.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:49   Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
12:40:49 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:49   Using cached attrs-26.1.0-py3-none-any.whl.metadata (8.8 kB)
12:40:49 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:49   Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (20 kB)
12:40:49 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:49   Using cached propcache-0.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (16 kB)
12:40:49 Collecting yarl<2.0,>=1.17.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:49   Using cached yarl-1.24.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (103 kB)
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12:40:49 Requirement already satisfied: idna>=2.0 in ./.venv3/lib64/python3.11/site-packages (from yarl<2.0,>=1.17.0->aiohttp->ome-zarr>=0.13.0->omero-cli-zarr) (3.18)
12:40:50 Collecting scipy>=1.11.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:50   Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
12:40:50 Collecting networkx>=3.0 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:50   Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
12:40:50 Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:50   Using cached imageio-2.37.4-py3-none-any.whl.metadata (9.6 kB)
12:40:50 Collecting tifffile>=2022.8.12 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:50   Using cached tifffile-2026.3.3-py3-none-any.whl.metadata (31 kB)
12:40:50 Collecting lazy-loader>=0.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
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12:40:50 Collecting donfig>=0.8 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
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12:40:50 Collecting google-crc32c>=1.5 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
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12:40:51 Collecting numcodecs>=0.14 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
12:40:51   Using cached numcodecs-0.16.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (3.4 kB)
12:40:51 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (3.4.9)
12:40:51 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (2026.7.22)
12:40:51 Using cached ome_zarr-0.18.0-py3-none-any.whl (57 kB)
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12:40:51 Using cached cloudpickle-3.1.2-py3-none-any.whl (22 kB)
12:40:51 Using cached fsspec-2026.6.0-py3-none-any.whl (203 kB)
12:40:51 Using cached importlib_metadata-9.0.0-py3-none-any.whl (27 kB)
12:40:51 Using cached ome_zarr_models-1.7-py3-none-any.whl (64 kB)
12:40:51 Using cached pydantic-2.12.5-py3-none-any.whl (463 kB)
12:40:51 Using cached pydantic_core-2.41.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
12:40:51 Using cached partd-1.4.2-py3-none-any.whl (18 kB)
12:40:51 Using cached pydantic_zarr-0.9.2-py3-none-any.whl (52 kB)
12:40:51 Using cached s3fs-2026.6.0-py3-none-any.whl (32 kB)
12:40:51 Using cached aiobotocore-3.8.0-py3-none-any.whl (91 kB)
12:40:51 Using cached aiohttp-3.14.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.8 MB)
12:40:51 Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB)
12:40:51 Using cached botocore-1.43.46-py3-none-any.whl (15.4 MB)
12:40:52 Using cached jmespath-1.1.0-py3-none-any.whl (20 kB)
12:40:52 Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
12:40:52 Using cached wrapt-2.2.2-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (159 kB)
12:40:52 Using cached yarl-1.24.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (111 kB)
12:40:52 Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl (15 kB)
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12:40:52 Using cached propcache-0.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (58 kB)
12:40:52 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (13.7 MB)
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12:40:52 Using cached tifffile-2026.3.3-py3-none-any.whl (243 kB)
12:40:52 Using cached toolz-1.1.0-py3-none-any.whl (58 kB)
12:40:52 Using cached zarr-3.1.6-py3-none-any.whl (295 kB)
12:40:52 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
12:40:52 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)
12:40:52 Using cached numcodecs-0.16.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (9.1 MB)
12:40:52 Using cached zipp-4.1.0-py3-none-any.whl (10 kB)
12:40:52 Using cached deprecated-1.3.1-py2.py3-none-any.whl (11 kB)
12:40:52 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
12:40:52 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
12:40:53 Building wheels for collected packages: omero-cli-zarr
12:40:53   Building wheel for omero-cli-zarr (pyproject.toml): started
12:40:53   Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
12:40:53   Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev162+g23736d7-py3-none-any.whl size=38288 sha256=8dd933677c9104b65f2ae09562c5a446df1825765f9162866a63b39551f2b4ed
12:40:53   Stored in directory: /tmp/pip-ephem-wheel-cache-gpfm1ds0/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
12:40:53 Successfully built omero-cli-zarr
12:40:53 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
12:41:30   Attempting uninstall: pydantic-core
12:41:30     Found existing installation: pydantic_core 2.46.4
12:41:30     Uninstalling pydantic_core-2.46.4:
12:41:30       Successfully uninstalled pydantic_core-2.46.4
12:42:05   Attempting uninstall: pydantic
12:42:05     Found existing installation: pydantic 2.13.4
12:42:05     Uninstalling pydantic-2.13.4:
12:42:05       Successfully uninstalled pydantic-2.13.4
12:42:48 
12:42:48 Successfully installed Deprecated-1.3.1 aiobotocore-3.8.0 aiohappyeyeballs-2.7.1 aiohttp-3.14.2 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-2.37.4 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.dev162+g23736d7 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-1.24.5 zarr-3.1.6 zipp-4.1.0
12:42:48 + pip install omero-certificates
12:42:49 Collecting omero-certificates
12:42:49   Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
12:42:49 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.22.1)
12:42:49 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
12:42:49 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
12:42:49 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.6)
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12:42:49 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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12:42:49 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)
12:42:49 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
12:42:50 Installing collected packages: omero-certificates
12:42:50 Successfully installed omero-certificates-0.4.0
12:42:50 + for x in *.tar.gz
12:42:50 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
12:42:51 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
12:42:51   Installing build dependencies: started
12:42:52   Installing build dependencies: finished with status 'done'
12:42:52   Getting requirements to build wheel: started
12:42:53   Getting requirements to build wheel: finished with status 'done'
12:42:53   Preparing metadata (pyproject.toml): started
12:42:53   Preparing metadata (pyproject.toml): finished with status 'done'
12:42:53 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.22.1)
12:42:53 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
12:42:53 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
12:42:53 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)
12:42:53 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)
12:42:53 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
12:42:53 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)
12:42:53 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
12:42:53 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
12:42:53 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)
12:42:53 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)
12:42:53 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)
12:42:53 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)
12:42:53 Building wheels for collected packages: omero-dropbox
12:42:53   Building wheel for omero-dropbox (pyproject.toml): started
12:42:53   Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
12:42:53   Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49153 sha256=a57cf18c94eff8902d80b1002f586423af9f9df698dc426013dfdd235c899e0a
12:42:53   Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
12:42:53 Successfully built omero-dropbox
12:42:53 Installing collected packages: omero-dropbox
12:42:54 Successfully installed omero-dropbox-5.7.1.dev0
12:42:54 + for x in *.tar.gz
12:42:54 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
12:42:55 Processing ./omero_marshal-0.9.2.dev0.tar.gz
12:42:55   Installing build dependencies: started
12:42:56   Installing build dependencies: finished with status 'done'
12:42:56   Getting requirements to build wheel: started
12:42:57   Getting requirements to build wheel: finished with status 'done'
12:42:57   Preparing metadata (pyproject.toml): started
12:42:57   Preparing metadata (pyproject.toml): finished with status 'done'
12:42:57 Building wheels for collected packages: omero_marshal
12:42:57   Building wheel for omero_marshal (pyproject.toml): started
12:42:57   Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
12:42:57   Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88129 sha256=60d6815d93007bf01a72744aaaa07ab83a16845d0a87be64c8349185cc56c878
12:42:57   Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
12:42:57 Successfully built omero_marshal
12:42:58 Installing collected packages: omero_marshal
12:43:00 Successfully installed omero_marshal-0.9.2.dev0
12:43:00 + for x in *.tar.gz
12:43:00 + pip install -U omero_py-5.22.2.dev0.tar.gz
12:43:01 Processing ./omero_py-5.22.2.dev0.tar.gz
12:43:01   Installing build dependencies: started
12:43:03   Installing build dependencies: finished with status 'done'
12:43:03   Getting requirements to build wheel: started
12:43:03   Getting requirements to build wheel: finished with status 'done'
12:43:03   Preparing metadata (pyproject.toml): started
12:43:04   Preparing metadata (pyproject.toml): finished with status 'done'
12:43:04 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.4.4)
12:43:04 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.0.0)
12:43:04 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.4.6)
12:43:04 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (12.3.0)
12:43:04 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (6.0.3)
12:43:04 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)
12:43:04 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.34.2)
12:43:04 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.2.0)
12:43:04 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)
12:43:04 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.18)
12:43:04 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)
12:43:04 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2026.7.22)
12:43:04 Building wheels for collected packages: omero-py
12:43:04   Building wheel for omero-py (pyproject.toml): started
12:43:05   Building wheel for omero-py (pyproject.toml): finished with status 'done'
12:43:05   Created wheel for omero-py: filename=omero_py-5.22.2.dev0-py3-none-any.whl size=2787060 sha256=3b0c4f74cb45a0e157f676b78d8bbea5f05be1d58e86d0289b53fc081c5dcead
12:43:05   Stored in directory: /home/omero/.cache/pip/wheels/ec/3f/72/4027ca0a7faf1f66d4577cc07619b0497ac8e99396d43dd8fa
12:43:05 Successfully built omero-py
12:43:05 Installing collected packages: omero-py
12:43:05   Attempting uninstall: omero-py
12:43:05     Found existing installation: omero-py 5.22.1
12:43:06     Uninstalling omero-py-5.22.1:
12:43:17       Successfully uninstalled omero-py-5.22.1
12:43:34 Successfully installed omero-py-5.22.2.dev0
12:43:34 + for x in *.tar.gz
12:43:34 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
12:43:35 Processing ./omero_scripts-5.10.1.dev0.tar.gz
12:43:35   Installing build dependencies: started
12:43:36   Installing build dependencies: finished with status 'done'
12:43:36   Getting requirements to build wheel: started
12:43:36   Getting requirements to build wheel: finished with status 'done'
12:43:36   Preparing metadata (pyproject.toml): started
12:43:37   Preparing metadata (pyproject.toml): finished with status 'done'
12:43:37 Building wheels for collected packages: omero-scripts
12:43:37   Building wheel for omero-scripts (pyproject.toml): started
12:43:37   Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
12:43:37   Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137216 sha256=273ef5343c56d9e644164907f19ab2d660721b95c13d21eb8b61a817d2c9482c
12:43:37   Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
12:43:37 Successfully built omero-scripts
12:43:37 Installing collected packages: omero-scripts
12:43:38 Successfully installed omero-scripts-5.10.1.dev0
12:43:38 + for x in *.tar.gz
12:43:38 + pip install -U omero_web-5.32.1.dev0.tar.gz
12:43:39 Processing ./omero_web-5.32.1.dev0.tar.gz
12:43:39   Installing build dependencies: started
12:43:41   Installing build dependencies: finished with status 'done'
12:43:41   Getting requirements to build wheel: started
12:43:41   Getting requirements to build wheel: finished with status 'done'
12:43:41   Preparing metadata (pyproject.toml): started
12:43:42   Preparing metadata (pyproject.toml): finished with status 'done'
12:43:42 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)
12:43:42 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.32.1.dev0)
12:43:42   Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
12:43:42 Collecting Django<5.3,>=5.2.9 (from omero-web==5.32.1.dev0)
12:43:42   Using cached django-5.2.16-py3-none-any.whl.metadata (4.1 kB)
12:43:42 Collecting django-pipeline>=4.1.0 (from omero-web==5.32.1.dev0)
12:43:42   Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
12:43:42 Collecting django-cors-headers==3.7.0 (from omero-web==5.32.1.dev0)
12:43:42   Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
12:43:42 Collecting whitenoise>=5.3.0 (from omero-web==5.32.1.dev0)
12:43:42   Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
12:43:43 Collecting gunicorn>=19.3 (from omero-web==5.32.1.dev0)
12:43:43   Using cached gunicorn-26.0.0-py3-none-any.whl.metadata (5.4 kB)
12:43:43 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)
12:43:43 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (12.3.0)
12:43:43 Collecting pytz (from omero-web==5.32.1.dev0)
12:43:43   Using cached pytz-2026.2-py2.py3-none-any.whl.metadata (22 kB)
12:43:43 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (3.2.0)
12:43:43 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (26.2)
12:43:43 Collecting importlib-resources (from omero-web==5.32.1.dev0)
12:43:43   Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
12:43:43 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
12:43:43   Using cached asgiref-3.12.1-py3-none-any.whl.metadata (9.4 kB)
12:43:43 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
12:43:43   Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
12:43:43 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)
12:43:43 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0)
12:43:43   Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 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)
12:43:43 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
12:43:43 Using cached django-5.2.16-py3-none-any.whl (8.3 MB)
12:43:43 Using cached asgiref-3.12.1-py3-none-any.whl (25 kB)
12:43:43 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
12:43:44 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
12:43:44 Using cached gunicorn-26.0.0-py3-none-any.whl (212 kB)
12:43:44 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
12:43:44 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
12:43:44 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
12:43:44 Using cached pytz-2026.2-py2.py3-none-any.whl (510 kB)
12:43:44 Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
12:43:44 Building wheels for collected packages: omero-web
12:43:44   Building wheel for omero-web (pyproject.toml): started
12:43:45   Building wheel for omero-web (pyproject.toml): finished with status 'done'
12:43:45   Created wheel for omero-web: filename=omero_web-5.32.1.dev0-py3-none-any.whl size=2820645 sha256=1fb474c29d9ab345a5d4aa84fa35fe6a83d0e70077b199d1957c33b95a0682f1
12:43:45   Stored in directory: /home/omero/.cache/pip/wheels/e6/f6/6f/ec36dda9edad720aabd7330edafa8a6a62d6ebfa4c7467248f
12:43:45 Successfully built omero-web
12:43:45 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
12:45:00 
12:45:01 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
12:45:01 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
12:45:01 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
12:45:01 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
12:45:01 --2026-07-22 12:45:01--  https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
12:45:01 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.108.133, 185.199.109.133, ...
12:45:01 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
12:45:01 HTTP request sent, awaiting response... 200 OK
12:45:02 Length: 139337 (136K) [text/plain]
12:45:02 Saving to: ‘Figure_To_Pdf.py’
12:45:02 
12:45:02      0K .......... .......... .......... .......... .......... 36% 2.75M 0s
12:45:02     50K .......... .......... .......... .......... .......... 73% 5.30M 0s
12:45:02    100K .......... .......... .......... ......               100% 6.70M=0.03s
12:45:02 
12:45:02 2026-07-22 12:45:02 (4.12 MB/s) - ‘Figure_To_Pdf.py’ saved [139337/139337]
12:45:02 
12:45:02 + chmod 755 Figure_To_Pdf.py
12:45:02 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
12:45:02 + omero config set omero.db.name OMERO-server
12:45:09 + omero config set omero.db.host pg
12:45:14 + omero config set omero.db.user postgres
12:45:18 + omero config set omero.data.dir /home/omero/omero-server-data
12:45:24 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
12:45:29 + omero config set omero.db.poolsize 25
12:45:34 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
12:45:39 + omero config set omero.security.trustStorePassword changeit
12:45:44 + omero config set omero.mail.config true
12:45:49 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
12:45:54 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
12:45:59 + omero certificates
12:46:04 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
12:46:04 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
12:46:04 + '[' false = true ']'
12:46:04 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
12:46:04 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
12:46:04 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG            dbcommand => upgrade
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG               dbhost => localhost
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG               dbname => OMERO-server
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG               dbpass => omero
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG               dbuser => omero
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG             rootpass => omero
12:46:04 2026-07-22 12:46:04,744 [    omego.db] DEBUG            serverdir => /home/omero/workspace/OMERO-server/OMERO.server
12:46:04 2026-07-22 12:46:04,745 [omego.extern] INFO  Executing : omero version
12:46:09 OMERO.py version:
12:46:09 OMERO.server version:
12:46:09 5.6.3-637-6181d3b055-ice36-b17
12:46:09 5.22.2.dev0
12:46:09 2026-07-22 12:46:09,802 [omego.extern] INFO  Completed [5.057 s]
12:46:09 2026-07-22 12:46:09,802 [omego.extern] DEBUG Using omero CLI from omero
12:46:09 2026-07-22 12:46:09,803 [    omego.db] INFO  DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
12:46:09 2026-07-22 12:46:09,803 [omego.extern] INFO  Running [current environment]: omero config get --show-password
12:46:09 2026-07-22 12:46:09,803 [omego.extern] INFO  Executing : omero config get --show-password
12:46:14 2026-07-22 12:46:14,684 [omego.extern] INFO  Completed [4.881 s]
12:46:14 2026-07-22 12:46:14,684 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
12:46:14 2026-07-22 12:46:14,684 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
12:46:14 2026-07-22 12:46:14,766 [omego.extern] INFO  Completed [0.082 s]
12:46:14 2026-07-22 12:46:14,766 [    omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.14\n'
12:46:14 2026-07-22 12:46:14,766 [    omego.db] INFO  psql version: psql (PostgreSQL) 16.14
12:46:14 
12:46:14 2026-07-22 12:46:14,766 [omego.extern] INFO  Running [current environment]: omero config get --show-password
12:46:14 2026-07-22 12:46:14,766 [omego.extern] INFO  Executing : omero config get --show-password
12:46:19 2026-07-22 12:46:19,771 [omego.extern] INFO  Completed [5.005 s]
12:46:19 2026-07-22 12:46:19,771 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
12:46:19 2026-07-22 12:46:19,771 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
12:46:19 2026-07-22 12:46:19,963 [omego.extern] INFO  Completed [0.192 s]
12:46:19 2026-07-22 12:46:19,963 [    omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.3") at port "5432".\n'
12:46:19 2026-07-22 12:46:19,963 [    omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
12:46:19 2026-07-22 12:46:19,963 [omego.extern] INFO  Running [current environment]: omero config get --show-password
12:46:19 2026-07-22 12:46:19,963 [omego.extern] INFO  Executing : omero config get --show-password
12:46:25 2026-07-22 12:46:25,237 [omego.extern] INFO  Completed [5.273 s]
12:46:25 2026-07-22 12:46:25,237 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
12:46:25 2026-07-22 12:46:25,237 [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
12:46:25 2026-07-22 12:46:25,993 [omego.extern] INFO  Completed [0.756 s]
12:46:25 2026-07-22 12:46:25,993 [    omego.db] DEBUG stdout: b'OMERO5.4|0\n'
12:46:25 2026-07-22 12:46:25,993 [    omego.db] INFO  Current omero db version: ('OMERO5.4', '0')
12:46:26 2026-07-22 12:46:26,044 [    omego.db] INFO  Database is already at OMERO5.4__0
12:46:26 + export LANG=en_US.UTF-8
12:46:26 + LANG=en_US.UTF-8
12:46:26 + export LANGUAGE=en_US:en
12:46:26 + LANGUAGE=en_US:en
12:46:26 + export LC_ALL=en_US.UTF-8
12:46:26 + LC_ALL=en_US.UTF-8
12:46:26 + BUILD_ID=DONT_KILL_ME
12:46:26 + omero admin start
12:46:38 WARNING: lock files in /home/omero/omero-server-data
12:46:38 ----------------------------------------
12:46:38 /home/omero/omero-server-data/.omero/repository/a3d421b1-9991-42f6-9eb8-867f8e8779af/.lock
12:46:38 ----------------------------------------
12:46:38 
12:46:38 You may want to stop all server processes and remove
12:46:38 these files manually. Lock files can remain after an
12:46:38 abrupt server outage and are especially frequent on
12:46:38 remotely mounted filesystems like NFS.
12:46:38 
12:46:38 No descriptor given. Using etc/grid/default.xml
12:46:50 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
12:46:50 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
12:46:50 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
12:46:50 Waiting on startup. Use CTRL-C to exit
12:46:51 + omero admin waitup
12:46:55 Waiting on startup. Use CTRL-C to exit
12:46:56 + omero admin diagnostics
12:47:00 
12:47:00 ================================================================================
12:47:00 OMERO Diagnostics (admin)
12:47:00 ================================================================================
12:47:00         
12:47:00 Commands:   java -version                  21.0.11   (/usr/bin/java)
12:47:00 Commands:   python -V                      3.11.13   (/home/omero/workspace/OMERO-server/.venv3/bin/python)
12:47:00 Commands:   icegridnode --version          3.6.5     (/opt/ice-3.6.5/bin/icegridnode)
12:47:00 Commands:   icegridadmin --version         3.6.5     (/opt/ice-3.6.5/bin/icegridadmin)
12:47:00 Commands:   psql --version                 16.14     (/usr/bin/psql)
12:47:00 Commands:   openssl version                3.5.527   (/usr/bin/openssl)
12:47:00 
12:47:00 Component:  OMERO.py                       5.22.2.dev0
12:47:00 Component:  OMERO.server                   5.6.3-637-6181d3b055-ice36-b17
12:47:00 
12:47:00 Server:     icegridnode                    running
12:47:00 Server:     Blitz-0                        active (pid = 3313, enabled)
12:47:00 Server:     Indexer-0                      active (pid = 3341, enabled)
12:47:00 Server:     OMERO.Glacier2                 active (pid = 3342, enabled)
12:47:00 Server:     OMERO.IceStorm                 active (pid = 3367, enabled)
12:47:00 Server:     Processor-0                    activating (enabled)
12:47:00 Server:     Tables-0                       activating (enabled)
12:47:00 
12:47:00 Log dir:    /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
12:47:00 Log files:  Blitz-0.log                    22.7 KB       errors=0    warnings=1   
12:47:00 Log files:  DropBox.log                    n/a
12:47:00 Log files:  FileServer.log                 n/a
12:47:00 Log files:  Indexer-0.log                  2.6 KB       
12:47:00 Log files:  MonitorServer.log              n/a
12:47:00 Log files:  Processor-0.log                592 B        
12:47:00 Log files:  Tables-0.log                   841 B        
12:47:00 Log files:  TestDropBox.log                n/a
12:47:00 Log files:  master.err                     empty
12:47:00 Log files:  master.out                     30.5 KB      
12:47:00 Log files:  Total size                     0.06 MB
12:47:00 
12:47:00 
12:47:00 Environment:OMERO_HOME=(unset)             
12:47:00 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 
12:47:00 Environment:OMERO_NODE=(unset)             
12:47:00 Environment:OMERO_MASTER=(unset)           
12:47:00 Environment:OMERO_USERDIR=(unset)          
12:47:00 Environment:OMERO_TMPDIR=(unset)           
12:47:00 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 
12:47:00 Environment:PYTHONPATH=(unset)             
12:47:00 Environment:ICE_HOME=/opt/ice-3.6.5        
12:47:00 Environment:LD_LIBRARY_PATH=(unset)        
12:47:00 Environment:DYLD_LIBRARY_PATH=(unset)      
12:47:00 
12:47:00 OMERO SSL port:4064                           
12:47:00 OMERO TCP port:4063                           
12:47:00 OMERO data dir:'/home/omero/omero-server-data' Exists? True	Is writable? True
12:47:00 OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)
12:47:00 
12:47:00 JVM settings: Blitz-${index}                -Xmx7200m
12:47:00 JVM settings: Indexer-${index}              -Xmx4800m
12:47:00 JVM settings: PixelData-${index}            -Xmx7200m
12:47:00 JVM settings: Repository-${index}           -Xmx4800m
12:47:00 
12:47:00 Jar:        lib/server/formats-api.jar     Bio-Formats API	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
12:47:00 Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
12:47:00 Jar:        lib/server/formats-gpl.jar     Bio-Formats library	8.5.0	18 March 2026	877c317e4e396381dc76e56c1539b24947f71dce
12:47:00 Jar:        lib/server/ome-codecs.jar      OME Codecs	1.1.3	26 February 2026	70fd9b72a9834f1af4852c1e5b5676c57a2c360e
12:47:00 Jar:        lib/server/ome-common.jar      OME Common Java	6.2.1	27 February 2026	a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
12:47:00 Jar:        lib/server/ome-jai.jar         OME JAI	0.1.5	30 June 2025	257a1c1410c0103485248d05752a5174262a38b6
12:47:00 Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)	5.3.4	25 June 2025	57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
12:47:00 Jar:        lib/server/ome-poi.jar         OME POI	5.3.11	11 November 2025	a2f3944ac71db9e7e51a6f64ec46beeb60613afb
12:47:00 Jar:        lib/server/ome-xml.jar         OME XML library	6.5.3	22 January 2026	21d1362abd9ce26e13888d2b2d028753d21ac96e
12:47:01 Jar:        lib/server/omero-blitz.jar     jar	5.8.6-SNAPSHOT		
12:47:01 Jar:        lib/server/omero-common.jar    jar	5.7.6-SNAPSHOT		
12:47:01 Jar:        lib/server/omero-gateway.jar   jar	5.11.1-SNAPSHOT		
12:47:01 Jar:        lib/server/omero-model.jar     jar	5.7.6-SNAPSHOT		
12:47:01 Jar:        lib/server/omero-renderer.jar  jar	5.6.6-SNAPSHOT		
12:47:01 Jar:        lib/server/omero-romio.jar     jar	5.8.6-SNAPSHOT		
12:47:01 Jar:        lib/server/omero-server.jar    jar	5.7.6-SNAPSHOT		
12:47:01 + deactivate
12:47:01 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
12:47:01 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
12:47:01 + export PATH
12:47:01 + unset _OLD_VIRTUAL_PATH
12:47:01 + '[' -n '' ']'
12:47:01 + hash -r
12:47:01 + '[' -n '' ']'
12:47:01 + unset VIRTUAL_ENV
12:47:01 + unset VIRTUAL_ENV_PROMPT
12:47:01 + '[' '!' '' = nondestructive ']'
12:47:01 + unset -f deactivate
12:47:01 Finished: SUCCESS