11:09:07 Started by upstream project "Trigger" build number 8
11:09:07 originally caused by:
11:09:07 Started by user devspace
11:09:07 Running as SYSTEM
11:09:07 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
11:09:07 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13238678278631401371.sh
11:09:07 + source /home/settings.env
11:09:07 ++ OMERO_DB_HOST=pg
11:09:07 ++ OMERO_DB_USER=postgres
11:09:07 ++ OMERO_DB_PASS=
11:09:07 ++ OMERO_ROOT_PASS=omero
11:09:07 ++ OMERO_DATA_DIR=/OMERO
11:09:07 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
11:09:07 + OMERO_DB_NAME=OMERO-server
11:09:07 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
11:09:07 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:09:07 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:09:07 + OMERO_DATA_DIR=/home/omero/omero-server-data
11:09:07 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
11:09:07 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
11:09:07 ++ deactivate nondestructive
11:09:07 ++ '[' -n '' ']'
11:09:07 ++ '[' -n '' ']'
11:09:07 ++ hash -r
11:09:07 ++ '[' -n '' ']'
11:09:07 ++ unset VIRTUAL_ENV
11:09:07 ++ unset VIRTUAL_ENV_PROMPT
11:09:07 ++ '[' '!' nondestructive = nondestructive ']'
11:09:07 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
11:09:07 ++ export VIRTUAL_ENV
11:09:07 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:09:07 ++ 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
11:09:07 ++ export PATH
11:09:07 ++ '[' -n '' ']'
11:09:07 ++ '[' -z '' ']'
11:09:07 ++ _OLD_VIRTUAL_PS1=
11:09:07 ++ PS1='(.venv3) '
11:09:07 ++ export PS1
11:09:07 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
11:09:07 ++ export VIRTUAL_ENV_PROMPT
11:09:07 ++ hash -r
11:09:07 + omero admin stop
11:09:40 Server not running
11:09:40 + echo not running
11:09:40 not running
11:09:40 + sleep 5
11:09:45 + deactivate
11:09:45 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
11:09:45 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:09:45 + export PATH
11:09:45 + unset _OLD_VIRTUAL_PATH
11:09:45 + '[' -n '' ']'
11:09:45 + hash -r
11:09:45 + '[' -n '' ']'
11:09:45 + unset VIRTUAL_ENV
11:09:45 + unset VIRTUAL_ENV_PROMPT
11:09:45 + '[' '!' '' = nondestructive ']'
11:09:45 + unset -f deactivate
11:09:45 + rm -rf /home/omero/workspace/OMERO-server/.venv3
11:12:27 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
11:12:46 + '[' true = true ']'
11:12:46 + dropdb -h pg -U postgres OMERO-server
11:12:53 + rm -rf /home/omero/omero-server-data
11:12:54 + rm -rf /home/omero/workspace/OMERO-server/omero-20260708-014756-227376.sql /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
11:13:00 Copied 1 artifact from "OMERO-build" build number 4
11:13:01 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 3
11:13:01 Copied 2 artifacts from "OMERO-build-build" build number 11
11:13:01 [OMERO-server] $ /bin/bash -xe /tmp/jenkins9766002537579649233.sh
11:13:01 + source /home/settings.env
11:13:01 ++ OMERO_DB_HOST=pg
11:13:01 ++ OMERO_DB_USER=postgres
11:13:01 ++ OMERO_DB_PASS=
11:13:01 ++ OMERO_ROOT_PASS=omero
11:13:01 ++ OMERO_DATA_DIR=/OMERO
11:13:01 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
11:13:01 + OMERO_DB_NAME=OMERO-server
11:13:01 + OMERO_DATA_DIR=/home/omero/omero-server-data
11:13:01 + mkdir -p /home/omero/omero-server-data
11:13:01 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
11:13:01 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:13:01 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:13:01 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
11:13:01 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
11:13:01 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
11:13:01 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
11:13:01 ++ ls OMERO.server-5.6.3-614-3c139506b6-ice36-b4.zip
11:13:01 + ZIP=OMERO.server-5.6.3-614-3c139506b6-ice36-b4.zip
11:13:01 + '[' '!' -z '' ']'
11:13:01 + DIST=OMERO.server-5.6.3-614-3c139506b6-ice36-b4
11:13:01 + unzip OMERO.server-5.6.3-614-3c139506b6-ice36-b4.zip
11:13:01 Archive: OMERO.server-5.6.3-614-3c139506b6-ice36-b4.zip
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/blitz/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/grid/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/profiles/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/error/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/grid/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/luts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/luts/janelia/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/luts/matplotlib/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/luts/ncsa_paledit/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/luts/seaborn/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/luts/wcif/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/analysis_scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/annotation_scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/export_scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/figure_scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/import_scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/scripts/omero/util_scripts/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/server/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/share/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/share/licenses/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/misc/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__1/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__10/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__11/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__2/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__3/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__4/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__5/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__6/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__7/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__8/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3A__9/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3__4/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3__5/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3__6/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO3__7/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO4.1__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO4.2__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO4.2__0/t/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO4.3__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO4.4__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO4__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.0__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.1__1/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.2__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.3__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4DEV__1/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4DEV__2/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4DEV__3/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/var/
11:13:01 creating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/var/tmp/
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/LICENSE.txt
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/backup.cfg
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/blitz/mail-senders.example
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/blitz/mail-server.example
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/build.properties
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/env.bat
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/env.sh
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/hibernate.properties
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/ice.config
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/logback-cli.xml
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/logback-indexing-cli.xml
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/logback-indexing.xml
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/logback.xml
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/mime.types
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/node1.cfg
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/node2.cfg
11:13:01 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/omero.properties
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/profiles/psql
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/rollover.cfg
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/Windows.cfg
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/error/maintainance.html
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/grid/README
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/grid/default.xml
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/grid/templates.xml
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/grid/windefault.xml
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/ice.config
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/internal.cfg
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/master.cfg
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/templates/robot.template
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/etc/testdropbox.config
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/history.rst
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/OMEZarrReader.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/accessors-smart.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/activation.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/aggdesigner-algorithm.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/aircompressor.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/antlr.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/aopalliance.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/apiguardian-api.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/asm.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/avatica-core.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/avatica-metrics.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/aws-java-sdk-core.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/aws-java-sdk-kms.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/aws-java-sdk-s3.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/base.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-anim.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-awt-util.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-bridge.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-codec.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-constants.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-css.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-dom.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-ext.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-gvt.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-i18n.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-parser.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-script.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-shared-resources.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-svg-dom.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-svggen.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-transcoder.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-util.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/batik-xml.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/btm.jar
11:13:02 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/calcite-core.jar
11:13:03 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/calcite-linq4j.jar
11:13:03 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/lib/client/cdm-core.jar
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11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/psql-footer.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/psql-header.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/schema.sql
11:13:15 inflating: OMERO.server-5.6.3-614-3c139506b6-ice36-b4/sql/psql/OMERO5.4__0/views.sql
11:13:15 + rm -f OMERO.server-5.6.3-614-3c139506b6-ice36-b4.zip
11:13:15 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-614-3c139506b6-ice36-b4 /home/omero/workspace/OMERO-server/OMERO.server
11:13:15 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
11:13:15 ++ deactivate nondestructive
11:13:15 ++ '[' -n '' ']'
11:13:15 ++ '[' -n '' ']'
11:13:15 ++ hash -r
11:13:15 ++ '[' -n '' ']'
11:13:15 ++ unset VIRTUAL_ENV
11:13:15 ++ unset VIRTUAL_ENV_PROMPT
11:13:15 ++ '[' '!' nondestructive = nondestructive ']'
11:13:15 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
11:13:15 ++ export VIRTUAL_ENV
11:13:15 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:13:15 ++ 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
11:13:15 ++ export PATH
11:13:15 ++ '[' -n '' ']'
11:13:15 ++ '[' -z '' ']'
11:13:15 ++ _OLD_VIRTUAL_PS1=
11:13:15 ++ PS1='(.venv3) '
11:13:15 ++ export PS1
11:13:15 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
11:13:15 ++ export VIRTUAL_ENV_PROMPT
11:13:15 ++ hash -r
11:13:15 + pip install -U pip
11:13:17 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
11:13:17 Collecting pip
11:13:17 Using cached pip-26.1.2-py3-none-any.whl (1.8 MB)
11:13:17 Installing collected packages: pip
11:13:17 Attempting uninstall: pip
11:13:17 Found existing installation: pip 22.3.1
11:13:18 Uninstalling pip-22.3.1:
11:13:18 Successfully uninstalled pip-22.3.1
11:13:30 Successfully installed pip-26.1.2
11:13:31 + pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
11:13:31 Collecting zeroc-ice==3.6.5
11:13:32 Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
11:13:35 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 13.5 MB/s 0:00:02
11:13:35 Installing collected packages: zeroc-ice
11:13:38 Successfully installed zeroc-ice-3.6.5
11:13:38 + pip install markdown
11:13:39 Collecting markdown
11:13:39 Using cached markdown-3.10.2-py3-none-any.whl.metadata (5.1 kB)
11:13:39 Using cached markdown-3.10.2-py3-none-any.whl (108 kB)
11:13:39 Installing collected packages: markdown
11:13:39 Successfully installed markdown-3.10.2
11:13:40 + pip install reportlab
11:13:40 Collecting reportlab
11:13:40 Using cached reportlab-5.0.0-py3-none-any.whl.metadata (1.6 kB)
11:13:41 Collecting pillow>=9.0.0 (from reportlab)
11:13:41 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
11:13:41 Collecting charset-normalizer (from reportlab)
11:13:41 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)
11:13:41 Using cached reportlab-5.0.0-py3-none-any.whl (2.0 MB)
11:13:41 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
11:13:41 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)
11:13:41 Installing collected packages: pillow, charset-normalizer, reportlab
11:13:49
11:13:49 Successfully installed charset-normalizer-3.4.9 pillow-12.3.0 reportlab-5.0.0
11:13:49 + pip install omego
11:13:50 Collecting omego
11:13:50 Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
11:13:50 Collecting future (from omego)
11:13:50 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
11:13:51 Collecting yaclifw>=0.1.1 (from omego)
11:13:51 Using cached yaclifw-0.2.0-py3-none-any.whl
11:13:51 Collecting six (from yaclifw>=0.1.1->omego)
11:13:51 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
11:13:51 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
11:13:51 Using cached future-1.0.0-py3-none-any.whl (491 kB)
11:13:51 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
11:13:51 Installing collected packages: six, future, yaclifw, omego
11:13:55
11:13:55 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
11:13:55 + pip install tables
11:13:56 Collecting tables
11:13:56 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)
11:13:57 Collecting numpy>=1.20.0 (from tables)
11:13:57 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
11:13:57 Collecting numexpr>=2.6.2 (from tables)
11:13:57 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
11:13:57 Collecting packaging (from tables)
11:13:57 Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
11:13:57 Collecting py-cpuinfo (from tables)
11:13:57 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
11:13:57 Collecting blosc2>=2.3.0 (from tables)
11:13:57 Using cached blosc2-4.7.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.8 kB)
11:13:57 Collecting ndindex (from blosc2>=2.3.0->tables)
11:13:57 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
11:13:57 Collecting msgpack (from blosc2>=2.3.0->tables)
11:13:57 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)
11:13:58 Collecting pydantic (from blosc2>=2.3.0->tables)
11:13:58 Using cached pydantic-2.13.4-py3-none-any.whl.metadata (109 kB)
11:13:58 Collecting requests (from blosc2>=2.3.0->tables)
11:13:58 Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
11:13:58 Collecting rich (from blosc2>=2.3.0->tables)
11:13:58 Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
11:13:58 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
11:13:58 Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
11:13:58 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
11:13:58 Using cached annotated_types-0.7.0-py3-none-any.whl.metadata (15 kB)
11:13:59 Collecting pydantic-core==2.46.4 (from pydantic->blosc2>=2.3.0->tables)
11:13:59 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
11:13:59 Collecting typing-extensions>=4.14.1 (from pydantic->blosc2>=2.3.0->tables)
11:13:59 Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
11:13:59 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
11:13:59 Using cached typing_inspection-0.4.2-py3-none-any.whl.metadata (2.6 kB)
11:13:59 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.9)
11:13:59 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
11:13:59 Using cached idna-3.18-py3-none-any.whl.metadata (6.1 kB)
11:13:59 Collecting urllib3<3,>=1.26 (from requests->blosc2>=2.3.0->tables)
11:13:59 Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
11:13:59 Collecting certifi>=2023.5.7 (from requests->blosc2>=2.3.0->tables)
11:13:59 Using cached certifi-2026.6.17-py3-none-any.whl.metadata (2.5 kB)
11:13:59 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
11:13:59 Using cached markdown_it_py-4.2.0-py3-none-any.whl.metadata (7.4 kB)
11:14:00 Collecting pygments<3.0.0,>=2.13.0 (from rich->blosc2>=2.3.0->tables)
11:14:00 Using cached pygments-2.20.0-py3-none-any.whl.metadata (2.5 kB)
11:14:00 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
11:14:00 Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
11:14:00 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)
11:14:00 Using cached blosc2-4.7.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (6.8 MB)
11:14:00 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
11:14:00 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
11:14:00 Using cached msgpack-1.2.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (423 kB)
11:14:00 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
11:14:00 Using cached packaging-26.2-py3-none-any.whl (100 kB)
11:14:00 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
11:14:00 Using cached pydantic-2.13.4-py3-none-any.whl (472 kB)
11:14:00 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
11:14:00 Using cached annotated_types-0.7.0-py3-none-any.whl (13 kB)
11:14:00 Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB)
11:14:00 Using cached typing_inspection-0.4.2-py3-none-any.whl (14 kB)
11:14:00 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
11:14:00 Using cached idna-3.18-py3-none-any.whl (65 kB)
11:14:00 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
11:14:00 Using cached certifi-2026.6.17-py3-none-any.whl (133 kB)
11:14:00 Using cached rich-15.0.0-py3-none-any.whl (310 kB)
11:14:00 Using cached pygments-2.20.0-py3-none-any.whl (1.2 MB)
11:14:00 Using cached markdown_it_py-4.2.0-py3-none-any.whl (91 kB)
11:14:00 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
11:14:00 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
11:14:01 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, threadpoolctl, pygments, packaging, numpy, ndindex, msgpack, mdurl, idna, certifi, annotated-types, typing-inspection, requests, pydantic-core, numexpr, markdown-it-py, rich, pydantic, blosc2, tables
11:14:42
11:14:42 Successfully installed annotated-types-0.7.0 blosc2-4.7.0 certifi-2026.6.17 idna-3.18 markdown-it-py-4.2.0 mdurl-0.1.2 msgpack-1.2.1 ndindex-1.10.1 numexpr-2.14.1 numpy-2.4.6 packaging-26.2 py-cpuinfo-9.0.0 pydantic-2.13.4 pydantic-core-2.46.4 pygments-2.20.0 requests-2.34.2 rich-15.0.0 tables-3.11.1 threadpoolctl-3.6.0 typing-extensions-4.16.0 typing-inspection-0.4.2 urllib3-2.7.0
11:14:42 + pip install jinja2
11:14:43 Collecting jinja2
11:14:43 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
11:14:44 Collecting MarkupSafe>=2.0 (from jinja2)
11:14:44 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)
11:14:44 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
11:14:44 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
11:14:44 Installing collected packages: MarkupSafe, jinja2
11:14:45
11:14:45 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
11:14:45 + pip install omero-py
11:14:46 Collecting omero-py
11:14:46 Using cached omero_py-5.22.1-py3-none-any.whl.metadata (6.5 kB)
11:14:46 Collecting appdirs (from omero-py)
11:14:46 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
11:14:46 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
11:14:46 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
11:14:46 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
11:14:46 Collecting PyYAML (from omero-py)
11:14:46 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)
11:14:46 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
11:14:46 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.34.2)
11:14:46 Collecting portalocker (from omero-py)
11:14:46 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
11:14:46 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.9)
11:14:46 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.18)
11:14:46 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.7.0)
11:14:46 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.6.17)
11:14:46 Using cached omero_py-5.22.1-py3-none-any.whl (2.8 MB)
11:14:46 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
11:14:46 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
11:14:46 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
11:14:46 Installing collected packages: appdirs, PyYAML, portalocker, omero-py
11:15:01
11:15:01 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.22.1 portalocker-3.2.0
11:15:01 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
11:15:02 Collecting omero-metadata
11:15:02 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-hmgmm4fq/omero-metadata_a520fe744aef481a94bf18824503af01
11:15:02 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-hmgmm4fq/omero-metadata_a520fe744aef481a94bf18824503af01
11:15:03 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit c11c984dee0371bac2c6057b02ffc087d7ede818
11:15:03 Installing build dependencies: started
11:15:04 Installing build dependencies: finished with status 'done'
11:15:04 Getting requirements to build wheel: started
11:15:05 Getting requirements to build wheel: finished with status 'done'
11:15:05 Preparing metadata (pyproject.toml): started
11:15:05 Preparing metadata (pyproject.toml): finished with status 'done'
11:15:05 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.22.1)
11:15:05 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
11:15:05 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
11:15:05 Collecting pandas (from omero-metadata)
11:15:05 Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
11:15:05 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
11:15:05 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
11:15:05 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.6)
11:15:05 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)
11:15:05 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
11:15:05 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
11:15:05 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
11:15:05 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
11:15:05 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
11:15:05 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
11:15:05 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)
11:15:05 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)
11:15:05 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)
11:15:05 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)
11:15:05 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.6.17)
11:15:05 Using cached pandas-3.0.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.3 MB)
11:15:06 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
11:15:06 Building wheels for collected packages: omero-metadata
11:15:06 Building wheel for omero-metadata (pyproject.toml): started
11:15:06 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
11:15:06 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=c0ad88efe0fab02196fca676a0fa2dfd230251838a6dfcdbbe776f2570ff1efd
11:15:06 Stored in directory: /tmp/pip-ephem-wheel-cache-_k83evwg/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
11:15:06 Successfully built omero-metadata
11:15:06 Installing collected packages: python-dateutil, pandas, omero-metadata
11:15:45
11:15:45 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.3 python-dateutil-2.9.0.post0
11:15:45 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
11:15:46 Collecting omero-cli-render
11:15:46 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-puaxmwwe/omero-cli-render_d382da31fc7d4fac99600205dc095c08
11:15:46 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-puaxmwwe/omero-cli-render_d382da31fc7d4fac99600205dc095c08
11:15:47 Running command git checkout -b merge_ci --track origin/merge_ci
11:15:48 Switched to a new branch 'merge_ci'
11:15:48 branch 'merge_ci' set up to track 'origin/merge_ci'.
11:15:48 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 0775cf6fc064609562e100aa3592008584339016
11:15:48 Installing build dependencies: started
11:15:49 Installing build dependencies: finished with status 'done'
11:15:49 Getting requirements to build wheel: started
11:15:49 Getting requirements to build wheel: finished with status 'done'
11:15:49 Preparing metadata (pyproject.toml): started
11:15:49 Preparing metadata (pyproject.toml): finished with status 'done'
11:15:49 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
11:15:49 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.22.1)
11:15:49 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
11:15:49 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
11:15:49 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)
11:15:49 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)
11:15:49 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)
11:15:49 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
11:15:49 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
11:15:49 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)
11:15:49 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)
11:15:49 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)
11:15:49 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.6.17)
11:15:49 Building wheels for collected packages: omero-cli-render
11:15:49 Building wheel for omero-cli-render (pyproject.toml): started
11:15:50 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
11:15:50 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19838 sha256=8dba06a7312e6af8b3b61c965f544baf13ecca9b7da48d73a8d679a026dcd579
11:15:50 Stored in directory: /tmp/pip-ephem-wheel-cache-wkvd57yf/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
11:15:50 Successfully built omero-cli-render
11:15:50 Installing collected packages: omero-cli-render
11:15:50 Successfully installed omero-cli-render-0.8.2.dev0
11:15:50 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
11:15:51 Collecting omero-cli-duplicate
11:15:51 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-7erh9uxu/omero-cli-duplicate_b5f4e2b14c604d32aaa79be5ca98c7df
11:15:51 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-7erh9uxu/omero-cli-duplicate_b5f4e2b14c604d32aaa79be5ca98c7df
11:15:52 Running command git checkout -b merge_ci --track origin/merge_ci
11:15:52 Switched to a new branch 'merge_ci'
11:15:52 branch 'merge_ci' set up to track 'origin/merge_ci'.
11:15:52 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit c58f1ee248c9f91a38322a9fd917707afff849bc
11:15:52 Installing build dependencies: started
11:15:53 Installing build dependencies: finished with status 'done'
11:15:53 Getting requirements to build wheel: started
11:15:54 Getting requirements to build wheel: finished with status 'done'
11:15:54 Preparing metadata (pyproject.toml): started
11:15:54 Preparing metadata (pyproject.toml): finished with status 'done'
11:15:54 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.22.1)
11:15:54 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
11:15:54 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
11:15:54 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
11:15:54 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)
11:15:54 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
11:15:54 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)
11:15:54 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.34.2)
11:15:54 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
11:15:54 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)
11:15:54 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)
11:15:54 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)
11:15:54 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.6.17)
11:15:54 Building wheels for collected packages: omero-cli-duplicate
11:15:54 Building wheel for omero-cli-duplicate (pyproject.toml): started
11:15:54 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
11:15:54 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=d912290962f8f55800b4a4d37d440a1b2971d5c142ef8ca706084adc4e512866
11:15:54 Stored in directory: /tmp/pip-ephem-wheel-cache-0jq910r_/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
11:15:54 Successfully built omero-cli-duplicate
11:15:54 Installing collected packages: omero-cli-duplicate
11:15:54 Successfully installed omero-cli-duplicate-0.4.1.dev0
11:15:54 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
11:15:55 Collecting omero-cli-zarr
11:15:55 Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-r0hu4th8/omero-cli-zarr_63c472cf627f4ab9b5308c63bcd80fb9
11:15:55 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-r0hu4th8/omero-cli-zarr_63c472cf627f4ab9b5308c63bcd80fb9
11:15:56 Running command git checkout -b merge_ci --track origin/merge_ci
11:15:56 Switched to a new branch 'merge_ci'
11:15:56 branch 'merge_ci' set up to track 'origin/merge_ci'.
11:15:56 Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit d699d417e172ab9bdb3fc022a584971ee3d4b07f
11:15:56 Installing build dependencies: started
11:15:58 Installing build dependencies: finished with status 'done'
11:15:58 Getting requirements to build wheel: started
11:15:58 Getting requirements to build wheel: finished with status 'done'
11:15:58 Installing backend dependencies: started
11:15:59 Installing backend dependencies: finished with status 'done'
11:15:59 Preparing metadata (pyproject.toml): started
11:16:00 Preparing metadata (pyproject.toml): finished with status 'done'
11:16:00 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.22.1)
11:16:00 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
11:16:00 Using cached ome_zarr-0.18.0-py3-none-any.whl.metadata (2.9 kB)
11:16:00 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.6)
11:16:00 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:00 Using cached dask-2026.7.0-py3-none-any.whl.metadata (3.8 kB)
11:16:00 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:00 Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
11:16:00 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)
11:16:00 Using cached fsspec-2026.6.0-py3-none-any.whl.metadata (10 kB)
11:16:01 Collecting aiohttp (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:01 Using cached aiohttp-3.14.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
11:16:01 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.34.2)
11:16:01 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:01 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
11:16:01 Collecting toolz (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:01 Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB)
11:16:02 Collecting rangehttpserver (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:02 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl.metadata (769 bytes)
11:16:02 Collecting ome-zarr-models>=1.6 (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:02 Using cached ome_zarr_models-1.7-py3-none-any.whl.metadata (3.0 kB)
11:16:02 Collecting Deprecated (from ome-zarr>=0.13.0->omero-cli-zarr)
11:16:02 Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB)
11:16:02 Collecting click>=8.1 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:02 Using cached click-8.4.2-py3-none-any.whl.metadata (2.6 kB)
11:16:02 Collecting cloudpickle>=3.0.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:02 Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB)
11:16:02 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)
11:16:02 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:02 Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
11:16:02 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)
11:16:02 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)
11:16:02 Using cached importlib_metadata-9.0.0-py3-none-any.whl.metadata (4.5 kB)
11:16:03 Collecting s3fs>2024.2.0 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:03 Using cached s3fs-2026.6.0-py3-none-any.whl.metadata (1.2 kB)
11:16:03 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)
11:16:03 Using cached zipp-4.1.0-py3-none-any.whl.metadata (3.6 kB)
11:16:03 Collecting pydantic-zarr>=0.8.2 (from ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:03 Using cached pydantic_zarr-0.9.2-py3-none-any.whl.metadata (4.0 kB)
11:16:03 Collecting pydantic<2.13,>=2.11.5 (from ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:03 Using cached pydantic-2.12.5-py3-none-any.whl.metadata (90 kB)
11:16:03 Requirement already satisfied: annotated-types>=0.6.0 in ./.venv3/lib64/python3.11/site-packages (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr) (0.7.0)
11:16:04 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)
11:16:04 Using cached pydantic_core-2.41.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.3 kB)
11:16:04 Requirement already satisfied: typing-extensions>=4.14.1 in ./.venv3/lib64/python3.11/site-packages (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr) (4.16.0)
11:16:04 Requirement already satisfied: typing-inspection>=0.4.2 in ./.venv3/lib64/python3.11/site-packages (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr) (0.4.2)
11:16:04 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
11:16:04 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.0.0)
11:16:04 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (12.3.0)
11:16:04 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (3.6.5)
11:16:04 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (3.2.0)
11:16:04 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)
11:16:04 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
11:16:04 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)
11:16:04 Using cached aiobotocore-3.7.0-py3-none-any.whl.metadata (28 kB)
11:16:04 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)
11:16:04 Using cached aioitertools-0.13.0-py3-none-any.whl.metadata (3.3 kB)
11:16:05 Collecting botocore<1.43.1,>=1.42.90 (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)
11:16:05 Using cached botocore-1.43.0-py3-none-any.whl.metadata (5.5 kB)
11:16:05 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)
11:16:05 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)
11:16:05 Using cached jmespath-1.1.0-py3-none-any.whl.metadata (7.6 kB)
11:16:05 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)
11:16:05 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)
11:16:05 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)
11:16:05 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)
11:16:05 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:05 Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl.metadata (5.9 kB)
11:16:05 Collecting aiosignal>=1.4.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:05 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
11:16:06 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:06 Using cached attrs-26.1.0-py3-none-any.whl.metadata (8.8 kB)
11:16:06 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:06 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)
11:16:06 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:06 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)
11:16:06 Collecting yarl<2.0,>=1.17.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:06 Using cached yarl-1.24.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (94 kB)
11:16:06 Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.43.1,>=1.42.90->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) (2.7.0)
11:16:06 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->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) (1.17.0)
11:16:06 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)
11:16:07 Collecting scipy>=1.11.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
11:16:07 Collecting networkx>=3.0 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
11:16:07 Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 Using cached imageio-2.37.3-py3-none-any.whl.metadata (9.7 kB)
11:16:07 Collecting tifffile>=2022.8.12 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 Using cached tifffile-2026.3.3-py3-none-any.whl.metadata (31 kB)
11:16:07 Collecting lazy-loader>=0.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 Using cached lazy_loader-0.5-py3-none-any.whl.metadata (5.9 kB)
11:16:07 Collecting donfig>=0.8 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
11:16:07 Collecting google-crc32c>=1.5 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 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.metadata (1.7 kB)
11:16:07 Collecting numcodecs>=0.14 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
11:16:07 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)
11:16:07 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)
11:16:07 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (2026.6.17)
11:16:07 Using cached ome_zarr-0.18.0-py3-none-any.whl (57 kB)
11:16:07 Using cached dask-2026.7.0-py3-none-any.whl (1.5 MB)
11:16:07 Using cached click-8.4.2-py3-none-any.whl (119 kB)
11:16:08 Using cached cloudpickle-3.1.2-py3-none-any.whl (22 kB)
11:16:08 Using cached fsspec-2026.6.0-py3-none-any.whl (203 kB)
11:16:08 Using cached importlib_metadata-9.0.0-py3-none-any.whl (27 kB)
11:16:08 Using cached ome_zarr_models-1.7-py3-none-any.whl (64 kB)
11:16:08 Using cached pydantic-2.12.5-py3-none-any.whl (463 kB)
11:16:08 Using cached pydantic_core-2.41.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
11:16:08 Using cached partd-1.4.2-py3-none-any.whl (18 kB)
11:16:08 Using cached pydantic_zarr-0.9.2-py3-none-any.whl (52 kB)
11:16:08 Using cached s3fs-2026.6.0-py3-none-any.whl (32 kB)
11:16:08 Using cached aiobotocore-3.7.0-py3-none-any.whl (89 kB)
11:16:08 Using cached aiohttp-3.14.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.8 MB)
11:16:08 Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB)
11:16:08 Using cached botocore-1.43.0-py3-none-any.whl (15.0 MB)
11:16:08 Using cached jmespath-1.1.0-py3-none-any.whl (20 kB)
11:16:08 Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
11:16:08 Using cached wrapt-2.2.2-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (159 kB)
11:16:08 Using cached yarl-1.24.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (106 kB)
11:16:08 Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl (15 kB)
11:16:08 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
11:16:08 Using cached attrs-26.1.0-py3-none-any.whl (67 kB)
11:16:08 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (231 kB)
11:16:08 Using cached propcache-0.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (58 kB)
11:16:08 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (13.7 MB)
11:16:08 Using cached imageio-2.37.3-py3-none-any.whl (317 kB)
11:16:08 Using cached lazy_loader-0.5-py3-none-any.whl (8.0 kB)
11:16:08 Using cached networkx-3.6.1-py3-none-any.whl (2.1 MB)
11:16:09 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.3 MB)
11:16:09 Using cached tifffile-2026.3.3-py3-none-any.whl (243 kB)
11:16:09 Using cached toolz-1.1.0-py3-none-any.whl (58 kB)
11:16:09 Using cached zarr-3.1.6-py3-none-any.whl (295 kB)
11:16:09 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
11:16:09 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)
11:16:09 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)
11:16:09 Using cached zipp-4.1.0-py3-none-any.whl (10 kB)
11:16:09 Using cached deprecated-1.3.1-py2.py3-none-any.whl (11 kB)
11:16:09 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
11:16:09 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
11:16:09 Building wheels for collected packages: omero-cli-zarr
11:16:09 Building wheel for omero-cli-zarr (pyproject.toml): started
11:16:10 Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
11:16:10 Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev162+gd699d41-py3-none-any.whl size=38288 sha256=743a6071087d69c47052fd0c5b29fc4bd841ceabc7e561bd9b0483597a2f5549
11:16:10 Stored in directory: /tmp/pip-ephem-wheel-cache-d14sbc9w/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
11:16:10 Successfully built omero-cli-zarr
11:16:10 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
11:16:42 Attempting uninstall: pydantic-core
11:16:42 Found existing installation: pydantic_core 2.46.4
11:16:42 Uninstalling pydantic_core-2.46.4:
11:16:42 Successfully uninstalled pydantic_core-2.46.4
11:17:17 Attempting uninstall: pydantic
11:17:17 Found existing installation: pydantic 2.13.4
11:17:17 Uninstalling pydantic-2.13.4:
11:17:17 Successfully uninstalled pydantic-2.13.4
11:17:58
11:17:58 Successfully installed Deprecated-1.3.1 aiobotocore-3.7.0 aiohappyeyeballs-2.7.1 aiohttp-3.14.1 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.0 click-8.4.2 cloudpickle-3.1.2 dask-2026.7.0 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.6.0 google-crc32c-1.8.0 imageio-2.37.3 importlib_metadata-9.0.0 jmespath-1.1.0 lazy-loader-0.5 locket-1.0.0 multidict-6.7.1 networkx-3.6.1 numcodecs-0.16.5 ome-zarr-0.18.0 ome-zarr-models-1.7 omero-cli-zarr-0.5.5.dev162+gd699d41 partd-1.4.2 propcache-0.5.2 pydantic-2.12.5 pydantic-core-2.41.5 pydantic-zarr-0.9.2 rangehttpserver-1.4.0 s3fs-2026.6.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 wrapt-2.2.2 yarl-1.24.2 zarr-3.1.6 zipp-4.1.0
11:17:59 + pip install omero-certificates
11:18:00 Collecting omero-certificates
11:18:00 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
11:18:00 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.22.1)
11:18:00 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
11:18:00 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
11:18:00 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.6)
11:18:00 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.3.0)
11:18:00 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
11:18:00 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
11:18:00 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.34.2)
11:18:00 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
11:18:00 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.9)
11:18:00 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.18)
11:18:00 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.7.0)
11:18:00 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.6.17)
11:18:00 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
11:18:00 Installing collected packages: omero-certificates
11:18:01 Successfully installed omero-certificates-0.4.0
11:18:01 + for x in *.tar.gz
11:18:01 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
11:18:01 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
11:18:01 Installing build dependencies: started
11:18:03 Installing build dependencies: finished with status 'done'
11:18:03 Getting requirements to build wheel: started
11:18:03 Getting requirements to build wheel: finished with status 'done'
11:18:03 Preparing metadata (pyproject.toml): started
11:18:03 Preparing metadata (pyproject.toml): finished with status 'done'
11:18:03 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.22.1)
11:18:03 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
11:18:03 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
11:18:03 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)
11:18:03 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)
11:18:03 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
11:18:03 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)
11:18:03 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
11:18:03 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
11:18:03 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)
11:18:03 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)
11:18:03 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)
11:18:03 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.6.17)
11:18:03 Building wheels for collected packages: omero-dropbox
11:18:03 Building wheel for omero-dropbox (pyproject.toml): started
11:18:04 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
11:18:04 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49153 sha256=8d90803efc2d04793e1f2efa2c2e6bb201c5f6c0b3286ce65f3b8016abf89ae6
11:18:04 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
11:18:04 Successfully built omero-dropbox
11:18:04 Installing collected packages: omero-dropbox
11:18:04 Successfully installed omero-dropbox-5.7.1.dev0
11:18:04 + for x in *.tar.gz
11:18:04 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
11:18:05 Processing ./omero_marshal-0.9.2.dev0.tar.gz
11:18:05 Installing build dependencies: started
11:18:06 Installing build dependencies: finished with status 'done'
11:18:06 Getting requirements to build wheel: started
11:18:07 Getting requirements to build wheel: finished with status 'done'
11:18:07 Preparing metadata (pyproject.toml): started
11:18:07 Preparing metadata (pyproject.toml): finished with status 'done'
11:18:07 Building wheels for collected packages: omero_marshal
11:18:07 Building wheel for omero_marshal (pyproject.toml): started
11:18:07 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
11:18:07 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88129 sha256=2f29480215993318905894fc3f90a06340820d91592246276d038b443cf1d367
11:18:07 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
11:18:07 Successfully built omero_marshal
11:18:08 Installing collected packages: omero_marshal
11:18:10 Successfully installed omero_marshal-0.9.2.dev0
11:18:10 + for x in *.tar.gz
11:18:10 + pip install -U omero_py-5.22.2.dev0.tar.gz
11:18:11 Processing ./omero_py-5.22.2.dev0.tar.gz
11:18:11 Installing build dependencies: started
11:18:12 Installing build dependencies: finished with status 'done'
11:18:12 Getting requirements to build wheel: started
11:18:13 Getting requirements to build wheel: finished with status 'done'
11:18:13 Preparing metadata (pyproject.toml): started
11:18:13 Preparing metadata (pyproject.toml): finished with status 'done'
11:18:13 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.4.4)
11:18:13 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.0.0)
11:18:13 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.4.6)
11:18:13 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (12.3.0)
11:18:13 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (6.0.3)
11:18:13 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)
11:18:13 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.34.2)
11:18:13 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.2.0)
11:18:13 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)
11:18:13 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.18)
11:18:13 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)
11:18:13 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2026.6.17)
11:18:13 Building wheels for collected packages: omero-py
11:18:13 Building wheel for omero-py (pyproject.toml): started
11:18:14 Building wheel for omero-py (pyproject.toml): finished with status 'done'
11:18:14 Created wheel for omero-py: filename=omero_py-5.22.2.dev0-py3-none-any.whl size=2787060 sha256=845cfd01816abf50dcfb5e93c2a78a974419453b8aa9e205833cc88ecfbdcfb5
11:18:14 Stored in directory: /home/omero/.cache/pip/wheels/ec/3f/72/4027ca0a7faf1f66d4577cc07619b0497ac8e99396d43dd8fa
11:18:14 Successfully built omero-py
11:18:14 Installing collected packages: omero-py
11:18:14 Attempting uninstall: omero-py
11:18:14 Found existing installation: omero-py 5.22.1
11:18:15 Uninstalling omero-py-5.22.1:
11:18:27 Successfully uninstalled omero-py-5.22.1
11:18:45 Successfully installed omero-py-5.22.2.dev0
11:18:45 + for x in *.tar.gz
11:18:45 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
11:18:46 Processing ./omero_scripts-5.10.1.dev0.tar.gz
11:18:46 Installing build dependencies: started
11:18:47 Installing build dependencies: finished with status 'done'
11:18:47 Getting requirements to build wheel: started
11:18:47 Getting requirements to build wheel: finished with status 'done'
11:18:47 Preparing metadata (pyproject.toml): started
11:18:48 Preparing metadata (pyproject.toml): finished with status 'done'
11:18:48 Building wheels for collected packages: omero-scripts
11:18:48 Building wheel for omero-scripts (pyproject.toml): started
11:18:48 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
11:18:48 Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=136999 sha256=51a3b1a1c1b73e2ecb65da1236c68d311c947badb2a17bd24fb147205da3d712
11:18:48 Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
11:18:48 Successfully built omero-scripts
11:18:48 Installing collected packages: omero-scripts
11:18:49 Successfully installed omero-scripts-5.10.1.dev0
11:18:49 + for x in *.tar.gz
11:18:49 + pip install -U omero_web-5.32.1.dev0.tar.gz
11:18:50 Processing ./omero_web-5.32.1.dev0.tar.gz
11:18:50 Installing build dependencies: started
11:18:52 Installing build dependencies: finished with status 'done'
11:18:52 Getting requirements to build wheel: started
11:18:52 Getting requirements to build wheel: finished with status 'done'
11:18:52 Preparing metadata (pyproject.toml): started
11:18:52 Preparing metadata (pyproject.toml): finished with status 'done'
11:18:52 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (5.22.2.dev0)
11:18:52 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.32.1.dev0)
11:18:52 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
11:18:53 Collecting Django<5.3,>=5.2.9 (from omero-web==5.32.1.dev0)
11:18:53 Using cached django-5.2.16-py3-none-any.whl.metadata (4.1 kB)
11:18:53 Collecting django-pipeline>=4.1.0 (from omero-web==5.32.1.dev0)
11:18:53 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
11:18:53 Collecting django-cors-headers==3.7.0 (from omero-web==5.32.1.dev0)
11:18:53 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
11:18:53 Collecting whitenoise>=5.3.0 (from omero-web==5.32.1.dev0)
11:18:53 Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
11:18:53 Collecting gunicorn>=19.3 (from omero-web==5.32.1.dev0)
11:18:53 Using cached gunicorn-26.0.0-py3-none-any.whl.metadata (5.4 kB)
11:18:53 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (0.9.2.dev0)
11:18:53 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (12.3.0)
11:18:53 Collecting pytz (from omero-web==5.32.1.dev0)
11:18:54 Using cached pytz-2026.2-py2.py3-none-any.whl.metadata (22 kB)
11:18:54 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (3.2.0)
11:18:54 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.32.1.dev0) (26.2)
11:18:54 Collecting importlib-resources (from omero-web==5.32.1.dev0)
11:18:54 Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
11:18:54 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
11:18:54 Using cached asgiref-3.11.1-py3-none-any.whl.metadata (9.3 kB)
11:18:54 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.32.1.dev0)
11:18:54 Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
11:18:54 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)
11:18:54 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.32.1.dev0)
11:18:54 Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 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)
11:18:54 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.32.1.dev0) (2026.6.17)
11:18:54 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
11:18:54 Using cached django-5.2.16-py3-none-any.whl (8.3 MB)
11:18:54 Using cached asgiref-3.11.1-py3-none-any.whl (24 kB)
11:18:54 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
11:18:54 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
11:18:54 Using cached gunicorn-26.0.0-py3-none-any.whl (212 kB)
11:18:54 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
11:18:54 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
11:18:54 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
11:18:54 Using cached pytz-2026.2-py2.py3-none-any.whl (510 kB)
11:18:54 Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
11:18:55 Building wheels for collected packages: omero-web
11:18:55 Building wheel for omero-web (pyproject.toml): started
11:18:56 Building wheel for omero-web (pyproject.toml): finished with status 'done'
11:18:56 Created wheel for omero-web: filename=omero_web-5.32.1.dev0-py3-none-any.whl size=2820645 sha256=5d0599ffc11086ddc7f51d959ecc59b25f882555a486ddf043f0bcd469469508
11:18:56 Stored in directory: /home/omero/.cache/pip/wheels/e6/f6/6f/ec36dda9edad720aabd7330edafa8a6a62d6ebfa4c7467248f
11:18:56 Successfully built omero-web
11:18:56 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
11:20:15
11:20:15 Successfully installed Django-5.2.16 asgiref-3.11.1 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
11:20:15 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
11:20:15 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
11:20:15 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
11:20:15 --2026-07-09 11:20:15-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
11:20:15 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.108.133, ...
11:20:15 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
11:20:15 HTTP request sent, awaiting response... 200 OK
11:20:16 Length: 139337 (136K) [text/plain]
11:20:16 Saving to: ‘Figure_To_Pdf.py’
11:20:16
11:20:16 0K .......... .......... .......... .......... .......... 36% 2.89M 0s
11:20:16 50K .......... .......... .......... .......... .......... 73% 10.6M 0s
11:20:16 100K .......... .......... .......... ...... 100% 3.57M=0.03s
11:20:16
11:20:16 2026-07-09 11:20:16 (4.23 MB/s) - ‘Figure_To_Pdf.py’ saved [139337/139337]
11:20:16
11:20:16 + chmod 755 Figure_To_Pdf.py
11:20:16 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
11:20:16 + omero config set omero.db.name OMERO-server
11:20:22 + omero config set omero.db.host pg
11:20:27 + omero config set omero.db.user postgres
11:20:31 + omero config set omero.data.dir /home/omero/omero-server-data
11:20:36 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
11:20:41 + omero config set omero.db.poolsize 25
11:20:46 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
11:20:50 + omero config set omero.security.trustStorePassword changeit
11:20:55 + omero config set omero.mail.config true
11:21:00 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
11:21:04 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
11:21:09 + omero certificates
11:21:13 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
11:21:13 certificates created: /home/omero/omero-server-data/certs/server.key /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
11:21:13 + '[' true = true ']'
11:21:13 + createdb -h pg -U postgres OMERO-server
11:21:18 + omego db init --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
11:21:18 2026-07-09 11:21:18,804 [omego.extern] INFO Executing : omero version
11:21:23 OMERO.py version:
11:21:23 OMERO.server version:
11:21:23 5.6.3-614-3c139506b6-ice36-b4
11:21:23 5.22.2.dev0
11:21:23 2026-07-09 11:21:23,679 [omego.extern] INFO Completed [4.875 s]
11:21:23 2026-07-09 11:21:23,680 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
11:21:23 2026-07-09 11:21:23,680 [omego.extern] INFO Running [current environment]: omero config get --show-password
11:21:23 2026-07-09 11:21:23,680 [omego.extern] INFO Executing : omero config get --show-password
11:21:28 2026-07-09 11:21:28,262 [omego.extern] INFO Completed [4.583 s]
11:21:28 2026-07-09 11:21:28,263 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
11:21:28 2026-07-09 11:21:28,263 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
11:21:28 2026-07-09 11:21:28,269 [omego.extern] INFO Completed [0.006 s]
11:21:28 2026-07-09 11:21:28,269 [ omego.db] INFO psql version: psql (PostgreSQL) 16.14
11:21:28
11:21:28 2026-07-09 11:21:28,269 [omego.extern] INFO Running [current environment]: omero config get --show-password
11:21:28 2026-07-09 11:21:28,269 [omego.extern] INFO Executing : omero config get --show-password
11:21:32 2026-07-09 11:21:32,616 [omego.extern] INFO Completed [4.347 s]
11:21:32 2026-07-09 11:21:32,617 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
11:21:32 2026-07-09 11:21:32,617 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
11:21:32 2026-07-09 11:21:32,666 [omego.extern] INFO Completed [0.049 s]
11:21:32 2026-07-09 11:21:32,666 [ omego.db] INFO Creating SQL: omero-20260709-112132-666897.sql
11:21:32 2026-07-09 11:21:32,666 [omego.extern] INFO Running [current environment]: omero db script -f omero-20260709-112132-666897.sql omero
11:21:32 2026-07-09 11:21:32,667 [omego.extern] INFO Executing : omero db script -f omero-20260709-112132-666897.sql omero
11:21:41 2026-07-09 11:21:41,244 [omego.extern] INFO Completed [8.577 s]
11:21:41 2026-07-09 11:21:41,244 [ omego.db] INFO Creating database using omero-20260709-112132-666897.sql
11:21:41 2026-07-09 11:21:41,244 [omego.extern] INFO Running [current environment]: omero config get --show-password
11:21:41 2026-07-09 11:21:41,244 [omego.extern] INFO Executing : omero config get --show-password
11:21:45 2026-07-09 11:21:45,801 [omego.extern] INFO Completed [4.558 s]
11:21:45 2026-07-09 11:21:45,802 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
11:21:45 2026-07-09 11:21:45,802 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -f omero-20260709-112132-666897.sql
11:22:05 2026-07-09 11:22:05,625 [omego.extern] INFO Completed [19.823 s]
11:22:05 2026-07-09 11:22:05,625 [ omego.db] WARNI stderr: b'psql:omero-20260709-112132-666897.sql:2842: NOTICE: identifier "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkcontraststretchingcontext_codomainmapcontext_id_codomainmapco"\npsql:omero-20260709-112132-666897.sql:4712: NOTICE: identifier "fklogicalchannel_photometricinterpretation_photometricinterpretation" will be truncated to "fklogicalchannel_photometricinterpretation_photometricinterpret"\npsql:omero-20260709-112132-666897.sql:5697: NOTICE: identifier "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcontext" will be truncated to "fkreverseintensitycontext_codomainmapcontext_id_codomainmapcont"\n'
11:22:05 + export LANG=en_US.UTF-8
11:22:05 + LANG=en_US.UTF-8
11:22:05 + export LANGUAGE=en_US:en
11:22:05 + LANGUAGE=en_US:en
11:22:05 + export LC_ALL=en_US.UTF-8
11:22:05 + LC_ALL=en_US.UTF-8
11:22:05 + BUILD_ID=DONT_KILL_ME
11:22:05 + omero admin start
11:22:15 No descriptor given. Using etc/grid/default.xml
11:22:28 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
11:22:28 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
11:22:28 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
11:22:28 Waiting on startup. Use CTRL-C to exit
11:22:28 + omero admin waitup
11:22:33 Waiting on startup. Use CTRL-C to exit
11:22:33 + omero admin diagnostics
11:22:38
11:22:38 ================================================================================
11:22:38 OMERO Diagnostics (admin)
11:22:38 ================================================================================
11:22:38
11:22:38 Commands: java -version 21.0.11 (/usr/bin/java)
11:22:38 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
11:22:38 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
11:22:38 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
11:22:38 Commands: psql --version 16.14 (/usr/bin/psql)
11:22:38 Commands: openssl version 3.5.527 (/usr/bin/openssl)
11:22:38
11:22:38 Component: OMERO.py 5.22.2.dev0
11:22:38 Component: OMERO.server 5.6.3-614-3c139506b6-ice36-b4
11:22:38
11:22:38 Server: icegridnode running
11:22:38 Server: Blitz-0 active (pid = 4158, enabled)
11:22:39 Server: Indexer-0 active (pid = 4191, enabled)
11:22:39 Server: OMERO.Glacier2 active (pid = 4213, enabled)
11:22:39 Server: OMERO.IceStorm active (pid = 4179, enabled)
11:22:39 Server: Processor-0 active (pid = 4217, enabled)
11:22:39 Server: Tables-0 active (pid = 4197, enabled)
11:22:39
11:22:39 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
11:22:39 Log files: Blitz-0.log 144.9 KB errors=0 warnings=1
11:22:39 Log files: DropBox.log n/a
11:22:39 Log files: FileServer.log n/a
11:22:39 Log files: Indexer-0.log 2.6 KB
11:22:39 Log files: MonitorServer.log n/a
11:22:39 Log files: Processor-0.log 856 B
11:22:39 Log files: Tables-0.log 1.1 KB
11:22:39 Log files: TestDropBox.log n/a
11:22:39 Log files: master.err empty
11:22:39 Log files: master.out 30.5 KB
11:22:39 Log files: Total size 0.18 MB
11:22:39
11:22:39
11:22:39 Environment:OMERO_HOME=(unset)
11:22:39 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
11:22:39 Environment:OMERO_NODE=(unset)
11:22:39 Environment:OMERO_MASTER=(unset)
11:22:39 Environment:OMERO_USERDIR=(unset)
11:22:39 Environment:OMERO_TMPDIR=(unset)
11:22:39 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
11:22:39 Environment:PYTHONPATH=(unset)
11:22:39 Environment:ICE_HOME=/opt/ice-3.6.5
11:22:39 Environment:LD_LIBRARY_PATH=(unset)
11:22:39 Environment:DYLD_LIBRARY_PATH=(unset)
11:22:39
11:22:39 OMERO SSL port:4064
11:22:39 OMERO TCP port:4063
11:22:39 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
11:22:39 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
11:22:39
11:22:39 JVM settings: Blitz-${index} -Xmx7200m
11:22:39 JVM settings: Indexer-${index} -Xmx4800m
11:22:39 JVM settings: PixelData-${index} -Xmx7200m
11:22:39 JVM settings: Repository-${index} -Xmx4800m
11:22:39
11:22:39 Jar: lib/server/formats-api.jar Bio-Formats API 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
11:22:39 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
11:22:39 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
11:22:39 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3 26 February 2026 70fd9b72a9834f1af4852c1e5b5676c57a2c360e
11:22:39 Jar: lib/server/ome-common.jar OME Common Java 6.2.1 27 February 2026 a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
11:22:39 Jar: lib/server/ome-jai.jar OME JAI 0.1.5 30 June 2025 257a1c1410c0103485248d05752a5174262a38b6
11:22:39 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4 25 June 2025 57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
11:22:39 Jar: lib/server/ome-poi.jar OME POI 5.3.11 11 November 2025 a2f3944ac71db9e7e51a6f64ec46beeb60613afb
11:22:39 Jar: lib/server/ome-xml.jar OME XML library 6.5.3 22 January 2026 21d1362abd9ce26e13888d2b2d028753d21ac96e
11:22:39 Jar: lib/server/omero-blitz.jar jar 5.8.6-SNAPSHOT
11:22:39 Jar: lib/server/omero-common.jar jar 5.7.6-SNAPSHOT
11:22:39 Jar: lib/server/omero-gateway.jar jar 5.11.1-SNAPSHOT
11:22:39 Jar: lib/server/omero-model.jar jar 5.7.6-SNAPSHOT
11:22:39 Jar: lib/server/omero-renderer.jar jar 5.6.6-SNAPSHOT
11:22:39 Jar: lib/server/omero-romio.jar jar 5.8.6-SNAPSHOT
11:22:39 Jar: lib/server/omero-server.jar jar 5.7.6-SNAPSHOT
11:22:39 + deactivate
11:22:39 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
11:22:39 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
11:22:39 + export PATH
11:22:39 + unset _OLD_VIRTUAL_PATH
11:22:39 + '[' -n '' ']'
11:22:39 + hash -r
11:22:39 + '[' -n '' ']'
11:22:39 + unset VIRTUAL_ENV
11:22:39 + unset VIRTUAL_ENV_PROMPT
11:22:39 + '[' '!' '' = nondestructive ']'
11:22:39 + unset -f deactivate
11:22:40 Finished: SUCCESS
