00:34:51 Started by upstream project "Trigger" build number 644
00:34:51 originally caused by:
00:34:51 Started by timer
00:34:51 Running as SYSTEM
00:34:51 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:34:51 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13433483559168854410.sh
00:34:51 + source /home/settings.env
00:34:51 ++ OMERO_DB_HOST=pg
00:34:51 ++ OMERO_DB_USER=postgres
00:34:51 ++ OMERO_DB_PASS=
00:34:51 ++ OMERO_ROOT_PASS=omero
00:34:51 ++ OMERO_DATA_DIR=/OMERO
00:34:51 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:34:51 + OMERO_DB_NAME=OMERO-server
00:34:51 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:34:51 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:34:51 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:34:51 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:34:51 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:34:51 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:34:51 ++ deactivate nondestructive
00:34:51 ++ '[' -n '' ']'
00:34:51 ++ '[' -n '' ']'
00:34:51 ++ hash -r
00:34:51 ++ '[' -n '' ']'
00:34:51 ++ unset VIRTUAL_ENV
00:34:51 ++ unset VIRTUAL_ENV_PROMPT
00:34:51 ++ '[' '!' nondestructive = nondestructive ']'
00:34:51 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:34:51 ++ export VIRTUAL_ENV
00:34:51 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:34:51 ++ 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
00:34:51 ++ export PATH
00:34:51 ++ '[' -n '' ']'
00:34:51 ++ '[' -z '' ']'
00:34:51 ++ _OLD_VIRTUAL_PS1=
00:34:51 ++ PS1='(.venv3) '
00:34:51 ++ export PS1
00:34:51 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:34:51 ++ export VIRTUAL_ENV_PROMPT
00:34:51 ++ hash -r
00:34:51 + omero admin stop
00:34:53 Waiting on shutdown. Use CTRL-C to exit
00:34:53 .+ sleep 5
00:35:08 + deactivate
00:35:08 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:35:08 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:35:08 + export PATH
00:35:08 + unset _OLD_VIRTUAL_PATH
00:35:08 + '[' -n '' ']'
00:35:08 + hash -r
00:35:08 + '[' -n '' ']'
00:35:08 + unset VIRTUAL_ENV
00:35:08 + unset VIRTUAL_ENV_PROMPT
00:35:08 + '[' '!' '' = nondestructive ']'
00:35:08 + unset -f deactivate
00:35:08 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:35:08 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:35:12 + '[' false = true ']'
00:35:12 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:35:12 Skipping PURGE_DATA:CleanDbAndRepo
00:35:12 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.4-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.21.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.29.3.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:35:14 Copied 1 artifact from "OMERO-build" build number 541
00:35:15 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 538
00:35:16 Copied 2 artifacts from "OMERO-build-build" build number 572
00:35:16 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 73
00:35:16 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13107027692733466400.sh
00:35:16 + source /home/settings.env
00:35:16 ++ OMERO_DB_HOST=pg
00:35:16 ++ OMERO_DB_USER=postgres
00:35:16 ++ OMERO_DB_PASS=
00:35:16 ++ OMERO_ROOT_PASS=omero
00:35:16 ++ OMERO_DATA_DIR=/OMERO
00:35:16 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:35:16 + OMERO_DB_NAME=OMERO-server
00:35:16 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:35:16 + mkdir -p /home/omero/omero-server-data
00:35:16 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:35:16 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:35:16 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:35:16 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:35:16 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:35:16 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:35:16 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:35:16 ++ ls OMERO.server-5.6.3-576-b406bad8dd-ice36-b541.zip
00:35:16 + ZIP=OMERO.server-5.6.3-576-b406bad8dd-ice36-b541.zip
00:35:16 + '[' '!' -z '' ']'
00:35:16 + DIST=OMERO.server-5.6.3-576-b406bad8dd-ice36-b541
00:35:16 + unzip OMERO.server-5.6.3-576-b406bad8dd-ice36-b541.zip
00:35:16 Archive: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541.zip
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/blitz/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/grid/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/profiles/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/error/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/grid/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/luts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/luts/janelia/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/luts/matplotlib/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/luts/ncsa_paledit/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/luts/seaborn/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/luts/wcif/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/analysis_scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/annotation_scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/export_scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/figure_scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/import_scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/scripts/omero/util_scripts/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/server/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/share/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/share/licenses/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/misc/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__1/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__10/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__11/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__2/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__3/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__4/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__5/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__6/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__7/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__8/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3A__9/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3__4/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3__5/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3__6/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO3__7/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO4.1__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO4.2__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO4.2__0/t/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO4.3__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO4.4__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO4__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.0__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.1__1/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.2__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.3__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4DEV__1/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4DEV__2/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4DEV__3/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/
00:35:16 creating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/var/
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/LICENSE.txt
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/backup.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/blitz/mail-senders.example
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/blitz/mail-server.example
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/build.properties
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/env.bat
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/env.sh
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/hibernate.properties
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/ice.config
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/logback-cli.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/logback-indexing-cli.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/logback-indexing.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/logback.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/mime.types
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/node1.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/node2.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/omero.properties
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/profiles/psql
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/rollover.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/Windows.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/error/maintainance.html
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/grid/README
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/grid/default.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/grid/templates.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/grid/windefault.xml
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/ice.config
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/internal.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/master.cfg
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/templates/robot.template
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/etc/testdropbox.config
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/history.rst
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/OMEZarrReader.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/accessors-smart.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/activation.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/aggdesigner-algorithm.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/aircompressor.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/antlr.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/aopalliance.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/apiguardian-api.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/asm.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/avatica-core.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/avatica-metrics.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/aws-java-sdk-core.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/aws-java-sdk-kms.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/aws-java-sdk-s3.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/base.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-anim.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-awt-util.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-bridge.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-codec.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-constants.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-css.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-dom.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-ext.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-gvt.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-i18n.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-parser.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-script.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-shared-resources.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-svg-dom.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-svggen.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-transcoder.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-util.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/batik-xml.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/btm.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/calcite-core.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/calcite-linq4j.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/cdm-core.jar
00:35:16 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/lib/client/checker-qual.jar
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00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/psql-footer.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/psql-header.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/schema.sql
00:35:18 inflating: OMERO.server-5.6.3-576-b406bad8dd-ice36-b541/sql/psql/OMERO5.4__0/views.sql
00:35:18 + rm -f OMERO.server-5.6.3-576-b406bad8dd-ice36-b541.zip
00:35:18 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-576-b406bad8dd-ice36-b541 /home/omero/workspace/OMERO-server/OMERO.server
00:35:18 ++ ls omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:35:18 + JAR=omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:35:18 ++ basename omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:35:18 + JAR_NAME=omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:35:18 + mv /home/omero/workspace/OMERO-server/omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:35:18 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:35:18 --2025-10-07 00:35:18-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:35:18 Resolving repo1.maven.org (repo1.maven.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
00:35:18 Connecting to repo1.maven.org (repo1.maven.org)|104.18.18.12|:443... connected.
00:35:18 HTTP request sent, awaiting response... 200 OK
00:35:18 Length: 889211 (868K) [application/java-archive]
00:35:18 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:35:18
00:35:18 0K .......... .......... .......... .......... .......... 5% 31.4M 0s
00:35:18 50K .......... .......... .......... .......... .......... 11% 5.49M 0s
00:35:18 100K .......... .......... .......... .......... .......... 17% 6.09M 0s
00:35:18 150K .......... .......... .......... .......... .......... 23% 42.4M 0s
00:35:18 200K .......... .......... .......... .......... .......... 28% 120M 0s
00:35:18 250K .......... .......... .......... .......... .......... 34% 122M 0s
00:35:18 300K .......... .......... .......... .......... .......... 40% 157M 0s
00:35:18 350K .......... .......... .......... .......... .......... 46% 6.33M 0s
00:35:18 400K .......... .......... .......... .......... .......... 51% 127M 0s
00:35:18 450K .......... .......... .......... .......... .......... 57% 111M 0s
00:35:18 500K .......... .......... .......... .......... .......... 63% 248M 0s
00:35:18 550K .......... .......... .......... .......... .......... 69% 102M 0s
00:35:18 600K .......... .......... .......... .......... .......... 74% 6.56M 0s
00:35:18 650K .......... .......... .......... .......... .......... 80% 89.9M 0s
00:35:18 700K .......... .......... .......... .......... .......... 86% 102M 0s
00:35:18 750K .......... .......... .......... .......... .......... 92% 81.4M 0s
00:35:18 800K .......... .......... .......... .......... .......... 97% 266M 0s
00:35:18 850K .......... ........ 100% 345M=0.04s
00:35:18
00:35:18 2025-10-07 00:35:18 (21.6 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:35:18
00:35:18 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:35:18 --2025-10-07 00:35:18-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:35:18 Resolving repo1.maven.org (repo1.maven.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
00:35:18 Connecting to repo1.maven.org (repo1.maven.org)|104.18.19.12|:443... connected.
00:35:19 HTTP request sent, awaiting response... 200 OK
00:35:19 Length: 73309 (72K) [application/java-archive]
00:35:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:35:19
00:35:19 0K .......... .......... .......... .......... .......... 69% 27.9M 0s
00:35:19 50K .......... .......... . 100% 2.79M=0.009s
00:35:19
00:35:19 2025-10-07 00:35:19 (7.52 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:35:19
00:35:19 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:35:19 --2025-10-07 00:35:19-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:35:19 Resolving repo1.maven.org (repo1.maven.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:130c, ...
00:35:19 Connecting to repo1.maven.org (repo1.maven.org)|104.18.19.12|:443... connected.
00:35:19 HTTP request sent, awaiting response... 200 OK
00:35:19 Length: 63303 (62K) [application/java-archive]
00:35:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:35:19
00:35:19 0K .......... .......... .......... .......... .......... 80% 31.3M 0s
00:35:19 50K .......... . 100% 124M=0.002s
00:35:19
00:35:19 2025-10-07 00:35:19 (36.5 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:35:19
00:35:19 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:35:19 --2025-10-07 00:35:19-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:35:19 Resolving repo1.maven.org (repo1.maven.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:130c, ...
00:35:19 Connecting to repo1.maven.org (repo1.maven.org)|104.18.19.12|:443... connected.
00:35:19 HTTP request sent, awaiting response... 200 OK
00:35:19 Length: 1271272 (1.2M) [application/java-archive]
00:35:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:35:19
00:35:19 0K .......... .......... .......... .......... .......... 4% 33.9M 0s
00:35:19 50K .......... .......... .......... .......... .......... 8% 5.41M 0s
00:35:19 100K .......... .......... .......... .......... .......... 12% 6.36M 0s
00:35:19 150K .......... .......... .......... .......... .......... 16% 36.8M 0s
00:35:19 200K .......... .......... .......... .......... .......... 20% 185M 0s
00:35:19 250K .......... .......... .......... .......... .......... 24% 58.7M 0s
00:35:19 300K .......... .......... .......... .......... .......... 28% 370M 0s
00:35:19 350K .......... .......... .......... .......... .......... 32% 6.26M 0s
00:35:19 400K .......... .......... .......... .......... .......... 36% 180M 0s
00:35:19 450K .......... .......... .......... .......... .......... 40% 60.4M 0s
00:35:19 500K .......... .......... .......... .......... .......... 44% 278M 0s
00:35:19 550K .......... .......... .......... .......... .......... 48% 108M 0s
00:35:19 600K .......... .......... .......... .......... .......... 52% 6.55M 0s
00:35:19 650K .......... .......... .......... .......... .......... 56% 268M 0s
00:35:19 700K .......... .......... .......... .......... .......... 60% 59.0M 0s
00:35:19 750K .......... .......... .......... .......... .......... 64% 84.6M 0s
00:35:19 800K .......... .......... .......... .......... .......... 68% 251M 0s
00:35:19 850K .......... .......... .......... .......... .......... 72% 6.56M 0s
00:35:19 900K .......... .......... .......... .......... .......... 76% 181M 0s
00:35:19 950K .......... .......... .......... .......... .......... 80% 77.2M 0s
00:35:19 1000K .......... .......... .......... .......... .......... 84% 84.3M 0s
00:35:19 1050K .......... .......... .......... .......... .......... 88% 230M 0s
00:35:19 1100K .......... .......... .......... .......... .......... 92% 7.31M 0s
00:35:19 1150K .......... .......... .......... .......... .......... 96% 37.3M 0s
00:35:19 1200K .......... .......... .......... .......... . 100% 267M=0.06s
00:35:19
00:35:19 2025-10-07 00:35:19 (21.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:35:19
00:35:19 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:35:19 ++ deactivate nondestructive
00:35:19 ++ '[' -n '' ']'
00:35:19 ++ '[' -n '' ']'
00:35:19 ++ hash -r
00:35:19 ++ '[' -n '' ']'
00:35:19 ++ unset VIRTUAL_ENV
00:35:19 ++ unset VIRTUAL_ENV_PROMPT
00:35:19 ++ '[' '!' nondestructive = nondestructive ']'
00:35:19 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:35:19 ++ export VIRTUAL_ENV
00:35:19 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:35:19 ++ 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
00:35:19 ++ export PATH
00:35:19 ++ '[' -n '' ']'
00:35:19 ++ '[' -z '' ']'
00:35:19 ++ _OLD_VIRTUAL_PS1=
00:35:19 ++ PS1='(.venv3) '
00:35:19 ++ export PS1
00:35:19 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:35:19 ++ export VIRTUAL_ENV_PROMPT
00:35:19 ++ hash -r
00:35:19 + pip install -U pip
00:35:19 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:35:20 Collecting pip
00:35:20 Using cached pip-25.2-py3-none-any.whl (1.8 MB)
00:35:20 Installing collected packages: pip
00:35:20 Attempting uninstall: pip
00:35:20 Found existing installation: pip 22.3.1
00:35:20 Uninstalling pip-22.3.1:
00:35:20 Successfully uninstalled pip-22.3.1
00:35:21 Successfully installed pip-25.2
00:35:21 WARNING: There was an error checking the latest version of pip.
00:35:21 + 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
00:35:21 Collecting zeroc-ice==3.6.5
00:35:21 Downloading https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
00:35:23 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 22.8 MB/s 0:00:01
00:35:23 Installing collected packages: zeroc-ice
00:35:24 Successfully installed zeroc-ice-3.6.5
00:35:24 + pip install markdown
00:35:24 Collecting markdown
00:35:24 Using cached markdown-3.9-py3-none-any.whl.metadata (5.1 kB)
00:35:24 Using cached markdown-3.9-py3-none-any.whl (107 kB)
00:35:24 Installing collected packages: markdown
00:35:24 Successfully installed markdown-3.9
00:35:25 + pip install reportlab
00:35:25 Collecting reportlab
00:35:25 Using cached reportlab-4.4.4-py3-none-any.whl.metadata (1.7 kB)
00:35:25 Collecting pillow>=9.0.0 (from reportlab)
00:35:25 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:35:25 Collecting charset-normalizer (from reportlab)
00:35:25 Using cached charset_normalizer-3.4.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (36 kB)
00:35:25 Using cached reportlab-4.4.4-py3-none-any.whl (2.0 MB)
00:35:25 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:35:25 Using cached charset_normalizer-3.4.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (150 kB)
00:35:25 Installing collected packages: pillow, charset-normalizer, reportlab
00:35:26
00:35:26 Successfully installed charset-normalizer-3.4.3 pillow-11.3.0 reportlab-4.4.4
00:35:26 + pip install pyarrow
00:35:27 Collecting pyarrow
00:35:27 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
00:35:27 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
00:35:27 Installing collected packages: pyarrow
00:35:28 Successfully installed pyarrow-21.0.0
00:35:28 + pip install omego
00:35:29 Collecting omego
00:35:29 Using cached omego-0.7.0-py3-none-any.whl
00:35:29 Collecting future (from omego)
00:35:29 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:35:29 Collecting yaclifw>=0.1.1 (from omego)
00:35:29 Using cached yaclifw-0.2.0-py3-none-any.whl
00:35:29 Collecting six (from yaclifw>=0.1.1->omego)
00:35:29 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:35:29 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:35:29 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:35:29 Installing collected packages: six, future, yaclifw, omego
00:35:29
00:35:29 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:35:29 + pip install tables
00:35:30 Collecting tables
00:35:30 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:35:30 Collecting numpy>=1.20.0 (from tables)
00:35:30 Using cached numpy-2.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
00:35:30 Collecting numexpr>=2.6.2 (from tables)
00:35:30 Using cached numexpr-2.13.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:35:30 Collecting packaging (from tables)
00:35:30 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:35:30 Collecting py-cpuinfo (from tables)
00:35:30 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:35:30 Collecting blosc2>=2.3.0 (from tables)
00:35:30 Using cached blosc2-3.9.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
00:35:30 Collecting typing-extensions>=4.4.0 (from tables)
00:35:30 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
00:35:30 Collecting ndindex (from blosc2>=2.3.0->tables)
00:35:30 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:35:30 Collecting msgpack (from blosc2>=2.3.0->tables)
00:35:30 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:35:30 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:35:30 Using cached platformdirs-4.4.0-py3-none-any.whl.metadata (12 kB)
00:35:30 Collecting requests (from blosc2>=2.3.0->tables)
00:35:30 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
00:35:30 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.3)
00:35:31 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:35:31 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:35:31 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:35:31 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
00:35:31 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:35:31 Using cached certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB)
00:35:31 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:35:31 Using cached blosc2-3.9.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
00:35:31 Using cached numexpr-2.13.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (441 kB)
00:35:31 Using cached numpy-2.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
00:35:31 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
00:35:31 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
00:35:31 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:35:31 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:35:31 Using cached platformdirs-4.4.0-py3-none-any.whl (18 kB)
00:35:31 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:35:31 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
00:35:31 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:35:31 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
00:35:31 Using cached certifi-2025.10.5-py3-none-any.whl (163 kB)
00:35:31 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:35:34
00:35:34 Successfully installed blosc2-3.9.1 certifi-2025.10.5 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.13.1 numpy-2.3.3 packaging-25.0 platformdirs-4.4.0 py-cpuinfo-9.0.0 requests-2.32.5 tables-3.10.2 typing-extensions-4.15.0 urllib3-2.5.0
00:35:34 + pip install jinja2
00:35:34 Collecting jinja2
00:35:34 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:35:35 Collecting MarkupSafe>=2.0 (from jinja2)
00:35:35 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)
00:35:35 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
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00:35:35 Installing collected packages: MarkupSafe, jinja2
00:35:35
00:35:35 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
00:35:35 + pip install zarr
00:35:35 Collecting zarr
00:35:35 Using cached zarr-3.1.3-py3-none-any.whl.metadata (10 kB)
00:35:35 Collecting donfig>=0.8 (from zarr)
00:35:35 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
00:35:35 Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr)
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00:35:35 Requirement already satisfied: numpy>=1.26 in ./.venv3/lib64/python3.11/site-packages (from zarr) (2.3.3)
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00:35:35 Collecting pyyaml (from donfig>=0.8->zarr)
00:35:35 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)
00:35:35 Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr)
00:35:35 Using cached crc32c-2.7.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.3 kB)
00:35:35 Using cached zarr-3.1.3-py3-none-any.whl (276 kB)
00:35:35 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
00:35:36 Using cached numcodecs-0.16.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.9 MB)
00:35:36 Using cached crc32c-2.7.1-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (53 kB)
00:35:36 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
00:35:36 Installing collected packages: pyyaml, numcodecs, crc32c, donfig, zarr
00:35:36
00:35:36 Successfully installed crc32c-2.7.1 donfig-0.8.1.post1 numcodecs-0.16.3 pyyaml-6.0.3 zarr-3.1.3
00:35:36 + pip install fsspec requests aiohttp s3fs
00:35:37 Collecting fsspec
00:35:37 Using cached fsspec-2025.9.0-py3-none-any.whl.metadata (10 kB)
00:35:37 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (2.32.5)
00:35:37 Collecting aiohttp
00:35:37 Downloading aiohttp-3.13.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
00:35:37 Collecting s3fs
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00:35:37 Collecting aiosignal>=1.4.0 (from aiohttp)
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00:35:37 Collecting attrs>=17.3.0 (from aiohttp)
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00:35:38 Collecting multidict<7.0,>=4.5 (from aiohttp)
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00:35:38 Collecting propcache>=0.2.0 (from aiohttp)
00:35:38 Using cached propcache-0.4.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)
00:35:38 Collecting yarl<2.0,>=1.17.0 (from aiohttp)
00:35:38 Downloading yarl-1.22.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (75 kB)
00:35:38 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs)
00:35:38 Using cached aiobotocore-2.24.2-py3-none-any.whl.metadata (25 kB)
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00:35:39 Collecting botocore<1.40.19,>=1.40.15 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
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00:35:39 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
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00:35:39 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
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00:35:39 Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:35:39 Using cached wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (6.4 kB)
00:35:39 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->aiobotocore<3.0.0,>=2.5.4->s3fs) (1.17.0)
00:35:39 Requirement already satisfied: typing-extensions>=4.2 in ./.venv3/lib64/python3.11/site-packages (from aiosignal>=1.4.0->aiohttp) (4.15.0)
00:35:39 Using cached fsspec-2025.9.0-py3-none-any.whl (199 kB)
00:35:39 Downloading aiohttp-3.13.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.7 MB)
00:35:39 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 20.6 MB/s 0:00:00
00:35:39 Downloading multidict-6.7.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
00:35:39 Downloading yarl-1.22.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (365 kB)
00:35:39 Using cached s3fs-2025.9.0-py3-none-any.whl (30 kB)
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00:35:39 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
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00:35:39 Using cached wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (82 kB)
00:35:39 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
00:35:39 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
00:35:39 Downloading attrs-25.4.0-py3-none-any.whl (67 kB)
00:35:39 Downloading frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (231 kB)
00:35:39 Using cached propcache-0.4.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (209 kB)
00:35:40 Installing collected packages: wrapt, python-dateutil, propcache, multidict, jmespath, fsspec, frozenlist, attrs, aioitertools, aiohappyeyeballs, yarl, botocore, aiosignal, aiohttp, aiobotocore, s3fs
00:35:41
00:35:41 Successfully installed aiobotocore-2.24.2 aiohappyeyeballs-2.6.1 aiohttp-3.13.0 aioitertools-0.12.0 aiosignal-1.4.0 attrs-25.4.0 botocore-1.40.18 frozenlist-1.8.0 fsspec-2025.9.0 jmespath-1.0.1 multidict-6.7.0 propcache-0.4.0 python-dateutil-2.9.0.post0 s3fs-2025.9.0 wrapt-1.17.3 yarl-1.22.0
00:35:41 + pip install omero-py
00:35:41 Collecting omero-py
00:35:41 Downloading omero_py-5.21.2-py3-none-any.whl.metadata (6.5 kB)
00:35:41 Collecting appdirs (from omero-py)
00:35:41 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:35:41 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:35:41 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.3)
00:35:41 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
00:35:41 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.3)
00:35:41 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:35:41 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
00:35:41 Collecting portalocker (from omero-py)
00:35:41 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:35:41 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.3)
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00:35:41 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.10.5)
00:35:41 Downloading omero_py-5.21.2-py3-none-any.whl (2.8 MB)
00:35:42 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 22.3 MB/s 0:00:00
00:35:42 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:35:42 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:35:42 Installing collected packages: appdirs, portalocker, omero-py
00:35:43
00:35:43 Successfully installed appdirs-1.4.4 omero-py-5.21.2 portalocker-3.2.0
00:35:44 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:35:44 Collecting omero-metadata
00:35:44 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-oh_1_wyh/omero-metadata_cfbf5ee22c664fc0aaa0b9d880882968
00:35:44 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-oh_1_wyh/omero-metadata_cfbf5ee22c664fc0aaa0b9d880882968
00:35:45 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 3cedcbe4a3ea3dc2bb43f1617714b51869ff2373
00:35:45 Installing build dependencies: started
00:35:45 Installing build dependencies: finished with status 'done'
00:35:45 Getting requirements to build wheel: started
00:35:46 Getting requirements to build wheel: finished with status 'done'
00:35:46 Preparing metadata (pyproject.toml): started
00:35:46 Preparing metadata (pyproject.toml): finished with status 'done'
00:35:46 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.2)
00:35:46 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
00:35:46 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:35:46 Collecting pandas (from omero-metadata)
00:35:46 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
00:35:46 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:35:46 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:35:46 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.3)
00:35:46 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (11.3.0)
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00:35:46 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
00:35:46 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:35:46 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
00:35:46 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:35:46 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:35:46 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:35:46 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:35:46 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
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00:35:46 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.10)
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00:35:46 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.10.5)
00:35:46 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB)
00:35:46 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:35:46 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:35:46 Building wheels for collected packages: omero-metadata
00:35:46 Building wheel for omero-metadata (pyproject.toml): started
00:35:47 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:35:47 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=bcd73370b5ce1b2f71ca2f11e9dcc9276a6980ba914740ab19f9528255453232
00:35:47 Stored in directory: /tmp/pip-ephem-wheel-cache-66ijxp82/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:35:47 Successfully built omero-metadata
00:35:47 Installing collected packages: pytz, tzdata, pandas, omero-metadata
00:35:51
00:35:51 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.3 pytz-2025.2 tzdata-2025.2
00:35:51 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:35:52 Collecting omero-cli-render
00:35:52 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-2opt52di/omero-cli-render_d533bc03bf274bb685ab06a5eee6d27b
00:35:52 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-2opt52di/omero-cli-render_d533bc03bf274bb685ab06a5eee6d27b
00:35:53 Running command git checkout -b merge_ci --track origin/merge_ci
00:35:53 Switched to a new branch 'merge_ci'
00:35:53 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:35:53 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 324d8ca8d467eb4db39e7409daea6e2ada92c2e6
00:35:53 Installing build dependencies: started
00:35:54 Installing build dependencies: finished with status 'done'
00:35:54 Getting requirements to build wheel: started
00:35:54 Getting requirements to build wheel: finished with status 'done'
00:35:54 Preparing metadata (pyproject.toml): started
00:35:54 Preparing metadata (pyproject.toml): finished with status 'done'
00:35:54 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
00:35:54 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.2)
00:35:54 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:35:54 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:35:54 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.3)
00:35:54 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.3.0)
00:35:54 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)
00:35:54 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
00:35:54 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:35:54 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.3)
00:35:54 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.10)
00:35:54 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.5.0)
00:35:54 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.10.5)
00:35:54 Building wheels for collected packages: omero-cli-render
00:35:54 Building wheel for omero-cli-render (pyproject.toml): started
00:35:55 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:35:55 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=b9880cbceaad5f34cab99d89f3730cb34fd44dd538aae8987ce8d5e16adf6881
00:35:55 Stored in directory: /tmp/pip-ephem-wheel-cache-5sc0qgb7/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:35:55 Successfully built omero-cli-render
00:35:55 Installing collected packages: omero-cli-render
00:35:55 Successfully installed omero-cli-render-0.8.2.dev0
00:35:55 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:35:55 Collecting omero-cli-duplicate
00:35:55 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-bpsutnw3/omero-cli-duplicate_2b773335801146f8849613a5d7274ca3
00:35:55 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-bpsutnw3/omero-cli-duplicate_2b773335801146f8849613a5d7274ca3
00:35:56 Running command git checkout -b merge_ci --track origin/merge_ci
00:35:56 Switched to a new branch 'merge_ci'
00:35:56 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:35:56 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit cd6b875affd6059e87bea9d714d9cd9b3433faf6
00:35:56 Installing build dependencies: started
00:35:57 Installing build dependencies: finished with status 'done'
00:35:57 Getting requirements to build wheel: started
00:35:57 Getting requirements to build wheel: finished with status 'done'
00:35:57 Preparing metadata (pyproject.toml): started
00:35:58 Preparing metadata (pyproject.toml): finished with status 'done'
00:35:58 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.2)
00:35:58 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:35:58 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:35:58 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.3)
00:35:58 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.3.0)
00:35:58 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
00:35:58 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)
00:35:58 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
00:35:58 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:35:58 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.3)
00:35:58 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.10)
00:35:58 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.5.0)
00:35:58 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.10.5)
00:35:58 Building wheels for collected packages: omero-cli-duplicate
00:35:58 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:35:58 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:35:58 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=6c5842adf0f534894f67470c9791a8668f53a54fd6ebc42d46022b1954f36b80
00:35:58 Stored in directory: /tmp/pip-ephem-wheel-cache-5ozswaih/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:35:58 Successfully built omero-cli-duplicate
00:35:58 Installing collected packages: omero-cli-duplicate
00:35:58 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:35:58 + pip install omero-certificates
00:35:59 Collecting omero-certificates
00:35:59 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:35:59 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.2)
00:35:59 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:35:59 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:35:59 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.3)
00:35:59 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (11.3.0)
00:35:59 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
00:35:59 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)
00:35:59 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
00:35:59 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:35:59 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.3)
00:35:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
00:35:59 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.5.0)
00:35:59 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.10.5)
00:35:59 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:35:59 Installing collected packages: omero-certificates
00:35:59 Successfully installed omero-certificates-0.4.0
00:35:59 + for x in *.tar.gz
00:35:59 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:35:59 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:35:59 Installing build dependencies: started
00:36:00 Installing build dependencies: finished with status 'done'
00:36:00 Getting requirements to build wheel: started
00:36:00 Getting requirements to build wheel: finished with status 'done'
00:36:00 Preparing metadata (pyproject.toml): started
00:36:00 Preparing metadata (pyproject.toml): finished with status 'done'
00:36:00 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.2)
00:36:00 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:36:00 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:36:00 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.3)
00:36:00 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.3.0)
00:36:00 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
00:36:00 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)
00:36:00 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
00:36:00 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:36:00 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.3)
00:36:00 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10)
00:36:00 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.5.0)
00:36:00 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.10.5)
00:36:00 Building wheels for collected packages: omero-dropbox
00:36:00 Building wheel for omero-dropbox (pyproject.toml): started
00:36:01 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:36:01 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=bafdf4dfa10ed3d12d4c09b7188a5b2bec4a835a7c981e5683b2a705649ab835
00:36:01 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:36:01 Successfully built omero-dropbox
00:36:01 Installing collected packages: omero-dropbox
00:36:01 Successfully installed omero-dropbox-5.7.1.dev0
00:36:01 + for x in *.tar.gz
00:36:01 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:36:01 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:36:01 Installing build dependencies: started
00:36:02 Installing build dependencies: finished with status 'done'
00:36:02 Getting requirements to build wheel: started
00:36:02 Getting requirements to build wheel: finished with status 'done'
00:36:02 Preparing metadata (pyproject.toml): started
00:36:03 Preparing metadata (pyproject.toml): finished with status 'done'
00:36:03 Building wheels for collected packages: omero_marshal
00:36:03 Building wheel for omero_marshal (pyproject.toml): started
00:36:03 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:36:03 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88121 sha256=a4e11956a5752db7d0877b6407749a1947c67fec362de4d30ec5856400d05ecc
00:36:03 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:36:03 Successfully built omero_marshal
00:36:03 Installing collected packages: omero_marshal
00:36:03 Successfully installed omero_marshal-0.9.1.dev0
00:36:03 + for x in *.tar.gz
00:36:03 + pip install -U omero_py-5.21.3.dev0.tar.gz
00:36:03 Processing ./omero_py-5.21.3.dev0.tar.gz
00:36:04 Installing build dependencies: started
00:36:04 Installing build dependencies: finished with status 'done'
00:36:04 Getting requirements to build wheel: started
00:36:05 Getting requirements to build wheel: finished with status 'done'
00:36:05 Preparing metadata (pyproject.toml): started
00:36:05 Preparing metadata (pyproject.toml): finished with status 'done'
00:36:05 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (1.4.4)
00:36:05 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (1.0.0)
00:36:05 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (2.3.3)
00:36:05 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (11.3.0)
00:36:05 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (6.0.3)
00:36:05 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (3.6.5)
00:36:05 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (2.32.5)
00:36:05 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (3.2.0)
00:36:05 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (3.4.3)
00:36:05 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (3.10)
00:36:05 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (2.5.0)
00:36:05 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (2025.10.5)
00:36:05 Building wheels for collected packages: omero-py
00:36:05 Building wheel for omero-py (pyproject.toml): started
00:36:06 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:36:06 Created wheel for omero-py: filename=omero_py-5.21.3.dev0-py3-none-any.whl size=2785643 sha256=f278bc6ac60a49a0b6887787d5903ae58f18b5af109bdc404f123558267d2580
00:36:06 Stored in directory: /home/omero/.cache/pip/wheels/b2/c3/69/7f46e8715cbcb96e4ea5a88612191cc747a1c318af7c8f681c
00:36:06 Successfully built omero-py
00:36:06 Installing collected packages: omero-py
00:36:06 Attempting uninstall: omero-py
00:36:06 Found existing installation: omero-py 5.21.2
00:36:06 Uninstalling omero-py-5.21.2:
00:36:07 Successfully uninstalled omero-py-5.21.2
00:36:08 Successfully installed omero-py-5.21.3.dev0
00:36:09 + for x in *.tar.gz
00:36:09 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:36:09 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:36:09 Installing build dependencies: started
00:36:10 Installing build dependencies: finished with status 'done'
00:36:10 Getting requirements to build wheel: started
00:36:10 Getting requirements to build wheel: finished with status 'done'
00:36:10 Preparing metadata (pyproject.toml): started
00:36:10 Preparing metadata (pyproject.toml): finished with status 'done'
00:36:10 Building wheels for collected packages: omero-scripts
00:36:10 Building wheel for omero-scripts (pyproject.toml): started
00:36:11 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:36:11 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=cdf0e1a62629e5fb820aba16cf4d1e4e9ae14aa734677bae48cb3d09f83eb0da
00:36:11 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:36:11 Successfully built omero-scripts
00:36:11 Installing collected packages: omero-scripts
00:36:11 Successfully installed omero-scripts-5.9.2.dev0
00:36:11 + for x in *.tar.gz
00:36:11 + pip install -U omero_web-5.29.3.dev0.tar.gz
00:36:11 Processing ./omero_web-5.29.3.dev0.tar.gz
00:36:12 Installing build dependencies: started
00:36:12 Installing build dependencies: finished with status 'done'
00:36:12 Getting requirements to build wheel: started
00:36:13 Getting requirements to build wheel: finished with status 'done'
00:36:13 Preparing metadata (pyproject.toml): started
00:36:13 Preparing metadata (pyproject.toml): finished with status 'done'
00:36:13 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (5.21.3.dev0)
00:36:13 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.3.dev0)
00:36:13 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:36:13 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.3.dev0)
00:36:13 Using cached django-4.2.25-py3-none-any.whl.metadata (4.2 kB)
00:36:13 Collecting django-pipeline (from omero-web==5.29.3.dev0)
00:36:13 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
00:36:13 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.3.dev0)
00:36:13 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:36:14 Collecting django-csp (from omero-web==5.29.3.dev0)
00:36:14 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:36:14 Collecting whitenoise>=5.3.0 (from omero-web==5.29.3.dev0)
00:36:14 Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
00:36:14 Collecting gunicorn>=19.3 (from omero-web==5.29.3.dev0)
00:36:14 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:36:14 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (0.9.1.dev0)
00:36:14 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (11.3.0)
00:36:14 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (2025.2)
00:36:14 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (3.2.0)
00:36:14 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (25.0)
00:36:14 Collecting importlib-resources (from omero-web==5.29.3.dev0)
00:36:14 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:36:14 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:36:14 Using cached asgiref-3.10.0-py3-none-any.whl.metadata (9.3 kB)
00:36:14 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:36:14 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:36:14 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (1.4.4)
00:36:14 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (1.0.0)
00:36:14 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.3.3)
00:36:14 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (6.0.3)
00:36:14 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (3.6.5)
00:36:14 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.32.5)
00:36:14 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.3.dev0) (65.5.1)
00:36:14 Collecting wheel (from django-pipeline->omero-web==5.29.3.dev0)
00:36:14 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:36:14 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (3.4.3)
00:36:14 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (3.10)
00:36:14 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.5.0)
00:36:14 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (2025.10.5)
00:36:14 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:36:14 Using cached django-4.2.25-py3-none-any.whl (8.0 MB)
00:36:14 Using cached asgiref-3.10.0-py3-none-any.whl (24 kB)
00:36:14 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:36:14 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:36:14 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:36:14 Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
00:36:14 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:36:14 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
00:36:14 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:36:14 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:36:14 Building wheels for collected packages: omero-web
00:36:14 Building wheel for omero-web (pyproject.toml): started
00:36:15 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:36:15 Created wheel for omero-web: filename=omero_web-5.29.3.dev0-py3-none-any.whl size=2818265 sha256=a4937e770d3113e79ba4b7b2376ac880082d1efa89cc0727e36a8e6eb4b58b02
00:36:15 Stored in directory: /home/omero/.cache/pip/wheels/22/5c/22/7feca3b3e1a26ce9fb6b16848ce79640a0079788b3a7d5450b
00:36:15 Successfully built omero-web
00:36:15 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:36:18
00:36:18 Successfully installed Django-4.2.25 asgiref-3.10.0 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.1.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.3.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.11.0
00:36:18 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:36:18 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:36:18 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:36:18 --2025-10-07 00:36:18-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:36:18 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.109.133, ...
00:36:18 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
00:36:18 HTTP request sent, awaiting response... 200 OK
00:36:18 Length: 125361 (122K) [text/plain]
00:36:18 Saving to: ‘Figure_To_Pdf.py’
00:36:18
00:36:18 0K .......... .......... .......... .......... .......... 40% 3.84M 0s
00:36:18 50K .......... .......... .......... .......... .......... 81% 13.6M 0s
00:36:18 100K .......... .......... .. 100% 4.47M=0.02s
00:36:18
00:36:18 2025-10-07 00:36:18 (5.64 MB/s) - ‘Figure_To_Pdf.py’ saved [125361/125361]
00:36:18
00:36:18 + chmod 755 Figure_To_Pdf.py
00:36:18 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:36:18 + omero config set omero.db.name OMERO-server
00:36:20 + omero config set omero.db.host pg
00:36:21 + omero config set omero.db.user postgres
00:36:22 + omero config set omero.data.dir /home/omero/omero-server-data
00:36:23 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:36:25 + omero config set omero.db.poolsize 25
00:36:26 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:36:27 + omero config set omero.security.trustStorePassword changeit
00:36:28 + omero config set omero.mail.config true
00:36:29 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:36:31 + omero config set omero.mail.host smtp.dundee.ac.uk
00:36:32 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:36:33 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:36:34 + omero certificates
00:36:35 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:36:35 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:36:36 + '[' false = true ']'
00:36:36 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:36:36 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:36:36 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG dbcommand => upgrade
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG dbhost => localhost
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG dbname => OMERO-server
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG dbpass => omero
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG dbuser => omero
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG rootpass => omero
00:36:36 2025-10-07 00:36:36,195 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:36:36 2025-10-07 00:36:36,195 [omego.extern] INFO Executing : omero version
00:36:37 OMERO.py version:
00:36:37 OMERO.server version:
00:36:37 5.6.3-576-b406bad8dd-ice36-b541
00:36:37 5.21.3.dev0
00:36:37 2025-10-07 00:36:37,449 [omego.extern] INFO Completed [1.254 s]
00:36:37 2025-10-07 00:36:37,449 [omego.extern] DEBUG Using omero CLI from omero
00:36:37 2025-10-07 00:36:37,449 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:36:37 2025-10-07 00:36:37,449 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:36:37 2025-10-07 00:36:37,450 [omego.extern] INFO Executing : omero config get --show-password
00:36:38 2025-10-07 00:36:38,649 [omego.extern] INFO Completed [1.199 s]
00:36:38 2025-10-07 00:36:38,649 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:36:38 2025-10-07 00:36:38,649 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:36:38 2025-10-07 00:36:38,655 [omego.extern] INFO Completed [0.006 s]
00:36:38 2025-10-07 00:36:38,655 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
00:36:38 2025-10-07 00:36:38,655 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
00:36:38
00:36:38 2025-10-07 00:36:38,655 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:36:38 2025-10-07 00:36:38,655 [omego.extern] INFO Executing : omero config get --show-password
00:36:39 2025-10-07 00:36:39,860 [omego.extern] INFO Completed [1.205 s]
00:36:39 2025-10-07 00:36:39,860 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:36:39 2025-10-07 00:36:39,860 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:36:39 2025-10-07 00:36:39,869 [omego.extern] INFO Completed [0.009 s]
00:36:39 2025-10-07 00:36:39,869 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.9") at port "5432".\n'
00:36:39 2025-10-07 00:36:39,869 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:36:39 2025-10-07 00:36:39,869 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:36:39 2025-10-07 00:36:39,869 [omego.extern] INFO Executing : omero config get --show-password
00:36:41 2025-10-07 00:36:41,120 [omego.extern] INFO Completed [1.251 s]
00:36:41 2025-10-07 00:36:41,120 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:36:41 2025-10-07 00:36:41,120 [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
00:36:41 2025-10-07 00:36:41,130 [omego.extern] INFO Completed [0.010 s]
00:36:41 2025-10-07 00:36:41,130 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:36:41 2025-10-07 00:36:41,130 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:36:41 2025-10-07 00:36:41,132 [ omego.db] INFO Database is already at OMERO5.4__0
00:36:41 + export LANG=en_US.UTF-8
00:36:41 + LANG=en_US.UTF-8
00:36:41 + export LANGUAGE=en_US:en
00:36:41 + LANGUAGE=en_US:en
00:36:41 + export LC_ALL=en_US.UTF-8
00:36:41 + LC_ALL=en_US.UTF-8
00:36:41 + BUILD_ID=DONT_KILL_ME
00:36:41 + omero admin start
00:36:45 No descriptor given. Using etc/grid/default.xml
00:36:54 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:36:54 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:36:54 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:36:54 Waiting on startup. Use CTRL-C to exit
00:36:54 + omero admin waitup
00:36:55 Waiting on startup. Use CTRL-C to exit
00:36:55 + omero admin diagnostics
00:36:56
00:36:56 ================================================================================
00:36:56 OMERO Diagnostics (admin)
00:36:56 ================================================================================
00:36:56
00:36:56 Commands: java -version 11.0.25 (/usr/bin/java)
00:36:56 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:36:56 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:36:56 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:36:56 Commands: psql --version 16.9 (/usr/bin/psql)
00:36:56 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:36:56
00:36:56 Component: OMERO.py 5.21.3.dev0
00:36:56 Component: OMERO.server 5.6.3-576-b406bad8dd-ice36-b541
00:36:56
00:36:56 Server: icegridnode running
00:36:56 Server: Blitz-0 active (pid = 54438, enabled)
00:36:56 Server: Indexer-0 activating (enabled)
00:36:56 Server: OMERO.Glacier2 active (pid = 54469, enabled)
00:36:56 Server: OMERO.IceStorm active (pid = 54493, enabled)
00:36:56 Server: Processor-0 activating (enabled)
00:36:56 Server: Tables-0 activating (enabled)
00:36:56
00:36:56 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:36:56 Log files: Blitz-0.log 23.7 KB errors=0 warnings=1
00:36:56 Log files: DropBox.log n/a
00:36:56 Log files: FileServer.log n/a
00:36:56 Log files: Indexer-0.log 114 B
00:36:56 Log files: MonitorServer.log n/a
00:36:56 Log files: Processor-0.log 281 B
00:36:56 Log files: Tables-0.log 281 B
00:36:56 Log files: TestDropBox.log n/a
00:36:56 Log files: master.err empty
00:36:56 Log files: master.out 30.5 KB
00:36:56 Log files: Total size 0.05 MB
00:36:56
00:36:56
00:36:56 Environment:OMERO_HOME=(unset)
00:36:56 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:36:56 Environment:OMERO_NODE=(unset)
00:36:56 Environment:OMERO_MASTER=(unset)
00:36:56 Environment:OMERO_USERDIR=(unset)
00:36:56 Environment:OMERO_TMPDIR=(unset)
00:36:56 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
00:36:56 Environment:PYTHONPATH=(unset)
00:36:56 Environment:ICE_HOME=/opt/ice-3.6.5
00:36:56 Environment:LD_LIBRARY_PATH=(unset)
00:36:56 Environment:DYLD_LIBRARY_PATH=(unset)
00:36:56
00:36:56 OMERO SSL port:4064
00:36:56 OMERO TCP port:4063
00:36:56 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:36:56 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:36:56
00:36:56 JVM settings: Blitz-${index} -Xmx7200m
00:36:56 JVM settings: Indexer-${index} -Xmx4800m
00:36:56 JVM settings: PixelData-${index} -Xmx7200m
00:36:56 JVM settings: Repository-${index} -Xmx4800m
00:36:56
00:36:56 Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 7 October 2025 75112a7cc905b8b7a4b3af26ee10fe28b2824e14
00:36:56 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 7 October 2025 75112a7cc905b8b7a4b3af26ee10fe28b2824e14
00:36:56 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 7 October 2025 75112a7cc905b8b7a4b3af26ee10fe28b2824e14
00:36:56 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 7 October 2025 7a28cd2fc4dee001f8d5b09ea9e8a361f809ee29
00:36:56 Jar: lib/server/ome-common.jar OME Common Java 6.1.1-SNAPSHOT 7 October 2025 7a28cd2fc4dee001f8d5b09ea9e8a361f809ee29
00:36:56 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 7 October 2025 7a28cd2fc4dee001f8d5b09ea9e8a361f809ee29
00:36:56 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 7 October 2025 7a28cd2fc4dee001f8d5b09ea9e8a361f809ee29
00:36:56 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 7 October 2025 7a28cd2fc4dee001f8d5b09ea9e8a361f809ee29
00:36:56 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 7 October 2025 7a28cd2fc4dee001f8d5b09ea9e8a361f809ee29
00:36:56 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:36:56 Jar: lib/server/omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.6.0-SNAPSHOT 94718ad42a948f25d469471ef7601986ac58a168
00:36:57 + deactivate
00:36:57 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:36:57 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:36:57 + export PATH
00:36:57 + unset _OLD_VIRTUAL_PATH
00:36:57 + '[' -n '' ']'
00:36:57 + hash -r
00:36:57 + '[' -n '' ']'
00:36:57 + unset VIRTUAL_ENV
00:36:57 + unset VIRTUAL_ENV_PROMPT
00:36:57 + '[' '!' '' = nondestructive ']'
00:36:57 + unset -f deactivate
00:36:57 Finished: SUCCESS
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