00:47:59 Started by upstream project "Trigger" build number 575
00:47:59 originally caused by:
00:47:59 Started by timer
00:47:59 Running as SYSTEM
00:47:59 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:47:59 [OMERO-server] $ /bin/bash -xe /tmp/jenkins6717762374227623219.sh
00:47:59 + source /home/settings.env
00:47:59 ++ OMERO_DB_HOST=pg
00:47:59 ++ OMERO_DB_USER=postgres
00:47:59 ++ OMERO_DB_PASS=
00:47:59 ++ OMERO_ROOT_PASS=omero
00:47:59 ++ OMERO_DATA_DIR=/OMERO
00:47:59 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:47:59 + OMERO_DB_NAME=OMERO-server
00:47:59 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:47:59 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:59 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:59 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:47:59 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:47:59 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:47:59 ++ deactivate nondestructive
00:47:59 ++ '[' -n '' ']'
00:47:59 ++ '[' -n '' ']'
00:47:59 ++ hash -r
00:47:59 ++ '[' -n '' ']'
00:47:59 ++ unset VIRTUAL_ENV
00:47:59 ++ unset VIRTUAL_ENV_PROMPT
00:47:59 ++ '[' '!' nondestructive = nondestructive ']'
00:47:59 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:47:59 ++ export VIRTUAL_ENV
00:47:59 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:47:59 ++ 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
00:47:59 ++ export PATH
00:47:59 ++ '[' -n '' ']'
00:47:59 ++ '[' -z '' ']'
00:47:59 ++ _OLD_VIRTUAL_PS1=
00:47:59 ++ PS1='(.venv3) '
00:47:59 ++ export PS1
00:47:59 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:47:59 ++ export VIRTUAL_ENV_PROMPT
00:47:59 ++ hash -r
00:47:59 + omero admin stop
00:48:00 Waiting on shutdown. Use CTRL-C to exit
00:48:00 .+ sleep 5
00:48:15 + deactivate
00:48:15 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:48:15 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:15 + export PATH
00:48:15 + unset _OLD_VIRTUAL_PATH
00:48:15 + '[' -n '' ']'
00:48:15 + hash -r
00:48:15 + '[' -n '' ']'
00:48:15 + unset VIRTUAL_ENV
00:48:15 + unset VIRTUAL_ENV_PROMPT
00:48:15 + '[' '!' '' = nondestructive ']'
00:48:15 + unset -f deactivate
00:48:15 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:48:16 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:48:19 + '[' false = true ']'
00:48:19 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:48:19 Skipping PURGE_DATA:CleanDbAndRepo
00:48:19 + 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-5.21.1.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-5.29.2.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:48:21 Copied 1 artifact from "OMERO-build" build number 484
00:48:21 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 477
00:48:21 Copied 2 artifacts from "OMERO-build-build" build number 511
00:48:21 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 17
00:48:21 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11460564474450470156.sh
00:48:21 + source /home/settings.env
00:48:21 ++ OMERO_DB_HOST=pg
00:48:21 ++ OMERO_DB_USER=postgres
00:48:21 ++ OMERO_DB_PASS=
00:48:21 ++ OMERO_ROOT_PASS=omero
00:48:21 ++ OMERO_DATA_DIR=/OMERO
00:48:21 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:48:21 + OMERO_DB_NAME=OMERO-server
00:48:21 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:48:21 + mkdir -p /home/omero/omero-server-data
00:48:21 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:48:21 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:21 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:21 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:21 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:21 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:21 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:21 ++ ls OMERO.server-5.6.3-574-6798e74085-ice36-b484.zip
00:48:21 + ZIP=OMERO.server-5.6.3-574-6798e74085-ice36-b484.zip
00:48:21 + '[' '!' -z '' ']'
00:48:21 + DIST=OMERO.server-5.6.3-574-6798e74085-ice36-b484
00:48:21 + unzip OMERO.server-5.6.3-574-6798e74085-ice36-b484.zip
00:48:21 Archive: OMERO.server-5.6.3-574-6798e74085-ice36-b484.zip
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/blitz/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/grid/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/profiles/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/error/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/grid/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/luts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/luts/janelia/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/luts/matplotlib/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/luts/ncsa_paledit/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/luts/seaborn/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/luts/wcif/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/analysis_scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/annotation_scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/export_scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/figure_scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/import_scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/scripts/omero/util_scripts/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/server/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/share/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/share/licenses/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/misc/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__1/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__10/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__11/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__2/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__3/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__4/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__5/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__6/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__7/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__8/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3A__9/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3__4/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3__5/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3__6/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO3__7/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO4.1__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO4.2__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO4.2__0/t/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO4.3__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO4.4__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO4__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.0__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.1__1/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.2__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.3__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4DEV__1/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4DEV__2/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4DEV__3/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4__0/
00:48:21 creating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/var/
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/LICENSE.txt
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/backup.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/blitz/mail-senders.example
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/blitz/mail-server.example
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/build.properties
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/env.bat
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/env.sh
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/hibernate.properties
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/ice.config
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/logback-cli.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/logback-indexing-cli.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/logback-indexing.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/logback.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/mime.types
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/node1.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/node2.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/omero.properties
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/profiles/psql
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/rollover.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/Windows.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/error/maintainance.html
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/grid/README
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/grid/default.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/grid/templates.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/grid/windefault.xml
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/ice.config
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/internal.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/master.cfg
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/templates/robot.template
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/etc/testdropbox.config
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/history.rst
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/OMEZarrReader.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/accessors-smart.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/activation.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/aggdesigner-algorithm.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/aircompressor.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/antlr.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/aopalliance.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/apiguardian-api.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/asm.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/avatica-core.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/avatica-metrics.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/aws-java-sdk-core.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/aws-java-sdk-kms.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/aws-java-sdk-s3.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/base.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-anim.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-awt-util.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-bridge.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-codec.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-constants.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-css.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-dom.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-ext.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-gvt.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-i18n.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-parser.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-script.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-shared-resources.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-svg-dom.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-svggen.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-transcoder.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-util.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/batik-xml.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/btm.jar
00:48:21 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/calcite-core.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/calcite-linq4j.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/cdm-core.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/checker-qual.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/commons-beanutils.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/commons-codec.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/commons-collections.jar
00:48:22 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/lib/client/commons-collections4.jar
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00:48:24 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4__0/psql-footer.sql
00:48:24 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4__0/psql-header.sql
00:48:24 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4__0/schema.sql
00:48:24 inflating: OMERO.server-5.6.3-574-6798e74085-ice36-b484/sql/psql/OMERO5.4__0/views.sql
00:48:24 + rm -f OMERO.server-5.6.3-574-6798e74085-ice36-b484.zip
00:48:24 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-574-6798e74085-ice36-b484 /home/omero/workspace/OMERO-server/OMERO.server
00:48:24 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:48:24 + JAR=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:48:24 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:48:24 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:48:24 + mv /home/omero/workspace/OMERO-server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:48:24 + 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
00:48:24 --2025-08-03 00:48:24-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:48:24 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:24 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:24 HTTP request sent, awaiting response... 200 OK
00:48:24 Length: 889211 (868K) [application/java-archive]
00:48:24 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:48:24
00:48:24 0K .......... .......... .......... .......... .......... 5% 3.81M 0s
00:48:24 50K .......... .......... .......... .......... .......... 11% 6.04M 0s
00:48:24 100K .......... .......... .......... .......... .......... 17% 22.8M 0s
00:48:24 150K .......... .......... .......... .......... .......... 23% 15.9M 0s
00:48:24 200K .......... .......... .......... .......... .......... 28% 8.85M 0s
00:48:24 250K .......... .......... .......... .......... .......... 34% 38.0M 0s
00:48:24 300K .......... .......... .......... .......... .......... 40% 23.6M 0s
00:48:24 350K .......... .......... .......... .......... .......... 46% 32.1M 0s
00:48:24 400K .......... .......... .......... .......... .......... 51% 113M 0s
00:48:24 450K .......... .......... .......... .......... .......... 57% 8.06M 0s
00:48:24 500K .......... .......... .......... .......... .......... 63% 34.1M 0s
00:48:24 550K .......... .......... .......... .......... .......... 69% 33.7M 0s
00:48:24 600K .......... .......... .......... .......... .......... 74% 159M 0s
00:48:24 650K .......... .......... .......... .......... .......... 80% 36.8M 0s
00:48:24 700K .......... .......... .......... .......... .......... 86% 7.98M 0s
00:48:24 750K .......... .......... .......... .......... .......... 92% 31.7M 0s
00:48:24 800K .......... .......... .......... .......... .......... 97% 36.5M 0s
00:48:24 850K .......... ........ 100% 181M=0.06s
00:48:24
00:48:24 2025-08-03 00:48:24 (15.0 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:48:24
00:48:24 + 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
00:48:24 --2025-08-03 00:48:24-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:48:24 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:24 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:24 HTTP request sent, awaiting response... 200 OK
00:48:24 Length: 73309 (72K) [application/java-archive]
00:48:24 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:48:24
00:48:24 0K .......... .......... .......... .......... .......... 69% 3.79M 0s
00:48:24 50K .......... .......... . 100% 21.3M=0.01s
00:48:24
00:48:24 2025-08-03 00:48:24 (5.04 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:48:24
00:48:24 + 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
00:48:24 --2025-08-03 00:48:24-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:48:24 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:24 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:24 HTTP request sent, awaiting response... 200 OK
00:48:24 Length: 63303 (62K) [application/java-archive]
00:48:24 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:48:24
00:48:24 0K .......... .......... .......... .......... .......... 80% 4.23M 0s
00:48:24 50K .......... . 100% 12.2M=0.01s
00:48:24
00:48:24 2025-08-03 00:48:24 (4.83 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:48:24
00:48:24 + 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
00:48:24 --2025-08-03 00:48:24-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:48:25 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:25 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:25 HTTP request sent, awaiting response... 200 OK
00:48:25 Length: 1271272 (1.2M) [application/java-archive]
00:48:25 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:48:25
00:48:25 0K .......... .......... .......... .......... .......... 4% 3.34M 0s
00:48:25 50K .......... .......... .......... .......... .......... 8% 9.07M 0s
00:48:25 100K .......... .......... .......... .......... .......... 12% 7.83M 0s
00:48:25 150K .......... .......... .......... .......... .......... 16% 20.7M 0s
00:48:25 200K .......... .......... .......... .......... .......... 20% 8.52M 0s
00:48:25 250K .......... .......... .......... .......... .......... 24% 30.8M 0s
00:48:25 300K .......... .......... .......... .......... .......... 28% 17.5M 0s
00:48:25 350K .......... .......... .......... .......... .......... 32% 136M 0s
00:48:25 400K .......... .......... .......... .......... .......... 36% 69.5M 0s
00:48:25 450K .......... .......... .......... .......... .......... 40% 9.59M 0s
00:48:25 500K .......... .......... .......... .......... .......... 44% 18.9M 0s
00:48:25 550K .......... .......... .......... .......... .......... 48% 145M 0s
00:48:25 600K .......... .......... .......... .......... .......... 52% 22.1M 0s
00:48:25 650K .......... .......... .......... .......... .......... 56% 30.8M 0s
00:48:25 700K .......... .......... .......... .......... .......... 60% 10.7M 0s
00:48:25 750K .......... .......... .......... .......... .......... 64% 23.4M 0s
00:48:25 800K .......... .......... .......... .......... .......... 68% 26.4M 0s
00:48:25 850K .......... .......... .......... .......... .......... 72% 103M 0s
00:48:25 900K .......... .......... .......... .......... .......... 76% 24.7M 0s
00:48:25 950K .......... .......... .......... .......... .......... 80% 11.9M 0s
00:48:25 1000K .......... .......... .......... .......... .......... 84% 27.4M 0s
00:48:25 1050K .......... .......... .......... .......... .......... 88% 65.5M 0s
00:48:25 1100K .......... .......... .......... .......... .......... 92% 24.6M 0s
00:48:25 1150K .......... .......... .......... .......... .......... 96% 22.5M 0s
00:48:25 1200K .......... .......... .......... .......... . 100% 14.5M=0.08s
00:48:25
00:48:25 2025-08-03 00:48:25 (15.9 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:48:25
00:48:25 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:48:25 ++ deactivate nondestructive
00:48:25 ++ '[' -n '' ']'
00:48:25 ++ '[' -n '' ']'
00:48:25 ++ hash -r
00:48:25 ++ '[' -n '' ']'
00:48:25 ++ unset VIRTUAL_ENV
00:48:25 ++ unset VIRTUAL_ENV_PROMPT
00:48:25 ++ '[' '!' nondestructive = nondestructive ']'
00:48:25 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:48:25 ++ export VIRTUAL_ENV
00:48:25 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:25 ++ 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
00:48:25 ++ export PATH
00:48:25 ++ '[' -n '' ']'
00:48:25 ++ '[' -z '' ']'
00:48:25 ++ _OLD_VIRTUAL_PS1=
00:48:25 ++ PS1='(.venv3) '
00:48:25 ++ export PS1
00:48:25 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:48:25 ++ export VIRTUAL_ENV_PROMPT
00:48:25 ++ hash -r
00:48:25 + pip install -U pip
00:48:25 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:48:25 Collecting pip
00:48:25 Using cached pip-25.2-py3-none-any.whl (1.8 MB)
00:48:25 Installing collected packages: pip
00:48:25 Attempting uninstall: pip
00:48:25 Found existing installation: pip 22.3.1
00:48:25 Uninstalling pip-22.3.1:
00:48:25 Successfully uninstalled pip-22.3.1
00:48:26 Successfully installed pip-25.2
00:48:26 WARNING: There was an error checking the latest version of pip.
00:48:26 + 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
00:48:27 Collecting zeroc-ice==3.6.5
00:48:27 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)
00:48:29 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 22.2 MB/s 0:00:01
00:48:29 Installing collected packages: zeroc-ice
00:48:31 Successfully installed zeroc-ice-3.6.5
00:48:31 + pip install markdown
00:48:31 Collecting markdown
00:48:31 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB)
00:48:31 Using cached markdown-3.8.2-py3-none-any.whl (106 kB)
00:48:31 Installing collected packages: markdown
00:48:31 Successfully installed markdown-3.8.2
00:48:31 + pip install reportlab
00:48:32 Collecting reportlab
00:48:32 Using cached reportlab-4.4.3-py3-none-any.whl.metadata (1.7 kB)
00:48:32 Collecting pillow>=9.0.0 (from reportlab)
00:48:32 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:48:32 Collecting charset-normalizer (from reportlab)
00:48:32 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
00:48:32 Using cached reportlab-4.4.3-py3-none-any.whl (2.0 MB)
00:48:32 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:48:32 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
00:48:32 Installing collected packages: pillow, charset-normalizer, reportlab
00:48:33
00:48:33 Successfully installed charset-normalizer-3.4.2 pillow-11.3.0 reportlab-4.4.3
00:48:33 + pip install pyarrow
00:48:33 Collecting pyarrow
00:48:33 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
00:48:33 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
00:48:34 Installing collected packages: pyarrow
00:48:35 Successfully installed pyarrow-21.0.0
00:48:35 + pip install omego
00:48:36 Collecting omego
00:48:36 Using cached omego-0.7.0-py3-none-any.whl
00:48:36 Collecting future (from omego)
00:48:36 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:48:36 Collecting yaclifw>=0.1.1 (from omego)
00:48:36 Using cached yaclifw-0.2.0-py3-none-any.whl
00:48:36 Collecting six (from yaclifw>=0.1.1->omego)
00:48:36 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:48:36 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:48:36 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:48:36 Installing collected packages: six, future, yaclifw, omego
00:48:36
00:48:36 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:48:36 + pip install tables
00:48:36 Collecting tables
00:48:36 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:48:37 Collecting numpy>=1.20.0 (from tables)
00:48:37 Using cached numpy-2.3.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
00:48:37 Collecting numexpr>=2.6.2 (from tables)
00:48:37 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:48:37 Collecting packaging (from tables)
00:48:37 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:48:37 Collecting py-cpuinfo (from tables)
00:48:37 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:48:37 Collecting blosc2>=2.3.0 (from tables)
00:48:37 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.0 kB)
00:48:37 Collecting typing-extensions>=4.4.0 (from tables)
00:48:37 Using cached typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB)
00:48:37 Collecting ndindex (from blosc2>=2.3.0->tables)
00:48:37 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:48:37 Collecting msgpack (from blosc2>=2.3.0->tables)
00:48:37 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:48:37 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:48:37 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
00:48:37 Collecting requests (from blosc2>=2.3.0->tables)
00:48:37 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB)
00:48:37 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2)
00:48:37 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:48:37 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:48:37 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:48:37 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
00:48:37 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:48:37 Using cached certifi-2025.7.14-py3-none-any.whl.metadata (2.4 kB)
00:48:37 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:48:37 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB)
00:48:37 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB)
00:48:37 Using cached numpy-2.3.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
00:48:37 Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB)
00:48:37 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
00:48:37 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:48:37 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:48:37 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
00:48:37 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:48:37 Using cached requests-2.32.4-py3-none-any.whl (64 kB)
00:48:37 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:48:37 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
00:48:37 Using cached certifi-2025.7.14-py3-none-any.whl (162 kB)
00:48:38 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:48:41
00:48:41 Successfully installed blosc2-3.6.1 certifi-2025.7.14 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.11.0 numpy-2.3.2 packaging-25.0 platformdirs-4.3.8 py-cpuinfo-9.0.0 requests-2.32.4 tables-3.10.2 typing-extensions-4.14.1 urllib3-2.5.0
00:48:41 + pip install jinja2
00:48:41 Collecting jinja2
00:48:41 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:48:41 Collecting MarkupSafe>=2.0 (from jinja2)
00:48:41 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:48:41 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:48:41 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
00:48:41 Installing collected packages: MarkupSafe, jinja2
00:48:42
00:48:42 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
00:48:42 + pip install zarr
00:48:42 Collecting zarr
00:48:42 Using cached zarr-3.1.1-py3-none-any.whl.metadata (10 kB)
00:48:42 Collecting donfig>=0.8 (from zarr)
00:48:42 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
00:48:42 Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr)
00:48:42 Using cached numcodecs-0.16.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.3 kB)
00:48:42 Requirement already satisfied: numpy>=1.26 in ./.venv3/lib64/python3.11/site-packages (from zarr) (2.3.2)
00:48:42 Requirement already satisfied: packaging>=22.0 in ./.venv3/lib64/python3.11/site-packages (from zarr) (25.0)
00:48:42 Requirement already satisfied: typing-extensions>=4.9 in ./.venv3/lib64/python3.11/site-packages (from zarr) (4.14.1)
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00:48:42 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:48:42 Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr)
00:48:42 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)
00:48:42 Using cached zarr-3.1.1-py3-none-any.whl (255 kB)
00:48:42 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
00:48:42 Using cached numcodecs-0.16.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.8 MB)
00:48:42 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)
00:48:42 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
00:48:43 Installing collected packages: pyyaml, numcodecs, crc32c, donfig, zarr
00:48:43
00:48:43 Successfully installed crc32c-2.7.1 donfig-0.8.1.post1 numcodecs-0.16.1 pyyaml-6.0.2 zarr-3.1.1
00:48:43 + pip install fsspec requests aiohttp s3fs
00:48:44 Collecting fsspec
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00:48:44 Collecting aiohttp
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00:48:44 Collecting s3fs
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00:48:44 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp)
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00:48:44 Collecting frozenlist>=1.1.1 (from aiohttp)
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00:48:45 Collecting multidict<7.0,>=4.5 (from aiohttp)
00:48:45 Using cached multidict-6.6.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
00:48:45 Collecting propcache>=0.2.0 (from aiohttp)
00:48:45 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
00:48:45 Collecting yarl<2.0,>=1.17.0 (from aiohttp)
00:48:45 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB)
00:48:45 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs)
00:48:45 Using cached aiobotocore-2.23.2-py3-none-any.whl.metadata (25 kB)
00:48:45 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:48:45 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
00:48:46 Collecting botocore<1.39.9,>=1.39.7 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:48:46 Using cached botocore-1.39.8-py3-none-any.whl.metadata (5.7 kB)
00:48:46 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
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00:48:46 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:48:46 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
00:48:46 Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:48:46 Using cached wrapt-1.17.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.4 kB)
00:48:46 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)
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00:48:46 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB)
00:48:46 Using cached multidict-6.6.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
00:48:46 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (348 kB)
00:48:46 Using cached s3fs-2025.7.0-py3-none-any.whl (30 kB)
00:48:46 Using cached aiobotocore-2.23.2-py3-none-any.whl (84 kB)
00:48:46 Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB)
00:48:46 Using cached botocore-1.39.8-py3-none-any.whl (13.9 MB)
00:48:46 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
00:48:46 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:48:46 Using cached wrapt-1.17.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (83 kB)
00:48:46 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
00:48:46 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
00:48:46 Using cached attrs-25.3.0-py3-none-any.whl (63 kB)
00:48:46 Using cached frozenlist-1.7.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (235 kB)
00:48:46 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB)
00:48:46 Installing collected packages: wrapt, python-dateutil, propcache, multidict, jmespath, fsspec, frozenlist, attrs, aioitertools, aiohappyeyeballs, yarl, botocore, aiosignal, aiohttp, aiobotocore, s3fs
00:48:47
00:48:47 Successfully installed aiobotocore-2.23.2 aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aioitertools-0.12.0 aiosignal-1.4.0 attrs-25.3.0 botocore-1.39.8 frozenlist-1.7.0 fsspec-2025.7.0 jmespath-1.0.1 multidict-6.6.3 propcache-0.3.2 python-dateutil-2.9.0.post0 s3fs-2025.7.0 wrapt-1.17.2 yarl-1.20.1
00:48:47 + pip install omero-py
00:48:48 Collecting omero-py
00:48:48 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB)
00:48:48 Collecting urllib3<2 (from omero-py)
00:48:48 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:48:48 Collecting appdirs (from omero-py)
00:48:48 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:48:48 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:48:48 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.2)
00:48:48 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
00:48:48 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.2)
00:48:48 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:48:48 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4)
00:48:48 Collecting portalocker (from omero-py)
00:48:48 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:48:48 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
00:48:48 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
00:48:48 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.7.14)
00:48:48 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB)
00:48:48 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:48:48 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:48:48 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:48:48 Installing collected packages: appdirs, urllib3, portalocker, omero-py
00:48:48 Attempting uninstall: urllib3
00:48:48 Found existing installation: urllib3 2.5.0
00:48:48 Uninstalling urllib3-2.5.0:
00:48:48 Successfully uninstalled urllib3-2.5.0
00:48:50
00:48:50 Successfully installed appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20
00:48:50 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:48:50 Collecting omero-metadata
00:48:50 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-g99ov152/omero-metadata_cb10a18d7f064008ab28ed5f21e5f50d
00:48:50 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-g99ov152/omero-metadata_cb10a18d7f064008ab28ed5f21e5f50d
00:48:51 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit ff19845b7d792f72a509975bc4ae7c0970d0eeb8
00:48:51 Installing build dependencies: started
00:48:52 Installing build dependencies: finished with status 'done'
00:48:52 Getting requirements to build wheel: started
00:48:52 Getting requirements to build wheel: finished with status 'done'
00:48:52 Preparing metadata (pyproject.toml): started
00:48:53 Preparing metadata (pyproject.toml): finished with status 'done'
00:48:53 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0)
00:48:53 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
00:48:53 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:48:53 Collecting pandas (from omero-metadata)
00:48:53 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
00:48:53 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:48:53 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:48:53 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:48:53 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.2)
00:48:53 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)
00:48:53 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)
00:48:53 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4)
00:48:53 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:48:53 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
00:48:53 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:48:53 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:48:53 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:48:53 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:48:53 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:48:53 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)
00:48:53 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.2)
00:48:53 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)
00:48:53 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.7.14)
00:48:53 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
00:48:53 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:48:53 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:48:53 Building wheels for collected packages: omero-metadata
00:48:53 Building wheel for omero-metadata (pyproject.toml): started
00:48:53 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:48:53 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=88f7ce98b460be342dedf551a870820b7c1e8666c72599e195c6975d45b8754e
00:48:53 Stored in directory: /tmp/pip-ephem-wheel-cache-x4nt642c/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:48:53 Successfully built omero-metadata
00:48:53 Installing collected packages: pytz, tzdata, pandas, omero-metadata
00:48:58
00:48:58 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.1 pytz-2025.2 tzdata-2025.2
00:48:58 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:48:58 Collecting omero-cli-render
00:48:58 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-ee0t4pbm/omero-cli-render_a02f28e749a94710b7d178fb1f6ff684
00:48:58 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-ee0t4pbm/omero-cli-render_a02f28e749a94710b7d178fb1f6ff684
00:48:59 Running command git checkout -b merge_ci --track origin/merge_ci
00:49:00 Switched to a new branch 'merge_ci'
00:49:00 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:49:00 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit e56f896d341d41a18b961b5cc30c51f561f8243b
00:49:00 Installing build dependencies: started
00:49:00 Installing build dependencies: finished with status 'done'
00:49:00 Getting requirements to build wheel: started
00:49:01 Getting requirements to build wheel: finished with status 'done'
00:49:01 Preparing metadata (pyproject.toml): started
00:49:01 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:01 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
00:49:01 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0)
00:49:01 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:49:01 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:49:01 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:49:01 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.2)
00:49:01 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)
00:49:01 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)
00:49:01 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4)
00:49:01 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:49:01 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.2)
00:49:01 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)
00:49:01 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.7.14)
00:49:01 Building wheels for collected packages: omero-cli-render
00:49:01 Building wheel for omero-cli-render (pyproject.toml): started
00:49:01 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:49:01 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=3c14e17cfdd6f3eca9a09e4339ddde9794a7d085aa9276813194767fb9a4fec1
00:49:01 Stored in directory: /tmp/pip-ephem-wheel-cache-edku_02x/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:49:01 Successfully built omero-cli-render
00:49:01 Installing collected packages: omero-cli-render
00:49:01 Successfully installed omero-cli-render-0.8.2.dev0
00:49:01 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:49:02 Collecting omero-cli-duplicate
00:49:02 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-q0dip7um/omero-cli-duplicate_bf8a91be8c7f4aaf92aae6a58cb0d3c3
00:49:02 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-q0dip7um/omero-cli-duplicate_bf8a91be8c7f4aaf92aae6a58cb0d3c3
00:49:03 Running command git checkout -b merge_ci --track origin/merge_ci
00:49:03 Switched to a new branch 'merge_ci'
00:49:03 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:49:03 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 80e3dfa37c66facef6e248fd62bbc4b6352360c8
00:49:03 Installing build dependencies: started
00:49:04 Installing build dependencies: finished with status 'done'
00:49:04 Getting requirements to build wheel: started
00:49:04 Getting requirements to build wheel: finished with status 'done'
00:49:04 Preparing metadata (pyproject.toml): started
00:49:04 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:04 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0)
00:49:04 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:49:04 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:49:04 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:49:04 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.2)
00:49:04 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)
00:49:04 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:49:04 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)
00:49:04 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4)
00:49:04 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:49:04 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.2)
00:49:04 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)
00:49:04 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.7.14)
00:49:04 Building wheels for collected packages: omero-cli-duplicate
00:49:04 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:49:05 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:49:05 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=059c71816c4c6c00cd7bfac323f274395fd1d5290e611a545b6d1a735f01810c
00:49:05 Stored in directory: /tmp/pip-ephem-wheel-cache-ogxcsuta/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:49:05 Successfully built omero-cli-duplicate
00:49:05 Installing collected packages: omero-cli-duplicate
00:49:05 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:49:05 + pip install omero-certificates
00:49:05 Collecting omero-certificates
00:49:05 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:49:05 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0)
00:49:05 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:49:05 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:49:05 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:49:05 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.2)
00:49:05 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)
00:49:05 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:49:05 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
00:49:05 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4)
00:49:05 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:49:05 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.2)
00:49:05 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
00:49:05 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.7.14)
00:49:05 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:49:05 Installing collected packages: omero-certificates
00:49:05 Successfully installed omero-certificates-0.4.0
00:49:05 + for x in *.tar.gz
00:49:05 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:49:06 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:49:06 Installing build dependencies: started
00:49:07 Installing build dependencies: finished with status 'done'
00:49:07 Getting requirements to build wheel: started
00:49:09 Getting requirements to build wheel: finished with status 'done'
00:49:09 Preparing metadata (pyproject.toml): started
00:49:09 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:09 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0)
00:49:09 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
00:49:09 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:49:09 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:49:09 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.2)
00:49:09 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)
00:49:09 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:49:09 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)
00:49:09 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4)
00:49:09 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:49:09 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.2)
00:49:09 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)
00:49:09 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.7.14)
00:49:09 Building wheels for collected packages: omero-dropbox
00:49:09 Building wheel for omero-dropbox (pyproject.toml): started
00:49:09 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:49:09 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=e4964b63925e44f5013ceec85bc14239bd268037a79f596c5c12777d4d3b0caa
00:49:09 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:49:09 Successfully built omero-dropbox
00:49:09 Installing collected packages: omero-dropbox
00:49:09 Successfully installed omero-dropbox-5.7.1.dev0
00:49:09 + for x in *.tar.gz
00:49:09 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:49:10 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:49:10 Installing build dependencies: started
00:49:11 Installing build dependencies: finished with status 'done'
00:49:11 Getting requirements to build wheel: started
00:49:11 Getting requirements to build wheel: finished with status 'done'
00:49:11 Preparing metadata (pyproject.toml): started
00:49:11 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:11 Building wheels for collected packages: omero_marshal
00:49:11 Building wheel for omero_marshal (pyproject.toml): started
00:49:12 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:49:12 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=4b4ab052536360726aed5e463f683f9184506f43fbcaf5567802f0570d9dfb8c
00:49:12 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:49:12 Successfully built omero_marshal
00:49:12 Installing collected packages: omero_marshal
00:49:12 Successfully installed omero_marshal-0.9.1.dev0
00:49:12 + for x in *.tar.gz
00:49:12 + pip install -U omero_py-5.21.1.dev0.tar.gz
00:49:12 Processing ./omero_py-5.21.1.dev0.tar.gz
00:49:13 Installing build dependencies: started
00:49:13 Installing build dependencies: finished with status 'done'
00:49:13 Getting requirements to build wheel: started
00:49:14 Getting requirements to build wheel: finished with status 'done'
00:49:14 Preparing metadata (pyproject.toml): started
00:49:14 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:14 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20)
00:49:14 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4)
00:49:14 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0)
00:49:14 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.2)
00:49:14 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0)
00:49:14 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2)
00:49:14 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.6.5)
00:49:14 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4)
00:49:14 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0)
00:49:14 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.4.2)
00:49:14 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10)
00:49:14 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.7.14)
00:49:14 Building wheels for collected packages: omero-py
00:49:14 Building wheel for omero-py (pyproject.toml): started
00:49:15 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:49:15 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783541 sha256=c6d55ecce70ea3a6bfffff69067fff04e3b6b73df9dcb583fe55ff542252161b
00:49:15 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d
00:49:15 Successfully built omero-py
00:49:15 Installing collected packages: omero-py
00:49:15 Attempting uninstall: omero-py
00:49:15 Found existing installation: omero-py 5.21.0
00:49:15 Uninstalling omero-py-5.21.0:
00:49:16 Successfully uninstalled omero-py-5.21.0
00:49:18 Successfully installed omero-py-5.21.1.dev0
00:49:18 + for x in *.tar.gz
00:49:18 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:49:18 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:49:18 Installing build dependencies: started
00:49:19 Installing build dependencies: finished with status 'done'
00:49:19 Getting requirements to build wheel: started
00:49:20 Getting requirements to build wheel: finished with status 'done'
00:49:20 Preparing metadata (pyproject.toml): started
00:49:20 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:20 Building wheels for collected packages: omero-scripts
00:49:20 Building wheel for omero-scripts (pyproject.toml): started
00:49:20 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:49:20 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=4d487b2f8cdb66097a286d5845b038d3050bbced7050f2fe73eba8ce877f9850
00:49:20 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:49:20 Successfully built omero-scripts
00:49:20 Installing collected packages: omero-scripts
00:49:21 Successfully installed omero-scripts-5.9.2.dev0
00:49:21 + for x in *.tar.gz
00:49:21 + pip install -U omero_web-5.29.2.dev0.tar.gz
00:49:22 Processing ./omero_web-5.29.2.dev0.tar.gz
00:49:22 Installing build dependencies: started
00:49:23 Installing build dependencies: finished with status 'done'
00:49:23 Getting requirements to build wheel: started
00:49:23 Getting requirements to build wheel: finished with status 'done'
00:49:23 Preparing metadata (pyproject.toml): started
00:49:24 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:24 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (5.21.1.dev0)
00:49:24 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0)
00:49:24 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:49:24 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0)
00:49:24 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB)
00:49:24 Collecting django-pipeline (from omero-web==5.29.2.dev0)
00:49:24 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
00:49:24 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0)
00:49:24 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:49:24 Collecting django-csp (from omero-web==5.29.2.dev0)
00:49:24 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:49:24 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0)
00:49:24 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
00:49:24 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0)
00:49:24 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:49:24 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (0.9.1.dev0)
00:49:24 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.3.0)
00:49:24 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2)
00:49:24 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0)
00:49:24 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0)
00:49:24 Collecting importlib-resources (from omero-web==5.29.2.dev0)
00:49:24 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:49:24 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
00:49:24 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB)
00:49:24 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0)
00:49:24 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:49:24 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.26.20)
00:49:24 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.4.4)
00:49:24 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.0.0)
00:49:24 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.3.2)
00:49:24 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (6.0.2)
00:49:24 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==5.29.2.dev0) (3.6.5)
00:49:24 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.32.4)
00:49:24 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1)
00:49:24 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0)
00:49:24 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:49:24 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.4.2)
00:49:24 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.10)
00:49:24 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (2025.7.14)
00:49:24 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:49:24 Using cached django-4.2.23-py3-none-any.whl (8.0 MB)
00:49:24 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB)
00:49:24 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:49:24 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:49:24 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:49:24 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
00:49:24 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:49:24 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
00:49:24 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:49:24 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:49:24 Building wheels for collected packages: omero-web
00:49:24 Building wheel for omero-web (pyproject.toml): started
00:49:26 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:49:26 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=38053a9a639cffa197d57b7d13ef8c656493bffb8dabb04d9163e50a87ebda53
00:49:26 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c
00:49:26 Successfully built omero-web
00:49:26 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:49:28
00:49:28 Successfully installed Django-4.2.23 asgiref-3.9.1 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.0.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.2.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.9.0
00:49:29 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:49:29 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:49:29 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:49:29 --2025-08-03 00:49:29-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:49:29 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.108.133, 185.199.111.133, ...
00:49:29 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.
00:49:29 HTTP request sent, awaiting response... 200 OK
00:49:29 Length: 125081 (122K) [text/plain]
00:49:29 Saving to: ‘Figure_To_Pdf.py’
00:49:29
00:49:29 0K .......... .......... .......... .......... .......... 40% 3.90M 0s
00:49:29 50K .......... .......... .......... .......... .......... 81% 5.85M 0s
00:49:29 100K .......... .......... .. 100% 48.0M=0.02s
00:49:29
00:49:29 2025-08-03 00:49:29 (5.60 MB/s) - ‘Figure_To_Pdf.py’ saved [125081/125081]
00:49:29
00:49:29 + chmod 755 Figure_To_Pdf.py
00:49:29 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:49:29 + omero config set omero.db.name OMERO-server
00:49:30 + omero config set omero.db.host pg
00:49:31 + omero config set omero.db.user postgres
00:49:33 + omero config set omero.data.dir /home/omero/omero-server-data
00:49:34 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:49:35 + omero config set omero.db.poolsize 25
00:49:37 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:49:38 + omero config set omero.security.trustStorePassword changeit
00:49:39 + omero config set omero.mail.config true
00:49:40 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:49:42 + omero config set omero.mail.host smtp.dundee.ac.uk
00:49:43 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:49:44 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:49:45 + omero certificates
00:49:46 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:49:47 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:49:47 + '[' false = true ']'
00:49:47 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:49:47 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:49:47 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:49:47 2025-08-03 00:49:47,361 [ omego.db] DEBUG dbcommand => upgrade
00:49:47 2025-08-03 00:49:47,361 [ omego.db] DEBUG dbhost => localhost
00:49:47 2025-08-03 00:49:47,361 [ omego.db] DEBUG dbname => OMERO-server
00:49:47 2025-08-03 00:49:47,361 [ omego.db] DEBUG dbpass => omero
00:49:47 2025-08-03 00:49:47,361 [ omego.db] DEBUG dbuser => omero
00:49:47 2025-08-03 00:49:47,362 [ omego.db] DEBUG rootpass => omero
00:49:47 2025-08-03 00:49:47,362 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:49:47 2025-08-03 00:49:47,362 [omego.extern] INFO Executing : omero version
00:49:48 OMERO.py version:
00:49:48 OMERO.server version:
00:49:48 5.6.3-574-6798e74085-ice36-b484
00:49:48 5.21.1.dev0
00:49:48 2025-08-03 00:49:48,673 [omego.extern] INFO Completed [1.311 s]
00:49:48 2025-08-03 00:49:48,673 [omego.extern] DEBUG Using omero CLI from omero
00:49:48 2025-08-03 00:49:48,673 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:49:48 2025-08-03 00:49:48,673 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:48 2025-08-03 00:49:48,673 [omego.extern] INFO Executing : omero config get --show-password
00:49:49 2025-08-03 00:49:49,963 [omego.extern] INFO Completed [1.290 s]
00:49:49 2025-08-03 00:49:49,964 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:49 2025-08-03 00:49:49,964 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:49:49 2025-08-03 00:49:49,970 [omego.extern] INFO Completed [0.006 s]
00:49:49 2025-08-03 00:49:49,970 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
00:49:49 2025-08-03 00:49:49,970 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
00:49:49
00:49:49 2025-08-03 00:49:49,970 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:49 2025-08-03 00:49:49,970 [omego.extern] INFO Executing : omero config get --show-password
00:49:51 2025-08-03 00:49:51,250 [omego.extern] INFO Completed [1.280 s]
00:49:51 2025-08-03 00:49:51,250 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:51 2025-08-03 00:49:51,250 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:49:51 2025-08-03 00:49:51,260 [omego.extern] INFO Completed [0.010 s]
00:49:51 2025-08-03 00:49:51,260 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.8") at port "5432".\n'
00:49:51 2025-08-03 00:49:51,261 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:49:51 2025-08-03 00:49:51,261 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:51 2025-08-03 00:49:51,261 [omego.extern] INFO Executing : omero config get --show-password
00:49:52 2025-08-03 00:49:52,556 [omego.extern] INFO Completed [1.296 s]
00:49:52 2025-08-03 00:49:52,557 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:52 2025-08-03 00:49:52,557 [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
00:49:52 2025-08-03 00:49:52,567 [omego.extern] INFO Completed [0.010 s]
00:49:52 2025-08-03 00:49:52,567 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:49:52 2025-08-03 00:49:52,567 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:49:52 2025-08-03 00:49:52,569 [ omego.db] INFO Database is already at OMERO5.4__0
00:49:52 + export LANG=en_US.UTF-8
00:49:52 + LANG=en_US.UTF-8
00:49:52 + export LANGUAGE=en_US:en
00:49:52 + LANGUAGE=en_US:en
00:49:52 + export LC_ALL=en_US.UTF-8
00:49:52 + LC_ALL=en_US.UTF-8
00:49:52 + BUILD_ID=DONT_KILL_ME
00:49:52 + omero admin start
00:49:57 No descriptor given. Using etc/grid/default.xml
00:50:07 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:50:07 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:50:07 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:50:07 Waiting on startup. Use CTRL-C to exit
00:50:07 + omero admin waitup
00:50:08 Waiting on startup. Use CTRL-C to exit
00:50:08 + omero admin diagnostics
00:50:12
00:50:12 ================================================================================
00:50:12 OMERO Diagnostics (admin)
00:50:12 ================================================================================
00:50:12
00:50:12 Commands: java -version 11.0.25 (/usr/bin/java)
00:50:12 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:50:12 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:50:12 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:50:12 Commands: psql --version 16.9 (/usr/bin/psql)
00:50:12 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:50:12
00:50:12 Component: OMERO.py 5.21.1.dev0
00:50:12 Component: OMERO.server 5.6.3-574-6798e74085-ice36-b484
00:50:12
00:50:12 Server: icegridnode running
00:50:12 Server: Blitz-0 active (pid = 31729, enabled)
00:50:12 Server: Indexer-0 activating (enabled)
00:50:12 Server: OMERO.Glacier2 active (pid = 31760, enabled)
00:50:12 Server: OMERO.IceStorm active (pid = 31767, enabled)
00:50:12 Server: Processor-0 active (pid = 31784, enabled)
00:50:12 Server: Tables-0 active (pid = 31799, enabled)
00:50:12
00:50:12 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:50:12 Log files: Blitz-0.log 33.1 KB errors=0 warnings=1
00:50:12 Log files: DropBox.log n/a
00:50:12 Log files: FileServer.log n/a
00:50:12 Log files: Indexer-0.log 598 B
00:50:12 Log files: MonitorServer.log n/a
00:50:12 Log files: Processor-0.log 735 B
00:50:12 Log files: Tables-0.log 961 B
00:50:12 Log files: TestDropBox.log n/a
00:50:12 Log files: master.err empty
00:50:12 Log files: master.out 30.5 KB
00:50:12 Log files: Total size 0.07 MB
00:50:12
00:50:12
00:50:12 Environment:OMERO_HOME=(unset)
00:50:12 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:50:12 Environment:OMERO_NODE=(unset)
00:50:12 Environment:OMERO_MASTER=(unset)
00:50:12 Environment:OMERO_USERDIR=(unset)
00:50:12 Environment:OMERO_TMPDIR=(unset)
00:50:12 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
00:50:12 Environment:PYTHONPATH=(unset)
00:50:12 Environment:ICE_HOME=/opt/ice-3.6.5
00:50:12 Environment:LD_LIBRARY_PATH=(unset)
00:50:12 Environment:DYLD_LIBRARY_PATH=(unset)
00:50:12
00:50:12 OMERO SSL port:4064
00:50:12 OMERO TCP port:4063
00:50:12 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:50:12 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:50:12
00:50:12 JVM settings: Blitz-${index} -Xmx7200m
00:50:12 JVM settings: Indexer-${index} -Xmx4800m
00:50:12 JVM settings: PixelData-${index} -Xmx7200m
00:50:12 JVM settings: Repository-${index} -Xmx4800m
00:50:12
00:50:12 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 3 August 2025 04b453e5836816f838b12379cc608f2637c22927
00:50:12 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 3 August 2025 04b453e5836816f838b12379cc608f2637c22927
00:50:12 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 3 August 2025 04b453e5836816f838b12379cc608f2637c22927
00:50:12 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 3 August 2025 ff878892ac5594e4a30a76cb64394ca4d8756d44
00:50:12 Jar: lib/server/ome-common.jar OME Common Java 6.1.1-SNAPSHOT 3 August 2025 ff878892ac5594e4a30a76cb64394ca4d8756d44
00:50:12 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 3 August 2025 ff878892ac5594e4a30a76cb64394ca4d8756d44
00:50:12 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 3 August 2025 ff878892ac5594e4a30a76cb64394ca4d8756d44
00:50:12 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 3 August 2025 ff878892ac5594e4a30a76cb64394ca4d8756d44
00:50:12 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 3 August 2025 ff878892ac5594e4a30a76cb64394ca4d8756d44
00:50:12 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:50:12 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT 305e9bee49283e687f8b45b0de0d08592c034e3f
00:50:12 + deactivate
00:50:12 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:50:12 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:12 + export PATH
00:50:12 + unset _OLD_VIRTUAL_PATH
00:50:12 + '[' -n '' ']'
00:50:12 + hash -r
00:50:12 + '[' -n '' ']'
00:50:12 + unset VIRTUAL_ENV
00:50:12 + unset VIRTUAL_ENV_PROMPT
00:50:12 + '[' '!' '' = nondestructive ']'
00:50:12 + unset -f deactivate
00:50:12 Finished: SUCCESS
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