00:51:52 Started by upstream project "Trigger" build number 605
00:51:52 originally caused by:
00:51:52 Started by timer
00:51:52 Running as SYSTEM
00:51:52 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:51:52 [OMERO-server] $ /bin/bash -xe /tmp/jenkins11593647594083512461.sh
00:51:52 + source /home/settings.env
00:51:52 ++ OMERO_DB_HOST=pg
00:51:52 ++ OMERO_DB_USER=postgres
00:51:52 ++ OMERO_DB_PASS=
00:51:52 ++ OMERO_ROOT_PASS=omero
00:51:52 ++ OMERO_DATA_DIR=/OMERO
00:51:52 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:51:52 + OMERO_DB_NAME=OMERO-server
00:51:52 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:51:52 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:51:52 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:51:52 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:51:52 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:51:52 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:51:52 ++ deactivate nondestructive
00:51:52 ++ '[' -n '' ']'
00:51:52 ++ '[' -n '' ']'
00:51:52 ++ hash -r
00:51:52 ++ '[' -n '' ']'
00:51:52 ++ unset VIRTUAL_ENV
00:51:52 ++ unset VIRTUAL_ENV_PROMPT
00:51:52 ++ '[' '!' nondestructive = nondestructive ']'
00:51:52 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:51:52 ++ export VIRTUAL_ENV
00:51:52 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:51:52 ++ 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
00:51:52 ++ export PATH
00:51:52 ++ '[' -n '' ']'
00:51:52 ++ '[' -z '' ']'
00:51:52 ++ _OLD_VIRTUAL_PS1=
00:51:52 ++ PS1='(.venv3) '
00:51:52 ++ export PS1
00:51:52 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:51:52 ++ export VIRTUAL_ENV_PROMPT
00:51:52 ++ hash -r
00:51:52 + omero admin stop
00:51:54 Waiting on shutdown. Use CTRL-C to exit
00:51:54 .+ sleep 5
00:52:09 + deactivate
00:52:09 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:52:09 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:52:09 + export PATH
00:52:09 + unset _OLD_VIRTUAL_PATH
00:52:09 + '[' -n '' ']'
00:52:09 + hash -r
00:52:09 + '[' -n '' ']'
00:52:09 + unset VIRTUAL_ENV
00:52:09 + unset VIRTUAL_ENV_PROMPT
00:52:09 + '[' '!' '' = nondestructive ']'
00:52:09 + unset -f deactivate
00:52:09 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:52:10 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:52:13 + '[' false = true ']'
00:52:13 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:52:13 Skipping PURGE_DATA:CleanDbAndRepo
00:52:13 + 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-5.29.3.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:52:15 Copied 1 artifact from "OMERO-build" build number 513
00:52:15 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 506
00:52:16 Copied 2 artifacts from "OMERO-build-build" build number 540
00:52:16 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 46
00:52:16 [OMERO-server] $ /bin/bash -xe /tmp/jenkins8734698143906551912.sh
00:52:16 + source /home/settings.env
00:52:16 ++ OMERO_DB_HOST=pg
00:52:16 ++ OMERO_DB_USER=postgres
00:52:16 ++ OMERO_DB_PASS=
00:52:16 ++ OMERO_ROOT_PASS=omero
00:52:16 ++ OMERO_DATA_DIR=/OMERO
00:52:16 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:52:16 + OMERO_DB_NAME=OMERO-server
00:52:16 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:52:16 + mkdir -p /home/omero/omero-server-data
00:52:16 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:52:16 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:52:16 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:52:16 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:52:16 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:52:16 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:52:16 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:52:16 ++ ls OMERO.server-5.6.3-574-3465a6037d-ice36-b513.zip
00:52:16 + ZIP=OMERO.server-5.6.3-574-3465a6037d-ice36-b513.zip
00:52:16 + '[' '!' -z '' ']'
00:52:16 + DIST=OMERO.server-5.6.3-574-3465a6037d-ice36-b513
00:52:16 + unzip OMERO.server-5.6.3-574-3465a6037d-ice36-b513.zip
00:52:16 Archive: OMERO.server-5.6.3-574-3465a6037d-ice36-b513.zip
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/blitz/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/grid/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/profiles/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/error/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/grid/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/luts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/luts/janelia/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/luts/matplotlib/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/luts/ncsa_paledit/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/luts/seaborn/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/luts/wcif/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/analysis_scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/annotation_scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/export_scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/figure_scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/import_scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/scripts/omero/util_scripts/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/server/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/share/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/share/licenses/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/misc/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__1/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__10/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__11/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__2/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__3/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__4/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__5/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__6/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__7/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__8/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3A__9/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3__4/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3__5/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3__6/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO3__7/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO4.1__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO4.2__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO4.2__0/t/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO4.3__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO4.4__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO4__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.0__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.1__1/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.2__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.3__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4DEV__1/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4DEV__2/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4DEV__3/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/
00:52:16 creating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/var/
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/LICENSE.txt
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/backup.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/blitz/mail-senders.example
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/blitz/mail-server.example
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/build.properties
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/env.bat
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/env.sh
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/hibernate.properties
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/ice.config
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/logback-cli.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/logback-indexing-cli.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/logback-indexing.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/logback.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/mime.types
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/node1.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/node2.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/omero.properties
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/profiles/psql
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/rollover.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/Windows.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/error/maintainance.html
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/grid/README
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/grid/default.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/grid/templates.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/grid/windefault.xml
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/ice.config
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/internal.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/master.cfg
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/templates/robot.template
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/etc/testdropbox.config
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/history.rst
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/OMEZarrReader.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/accessors-smart.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/activation.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/aggdesigner-algorithm.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/aircompressor.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/antlr.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/aopalliance.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/apiguardian-api.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/asm.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/avatica-core.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/avatica-metrics.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/aws-java-sdk-core.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/aws-java-sdk-kms.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/aws-java-sdk-s3.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/base.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-anim.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-awt-util.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-bridge.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-codec.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-constants.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-css.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-dom.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-ext.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-gvt.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-i18n.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-parser.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-script.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-shared-resources.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-svg-dom.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-svggen.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-transcoder.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-util.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/batik-xml.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/btm.jar
00:52:16 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/calcite-core.jar
00:52:17 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/calcite-linq4j.jar
00:52:17 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/cdm-core.jar
00:52:17 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/checker-qual.jar
00:52:17 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/lib/client/commons-beanutils.jar
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00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/psql-footer.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/psql-header.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/schema.sql
00:52:19 inflating: OMERO.server-5.6.3-574-3465a6037d-ice36-b513/sql/psql/OMERO5.4__0/views.sql
00:52:19 + rm -f OMERO.server-5.6.3-574-3465a6037d-ice36-b513.zip
00:52:19 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-574-3465a6037d-ice36-b513 /home/omero/workspace/OMERO-server/OMERO.server
00:52:19 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:52:19 + JAR=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:52:19 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:52:19 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar
00:52:19 + 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
00:52:19 + 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
00:52:19 --2025-09-02 00:52:19-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:52:19 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:52:19 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:52:19 HTTP request sent, awaiting response... 200 OK
00:52:19 Length: 889211 (868K) [application/java-archive]
00:52:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:52:19
00:52:19 0K .......... .......... .......... .......... .......... 5% 3.88M 0s
00:52:19 50K .......... .......... .......... .......... .......... 11% 5.77M 0s
00:52:19 100K .......... .......... .......... .......... .......... 17% 21.7M 0s
00:52:19 150K .......... .......... .......... .......... .......... 23% 25.1M 0s
00:52:19 200K .......... .......... .......... .......... .......... 28% 7.67M 0s
00:52:19 250K .......... .......... .......... .......... .......... 34% 44.1M 0s
00:52:19 300K .......... .......... .......... .......... .......... 40% 23.9M 0s
00:52:19 350K .......... .......... .......... .......... .......... 46% 91.1M 0s
00:52:19 400K .......... .......... .......... .......... .......... 51% 33.3M 0s
00:52:19 450K .......... .......... .......... .......... .......... 57% 8.24M 0s
00:52:19 500K .......... .......... .......... .......... .......... 63% 32.0M 0s
00:52:19 550K .......... .......... .......... .......... .......... 69% 31.4M 0s
00:52:19 600K .......... .......... .......... .......... .......... 74% 155M 0s
00:52:19 650K .......... .......... .......... .......... .......... 80% 33.2M 0s
00:52:19 700K .......... .......... .......... .......... .......... 86% 8.27M 0s
00:52:19 750K .......... .......... .......... .......... .......... 92% 30.8M 0s
00:52:19 800K .......... .......... .......... .......... .......... 97% 46.2M 0s
00:52:19 850K .......... ........ 100% 124M=0.06s
00:52:19
00:52:19 2025-09-02 00:52:19 (15.1 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:52:19
00:52:19 + 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
00:52:19 --2025-09-02 00:52:19-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:52:19 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:52:19 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:52:19 HTTP request sent, awaiting response... 200 OK
00:52:19 Length: 73309 (72K) [application/java-archive]
00:52:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:52:19
00:52:19 0K .......... .......... .......... .......... .......... 69% 4.11M 0s
00:52:19 50K .......... .......... . 100% 10.9M=0.01s
00:52:19
00:52:19 2025-09-02 00:52:19 (5.06 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:52:19
00:52:19 + 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
00:52:19 --2025-09-02 00:52:19-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:52:19 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:52:19 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:52:19 HTTP request sent, awaiting response... 200 OK
00:52:19 Length: 63303 (62K) [application/java-archive]
00:52:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:52:19
00:52:19 0K .......... .......... .......... .......... .......... 80% 4.17M 0s
00:52:19 50K .......... . 100% 10.6M=0.01s
00:52:19
00:52:19 2025-09-02 00:52:19 (4.72 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:52:19
00:52:19 + 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
00:52:19 --2025-09-02 00:52:19-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:52:19 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:52:19 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:52:19 HTTP request sent, awaiting response... 200 OK
00:52:19 Length: 1271272 (1.2M) [application/java-archive]
00:52:19 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:52:19
00:52:19 0K .......... .......... .......... .......... .......... 4% 4.15M 0s
00:52:20 50K .......... .......... .......... .......... .......... 8% 10.9M 0s
00:52:20 100K .......... .......... .......... .......... .......... 12% 6.86M 0s
00:52:20 150K .......... .......... .......... .......... .......... 16% 23.1M 0s
00:52:20 200K .......... .......... .......... .......... .......... 20% 8.11M 0s
00:52:20 250K .......... .......... .......... .......... .......... 24% 36.0M 0s
00:52:20 300K .......... .......... .......... .......... .......... 28% 23.1M 0s
00:52:20 350K .......... .......... .......... .......... .......... 32% 115M 0s
00:52:20 400K .......... .......... .......... .......... .......... 36% 24.3M 0s
00:52:20 450K .......... .......... .......... .......... .......... 40% 9.92M 0s
00:52:20 500K .......... .......... .......... .......... .......... 44% 25.2M 0s
00:52:20 550K .......... .......... .......... .......... .......... 48% 108M 0s
00:52:20 600K .......... .......... .......... .......... .......... 52% 32.5M 0s
00:52:20 650K .......... .......... .......... .......... .......... 56% 23.2M 0s
00:52:20 700K .......... .......... .......... .......... .......... 60% 9.85M 0s
00:52:20 750K .......... .......... .......... .......... .......... 64% 27.2M 0s
00:52:20 800K .......... .......... .......... .......... .......... 68% 106M 0s
00:52:20 850K .......... .......... .......... .......... .......... 72% 42.1M 0s
00:52:20 900K .......... .......... .......... .......... .......... 76% 23.5M 0s
00:52:20 950K .......... .......... .......... .......... .......... 80% 9.57M 0s
00:52:20 1000K .......... .......... .......... .......... .......... 84% 41.0M 0s
00:52:20 1050K .......... .......... .......... .......... .......... 88% 43.2M 0s
00:52:20 1100K .......... .......... .......... .......... .......... 92% 38.0M 0s
00:52:20 1150K .......... .......... .......... .......... .......... 96% 24.3M 0s
00:52:20 1200K .......... .......... .......... .......... . 100% 175M=0.07s
00:52:20
00:52:20 2025-09-02 00:52:20 (17.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:52:20
00:52:20 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:52:20 ++ deactivate nondestructive
00:52:20 ++ '[' -n '' ']'
00:52:20 ++ '[' -n '' ']'
00:52:20 ++ hash -r
00:52:20 ++ '[' -n '' ']'
00:52:20 ++ unset VIRTUAL_ENV
00:52:20 ++ unset VIRTUAL_ENV_PROMPT
00:52:20 ++ '[' '!' nondestructive = nondestructive ']'
00:52:20 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:52:20 ++ export VIRTUAL_ENV
00:52:20 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:52:20 ++ 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
00:52:20 ++ export PATH
00:52:20 ++ '[' -n '' ']'
00:52:20 ++ '[' -z '' ']'
00:52:20 ++ _OLD_VIRTUAL_PS1=
00:52:20 ++ PS1='(.venv3) '
00:52:20 ++ export PS1
00:52:20 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:52:20 ++ export VIRTUAL_ENV_PROMPT
00:52:20 ++ hash -r
00:52:20 + pip install -U pip
00:52:20 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:52:20 Collecting pip
00:52:20 Using cached pip-25.2-py3-none-any.whl (1.8 MB)
00:52:20 Installing collected packages: pip
00:52:20 Attempting uninstall: pip
00:52:20 Found existing installation: pip 22.3.1
00:52:20 Uninstalling pip-22.3.1:
00:52:20 Successfully uninstalled pip-22.3.1
00:52:21 Successfully installed pip-25.2
00:52:21 WARNING: There was an error checking the latest version of pip.
00:52:21 + 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
00:52:22 Collecting zeroc-ice==3.6.5
00:52:22 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)
00:52:23 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 23.3 MB/s 0:00:01
00:52:24 Installing collected packages: zeroc-ice
00:52:25 Successfully installed zeroc-ice-3.6.5
00:52:25 + pip install markdown
00:52:25 Collecting markdown
00:52:25 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB)
00:52:25 Using cached markdown-3.8.2-py3-none-any.whl (106 kB)
00:52:25 Installing collected packages: markdown
00:52:25 Successfully installed markdown-3.8.2
00:52:25 + pip install reportlab
00:52:26 Collecting reportlab
00:52:26 Using cached reportlab-4.4.3-py3-none-any.whl.metadata (1.7 kB)
00:52:26 Collecting pillow>=9.0.0 (from reportlab)
00:52:26 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:52:26 Collecting charset-normalizer (from reportlab)
00:52:26 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)
00:52:26 Using cached reportlab-4.4.3-py3-none-any.whl (2.0 MB)
00:52:26 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:52:26 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)
00:52:26 Installing collected packages: pillow, charset-normalizer, reportlab
00:52:27
00:52:27 Successfully installed charset-normalizer-3.4.3 pillow-11.3.0 reportlab-4.4.3
00:52:27 + pip install pyarrow
00:52:27 Collecting pyarrow
00:52:28 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
00:52:28 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
00:52:28 Installing collected packages: pyarrow
00:52:29 Successfully installed pyarrow-21.0.0
00:52:29 + pip install omego
00:52:30 Collecting omego
00:52:30 Using cached omego-0.7.0-py3-none-any.whl
00:52:30 Collecting future (from omego)
00:52:30 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:52:30 Collecting yaclifw>=0.1.1 (from omego)
00:52:30 Using cached yaclifw-0.2.0-py3-none-any.whl
00:52:30 Collecting six (from yaclifw>=0.1.1->omego)
00:52:30 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:52:30 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:52:30 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:52:30 Installing collected packages: six, future, yaclifw, omego
00:52:30
00:52:30 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:52:30 + pip install tables
00:52:30 Collecting tables
00:52:30 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:52:31 Collecting numpy>=1.20.0 (from tables)
00:52:31 Using cached numpy-2.3.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
00:52:31 Collecting numexpr>=2.6.2 (from tables)
00:52:31 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:52:31 Collecting packaging (from tables)
00:52:31 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:52:31 Collecting py-cpuinfo (from tables)
00:52:31 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:52:31 Collecting blosc2>=2.3.0 (from tables)
00:52:31 Using cached blosc2-3.7.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
00:52:31 Collecting typing-extensions>=4.4.0 (from tables)
00:52:31 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
00:52:31 Collecting ndindex (from blosc2>=2.3.0->tables)
00:52:31 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:52:31 Collecting msgpack (from blosc2>=2.3.0->tables)
00:52:31 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:52:31 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:52:31 Using cached platformdirs-4.4.0-py3-none-any.whl.metadata (12 kB)
00:52:31 Collecting requests (from blosc2>=2.3.0->tables)
00:52:31 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
00:52:31 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.3)
00:52:31 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:52:31 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:52:31 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:52:31 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
00:52:31 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:52:31 Using cached certifi-2025.8.3-py3-none-any.whl.metadata (2.4 kB)
00:52:31 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:52:31 Using cached blosc2-3.7.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
00:52:31 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB)
00:52:31 Using cached numpy-2.3.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
00:52:31 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
00:52:31 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB)
00:52:31 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:52:31 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:52:31 Using cached platformdirs-4.4.0-py3-none-any.whl (18 kB)
00:52:31 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:52:31 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
00:52:31 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:52:31 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
00:52:31 Using cached certifi-2025.8.3-py3-none-any.whl (161 kB)
00:52:32 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:52:35
00:52:35 Successfully installed blosc2-3.7.2 certifi-2025.8.3 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.11.0 numpy-2.3.2 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
00:52:35 + pip install jinja2
00:52:35 Collecting jinja2
00:52:35 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:52:35 Collecting MarkupSafe>=2.0 (from jinja2)
00:52:35 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:52:35 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:52:35 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
00:52:35 Installing collected packages: MarkupSafe, jinja2
00:52:36
00:52:36 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
00:52:36 + pip install zarr
00:52:36 Collecting zarr
00:52:36 Using cached zarr-3.1.2-py3-none-any.whl.metadata (10 kB)
00:52:36 Collecting donfig>=0.8 (from zarr)
00:52:36 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
00:52:36 Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr)
00:52:36 Using cached numcodecs-0.16.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.3 kB)
00:52:36 Requirement already satisfied: numpy>=1.26 in ./.venv3/lib64/python3.11/site-packages (from zarr) (2.3.2)
00:52:36 Requirement already satisfied: packaging>=22.0 in ./.venv3/lib64/python3.11/site-packages (from zarr) (25.0)
00:52:36 Requirement already satisfied: typing-extensions>=4.9 in ./.venv3/lib64/python3.11/site-packages (from zarr) (4.15.0)
00:52:36 Collecting pyyaml (from donfig>=0.8->zarr)
00:52:36 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:52:36 Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr)
00:52:36 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.metadata (7.3 kB)
00:52:36 Using cached zarr-3.1.2-py3-none-any.whl (261 kB)
00:52:36 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
00:52:36 Using cached numcodecs-0.16.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.8 MB)
00:52:36 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)
00:52:36 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
00:52:36 Installing collected packages: pyyaml, numcodecs, crc32c, donfig, zarr
00:52:37
00:52:37 Successfully installed crc32c-2.7.1 donfig-0.8.1.post1 numcodecs-0.16.2 pyyaml-6.0.2 zarr-3.1.2
00:52:37 + pip install fsspec requests aiohttp s3fs
00:52:37 Collecting fsspec
00:52:37 Using cached fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB)
00:52:37 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (2.32.5)
00:52:38 Collecting aiohttp
00:52:38 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.7 kB)
00:52:38 Collecting s3fs
00:52:38 Using cached s3fs-2025.7.0-py3-none-any.whl.metadata (1.4 kB)
00:52:38 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests) (3.4.3)
00:52:38 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests) (3.10)
00:52:38 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests) (2.5.0)
00:52:38 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests) (2025.8.3)
00:52:38 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp)
00:52:38 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
00:52:38 Collecting aiosignal>=1.4.0 (from aiohttp)
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00:52:38 Collecting attrs>=17.3.0 (from aiohttp)
00:52:38 Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)
00:52:38 Collecting frozenlist>=1.1.1 (from aiohttp)
00:52:38 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.metadata (18 kB)
00:52:39 Collecting multidict<7.0,>=4.5 (from aiohttp)
00:52:39 Using cached multidict-6.6.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
00:52:39 Collecting propcache>=0.2.0 (from aiohttp)
00:52:39 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
00:52:39 Collecting yarl<2.0,>=1.17.0 (from aiohttp)
00:52:39 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB)
00:52:39 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs)
00:52:39 Using cached aiobotocore-2.24.1-py3-none-any.whl.metadata (25 kB)
00:52:39 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:52:39 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
00:52:39 Collecting botocore<1.39.12,>=1.39.9 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:52:39 Using cached botocore-1.39.11-py3-none-any.whl.metadata (5.7 kB)
00:52:39 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:52:40 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:52:40 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:52:40 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
00:52:40 Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:52:40 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)
00:52:40 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)
00:52:40 Requirement already satisfied: typing-extensions>=4.2 in ./.venv3/lib64/python3.11/site-packages (from aiosignal>=1.4.0->aiohttp) (4.15.0)
00:52:40 Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB)
00:52:40 Using cached aiohttp-3.12.15-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB)
00:52:40 Using cached multidict-6.6.4-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
00:52:40 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (348 kB)
00:52:40 Using cached s3fs-2025.7.0-py3-none-any.whl (30 kB)
00:52:40 Using cached aiobotocore-2.24.1-py3-none-any.whl (85 kB)
00:52:40 Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB)
00:52:40 Using cached botocore-1.39.11-py3-none-any.whl (13.9 MB)
00:52:40 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
00:52:40 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:52:40 Using cached wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (82 kB)
00:52:40 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
00:52:40 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
00:52:40 Using cached attrs-25.3.0-py3-none-any.whl (63 kB)
00:52:40 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)
00:52:40 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB)
00:52:40 Installing collected packages: wrapt, python-dateutil, propcache, multidict, jmespath, fsspec, frozenlist, attrs, aioitertools, aiohappyeyeballs, yarl, botocore, aiosignal, aiohttp, aiobotocore, s3fs
00:52:41
00:52:41 Successfully installed aiobotocore-2.24.1 aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aioitertools-0.12.0 aiosignal-1.4.0 attrs-25.3.0 botocore-1.39.11 frozenlist-1.7.0 fsspec-2025.7.0 jmespath-1.0.1 multidict-6.6.4 propcache-0.3.2 python-dateutil-2.9.0.post0 s3fs-2025.7.0 wrapt-1.17.3 yarl-1.20.1
00:52:41 + pip install omero-py
00:52:42 Collecting omero-py
00:52:42 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB)
00:52:42 Collecting urllib3<2 (from omero-py)
00:52:42 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:52:42 Collecting appdirs (from omero-py)
00:52:42 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:52:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:52:42 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.2)
00:52:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
00:52:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.2)
00:52:42 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:52:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
00:52:42 Collecting portalocker (from omero-py)
00:52:42 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:52:42 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.3)
00:52:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
00:52:42 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.8.3)
00:52:42 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB)
00:52:42 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:52:42 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:52:42 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:52:42 Installing collected packages: appdirs, urllib3, portalocker, omero-py
00:52:42 Attempting uninstall: urllib3
00:52:42 Found existing installation: urllib3 2.5.0
00:52:42 Uninstalling urllib3-2.5.0:
00:52:42 Successfully uninstalled urllib3-2.5.0
00:52:44
00:52:44 Successfully installed appdirs-1.4.4 omero-py-5.21.0 portalocker-3.2.0 urllib3-1.26.20
00:52:44 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:52:44 Collecting omero-metadata
00:52:44 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-wwz79crp/omero-metadata_d061ac7e32a0429c8e553277ce860107
00:52:44 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-wwz79crp/omero-metadata_d061ac7e32a0429c8e553277ce860107
00:52:45 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit ed2caaeb65fb81ab50ba28d12c6a493726ed56ce
00:52:45 Installing build dependencies: started
00:52:46 Installing build dependencies: finished with status 'done'
00:52:46 Getting requirements to build wheel: started
00:52:47 Getting requirements to build wheel: finished with status 'done'
00:52:47 Preparing metadata (pyproject.toml): started
00:52:47 Preparing metadata (pyproject.toml): finished with status 'done'
00:52:47 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0)
00:52:47 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
00:52:47 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:52:47 Collecting pandas (from omero-metadata)
00:52:47 Using cached pandas-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB)
00:52:47 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:52:47 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:52:47 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:52:47 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.2)
00:52:47 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)
00:52:47 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)
00:52:47 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
00:52:47 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:52:47 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
00:52:47 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:52:47 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:52:47 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:52:47 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:52:47 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:52:47 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)
00:52:47 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.3)
00:52:47 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)
00:52:47 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.8.3)
00:52:47 Using cached pandas-2.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB)
00:52:47 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:52:47 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:52:47 Building wheels for collected packages: omero-metadata
00:52:47 Building wheel for omero-metadata (pyproject.toml): started
00:52:48 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:52:48 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=44c5a5605150504624d0d5083355a4297ba0550564b60149819d56cf7cf3f2cb
00:52:48 Stored in directory: /tmp/pip-ephem-wheel-cache-wy_62r52/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:52:48 Successfully built omero-metadata
00:52:48 Installing collected packages: pytz, tzdata, pandas, omero-metadata
00:52:52
00:52:52 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.2 pytz-2025.2 tzdata-2025.2
00:52:53 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:52:53 Collecting omero-cli-render
00:52:53 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-9k2ojuy5/omero-cli-render_204f3bd3bd794f8fba54f416180053d4
00:52:53 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-9k2ojuy5/omero-cli-render_204f3bd3bd794f8fba54f416180053d4
00:52:54 Running command git checkout -b merge_ci --track origin/merge_ci
00:52:54 Switched to a new branch 'merge_ci'
00:52:54 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:52:54 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 2226d8c73666ab1417a42a4f14f12a0d80f66144
00:52:54 Installing build dependencies: started
00:52:55 Installing build dependencies: finished with status 'done'
00:52:55 Getting requirements to build wheel: started
00:52:55 Getting requirements to build wheel: finished with status 'done'
00:52:55 Preparing metadata (pyproject.toml): started
00:52:55 Preparing metadata (pyproject.toml): finished with status 'done'
00:52:55 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
00:52:55 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0)
00:52:55 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:52:55 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:52:55 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:52:55 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.2)
00:52:55 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)
00:52:55 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)
00:52:55 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
00:52:55 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:52:55 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)
00:52:55 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)
00:52:55 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.8.3)
00:52:55 Building wheels for collected packages: omero-cli-render
00:52:55 Building wheel for omero-cli-render (pyproject.toml): started
00:52:56 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:52:56 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=6b39365649e84129ed9d8388e39401ab24796fbc810d73f3e6d1fb83a6a04693
00:52:56 Stored in directory: /tmp/pip-ephem-wheel-cache-tzjzvibn/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:52:56 Successfully built omero-cli-render
00:52:56 Installing collected packages: omero-cli-render
00:52:56 Successfully installed omero-cli-render-0.8.2.dev0
00:52:56 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:52:56 Collecting omero-cli-duplicate
00:52:56 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-bbzjzlbl/omero-cli-duplicate_07281101746946d9a129e8d9528c3098
00:52:56 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-bbzjzlbl/omero-cli-duplicate_07281101746946d9a129e8d9528c3098
00:52:57 Running command git checkout -b merge_ci --track origin/merge_ci
00:52:57 Switched to a new branch 'merge_ci'
00:52:57 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:52:57 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 72a06bd1d3c5cfccb19b5d6502add0d0d1287b6d
00:52:57 Installing build dependencies: started
00:52:58 Installing build dependencies: finished with status 'done'
00:52:58 Getting requirements to build wheel: started
00:52:58 Getting requirements to build wheel: finished with status 'done'
00:52:58 Preparing metadata (pyproject.toml): started
00:52:59 Preparing metadata (pyproject.toml): finished with status 'done'
00:52:59 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0)
00:52:59 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:52:59 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:52:59 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:52:59 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.2)
00:52:59 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)
00:52:59 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:52:59 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)
00:52:59 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
00:52:59 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:52:59 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)
00:52:59 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)
00:52:59 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.8.3)
00:52:59 Building wheels for collected packages: omero-cli-duplicate
00:52:59 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:52:59 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:52:59 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=5ad09e1b88c22e799e2eab2422259e18a85422b60bd4ccc007e2b49038e18477
00:52:59 Stored in directory: /tmp/pip-ephem-wheel-cache-zmvch0dl/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:52:59 Successfully built omero-cli-duplicate
00:52:59 Installing collected packages: omero-cli-duplicate
00:52:59 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:52:59 + pip install omero-certificates
00:53:00 Collecting omero-certificates
00:53:00 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:53:00 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0)
00:53:00 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:53:00 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:53:00 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:53:00 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.2)
00:53:00 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)
00:53:00 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:53:00 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
00:53:00 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
00:53:00 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:53:00 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.3)
00:53:00 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
00:53:00 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.8.3)
00:53:00 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:53:00 Installing collected packages: omero-certificates
00:53:00 Successfully installed omero-certificates-0.4.0
00:53:00 + for x in *.tar.gz
00:53:00 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:53:00 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:53:00 Installing build dependencies: started
00:53:01 Installing build dependencies: finished with status 'done'
00:53:01 Getting requirements to build wheel: started
00:53:02 Getting requirements to build wheel: finished with status 'done'
00:53:02 Preparing metadata (pyproject.toml): started
00:53:03 Preparing metadata (pyproject.toml): finished with status 'done'
00:53:03 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0)
00:53:03 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
00:53:03 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:53:03 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:53:03 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.2)
00:53:03 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)
00:53:03 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:53:03 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5)
00:53:03 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
00:53:03 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:53:03 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.3)
00:53:03 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10)
00:53:03 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.8.3)
00:53:03 Building wheels for collected packages: omero-dropbox
00:53:03 Building wheel for omero-dropbox (pyproject.toml): started
00:53:03 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:53:03 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=8d2f6ccbadb158aabc85be4db4ab418b8635e5dbb6661188954121470e12bdab
00:53:03 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:53:03 Successfully built omero-dropbox
00:53:03 Installing collected packages: omero-dropbox
00:53:04 Successfully installed omero-dropbox-5.7.1.dev0
00:53:04 + for x in *.tar.gz
00:53:04 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:53:04 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:53:04 Installing build dependencies: started
00:53:05 Installing build dependencies: finished with status 'done'
00:53:05 Getting requirements to build wheel: started
00:53:05 Getting requirements to build wheel: finished with status 'done'
00:53:05 Preparing metadata (pyproject.toml): started
00:53:05 Preparing metadata (pyproject.toml): finished with status 'done'
00:53:05 Building wheels for collected packages: omero_marshal
00:53:05 Building wheel for omero_marshal (pyproject.toml): started
00:53:06 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:53:06 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=49c2cc9febb4b9760a3888450de2a76df3754c030d929ed5cc9e1fb02b57c3fa
00:53:06 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:53:06 Successfully built omero_marshal
00:53:06 Installing collected packages: omero_marshal
00:53:06 Successfully installed omero_marshal-0.9.1.dev0
00:53:06 + for x in *.tar.gz
00:53:06 + pip install -U omero_py-5.21.1.dev0.tar.gz
00:53:06 Processing ./omero_py-5.21.1.dev0.tar.gz
00:53:07 Installing build dependencies: started
00:53:08 Installing build dependencies: finished with status 'done'
00:53:08 Getting requirements to build wheel: started
00:53:08 Getting requirements to build wheel: finished with status 'done'
00:53:08 Preparing metadata (pyproject.toml): started
00:53:08 Preparing metadata (pyproject.toml): finished with status 'done'
00:53:08 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4)
00:53:08 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0)
00:53:08 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.2)
00:53:08 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0)
00:53:08 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2)
00:53:08 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)
00:53:08 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.5)
00:53:08 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0)
00:53:08 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.4.3)
00:53:08 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10)
00:53:08 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (1.26.20)
00:53:08 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.8.3)
00:53:08 Building wheels for collected packages: omero-py
00:53:08 Building wheel for omero-py (pyproject.toml): started
00:53:09 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:53:09 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783450 sha256=694d0d545a9bc6de9f9c7de7734580a49fb53303804a316eed5ba3af66108a46
00:53:09 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d
00:53:09 Successfully built omero-py
00:53:10 Installing collected packages: omero-py
00:53:10 Attempting uninstall: omero-py
00:53:10 Found existing installation: omero-py 5.21.0
00:53:10 Uninstalling omero-py-5.21.0:
00:53:10 Successfully uninstalled omero-py-5.21.0
00:53:12 Successfully installed omero-py-5.21.1.dev0
00:53:12 + for x in *.tar.gz
00:53:12 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:53:12 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:53:12 Installing build dependencies: started
00:53:13 Installing build dependencies: finished with status 'done'
00:53:13 Getting requirements to build wheel: started
00:53:14 Getting requirements to build wheel: finished with status 'done'
00:53:14 Preparing metadata (pyproject.toml): started
00:53:14 Preparing metadata (pyproject.toml): finished with status 'done'
00:53:14 Building wheels for collected packages: omero-scripts
00:53:14 Building wheel for omero-scripts (pyproject.toml): started
00:53:14 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:53:14 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=8f6338a8a6c6efc9b99edec578da3e5a84655a783a126212b960f63025867f71
00:53:14 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:53:14 Successfully built omero-scripts
00:53:15 Installing collected packages: omero-scripts
00:53:16 Successfully installed omero-scripts-5.9.2.dev0
00:53:16 + for x in *.tar.gz
00:53:16 + pip install -U omero_web-5.29.3.dev0.tar.gz
00:53:16 Processing ./omero_web-5.29.3.dev0.tar.gz
00:53:16 Installing build dependencies: started
00:53:18 Installing build dependencies: finished with status 'done'
00:53:18 Getting requirements to build wheel: started
00:53:18 Getting requirements to build wheel: finished with status 'done'
00:53:18 Preparing metadata (pyproject.toml): started
00:53:18 Preparing metadata (pyproject.toml): finished with status 'done'
00:53:18 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (5.21.1.dev0)
00:53:18 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.3.dev0)
00:53:18 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:53:19 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.3.dev0)
00:53:19 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB)
00:53:19 Collecting django-pipeline (from omero-web==5.29.3.dev0)
00:53:19 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
00:53:19 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.3.dev0)
00:53:19 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:53:19 Collecting django-csp (from omero-web==5.29.3.dev0)
00:53:19 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:53:19 Collecting whitenoise>=5.3.0 (from omero-web==5.29.3.dev0)
00:53:19 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
00:53:19 Collecting gunicorn>=19.3 (from omero-web==5.29.3.dev0)
00:53:19 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:53:19 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)
00:53:19 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (11.3.0)
00:53:19 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (2025.2)
00:53:19 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (3.2.0)
00:53:19 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (25.0)
00:53:19 Collecting importlib-resources (from omero-web==5.29.3.dev0)
00:53:19 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:53:19 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:53:19 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB)
00:53:19 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:53:19 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:53:19 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)
00:53:19 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)
00:53:19 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.3.2)
00:53:19 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (6.0.2)
00:53:19 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)
00:53:19 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)
00:53:19 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.3.dev0) (65.5.1)
00:53:19 Collecting wheel (from django-pipeline->omero-web==5.29.3.dev0)
00:53:19 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:53:19 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)
00:53:19 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)
00:53:19 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) (1.26.20)
00:53:19 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) (2025.8.3)
00:53:19 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:53:19 Using cached django-4.2.23-py3-none-any.whl (8.0 MB)
00:53:19 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB)
00:53:19 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:53:19 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:53:19 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:53:19 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
00:53:19 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:53:19 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
00:53:19 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:53:19 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:53:19 Building wheels for collected packages: omero-web
00:53:19 Building wheel for omero-web (pyproject.toml): started
00:53:20 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:53:20 Created wheel for omero-web: filename=omero_web-5.29.3.dev0-py3-none-any.whl size=2817942 sha256=b2c7d214dd08baba425807ca0a6ea9f313b64f07533dd4a2bbd32583ac3e8d53
00:53:20 Stored in directory: /home/omero/.cache/pip/wheels/22/5c/22/7feca3b3e1a26ce9fb6b16848ce79640a0079788b3a7d5450b
00:53:20 Successfully built omero-web
00:53:20 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:53:23
00:53:23 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-5.29.3.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.9.0
00:53:23 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:53:23 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:53:23 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:53:23 --2025-09-02 00:53:23-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:53:24 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.110.133, ...
00:53:24 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
00:53:24 HTTP request sent, awaiting response... 200 OK
00:53:24 Length: 125081 (122K) [text/plain]
00:53:24 Saving to: ‘Figure_To_Pdf.py’
00:53:24
00:53:24 0K .......... .......... .......... .......... .......... 40% 4.03M 0s
00:53:24 50K .......... .......... .......... .......... .......... 81% 11.7M 0s
00:53:24 100K .......... .......... .. 100% 4.48M=0.02s
00:53:24
00:53:24 2025-09-02 00:53:24 (5.65 MB/s) - ‘Figure_To_Pdf.py’ saved [125081/125081]
00:53:24
00:53:24 + chmod 755 Figure_To_Pdf.py
00:53:24 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:53:24 + omero config set omero.db.name OMERO-server
00:53:25 + omero config set omero.db.host pg
00:53:26 + omero config set omero.db.user postgres
00:53:28 + omero config set omero.data.dir /home/omero/omero-server-data
00:53:29 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:53:30 + omero config set omero.db.poolsize 25
00:53:31 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:53:33 + omero config set omero.security.trustStorePassword changeit
00:53:34 + omero config set omero.mail.config true
00:53:35 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:53:36 + omero config set omero.mail.host smtp.dundee.ac.uk
00:53:38 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:53:39 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:53:40 + omero certificates
00:53:41 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:53:41 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:53:41 + '[' false = true ']'
00:53:41 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:53:41 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:53:41 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG dbcommand => upgrade
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG dbhost => localhost
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG dbname => OMERO-server
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG dbpass => omero
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG dbuser => omero
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG rootpass => omero
00:53:42 2025-09-02 00:53:42,082 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:53:42 2025-09-02 00:53:42,082 [omego.extern] INFO Executing : omero version
00:53:43 OMERO.py version:
00:53:43 OMERO.server version:
00:53:43 5.6.3-574-3465a6037d-ice36-b513
00:53:43 5.21.1.dev0
00:53:43 2025-09-02 00:53:43,371 [omego.extern] INFO Completed [1.288 s]
00:53:43 2025-09-02 00:53:43,371 [omego.extern] DEBUG Using omero CLI from omero
00:53:43 2025-09-02 00:53:43,371 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:53:43 2025-09-02 00:53:43,371 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:53:43 2025-09-02 00:53:43,371 [omego.extern] INFO Executing : omero config get --show-password
00:53:44 2025-09-02 00:53:44,602 [omego.extern] INFO Completed [1.231 s]
00:53:44 2025-09-02 00:53:44,603 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:53:44 2025-09-02 00:53:44,603 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:53:44 2025-09-02 00:53:44,610 [omego.extern] INFO Completed [0.007 s]
00:53:44 2025-09-02 00:53:44,610 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
00:53:44 2025-09-02 00:53:44,610 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
00:53:44
00:53:44 2025-09-02 00:53:44,610 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:53:44 2025-09-02 00:53:44,610 [omego.extern] INFO Executing : omero config get --show-password
00:53:45 2025-09-02 00:53:45,886 [omego.extern] INFO Completed [1.276 s]
00:53:45 2025-09-02 00:53:45,886 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:53:45 2025-09-02 00:53:45,886 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:53:45 2025-09-02 00:53:45,897 [omego.extern] INFO Completed [0.011 s]
00:53:45 2025-09-02 00:53:45,897 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.6") at port "5432".\n'
00:53:45 2025-09-02 00:53:45,898 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:53:45 2025-09-02 00:53:45,898 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:53:45 2025-09-02 00:53:45,898 [omego.extern] INFO Executing : omero config get --show-password
00:53:47 2025-09-02 00:53:47,134 [omego.extern] INFO Completed [1.236 s]
00:53:47 2025-09-02 00:53:47,134 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:53:47 2025-09-02 00:53:47,134 [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
00:53:47 2025-09-02 00:53:47,145 [omego.extern] INFO Completed [0.011 s]
00:53:47 2025-09-02 00:53:47,145 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:53:47 2025-09-02 00:53:47,145 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:53:47 2025-09-02 00:53:47,147 [ omego.db] INFO Database is already at OMERO5.4__0
00:53:47 + export LANG=en_US.UTF-8
00:53:47 + LANG=en_US.UTF-8
00:53:47 + export LANGUAGE=en_US:en
00:53:47 + LANGUAGE=en_US:en
00:53:47 + export LC_ALL=en_US.UTF-8
00:53:47 + LC_ALL=en_US.UTF-8
00:53:47 + BUILD_ID=DONT_KILL_ME
00:53:47 + omero admin start
00:53:52 No descriptor given. Using etc/grid/default.xml
00:54:00 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:54:00 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:54:00 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:54:00 Waiting on startup. Use CTRL-C to exit
00:54:00 + omero admin waitup
00:54:01 Waiting on startup. Use CTRL-C to exit
00:54:01 + omero admin diagnostics
00:54:03
00:54:03 ================================================================================
00:54:03 OMERO Diagnostics (admin)
00:54:03 ================================================================================
00:54:03
00:54:03 Commands: java -version 11.0.25 (/usr/bin/java)
00:54:03 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:54:03 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:54:03 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:54:03 Commands: psql --version 16.9 (/usr/bin/psql)
00:54:03 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:54:03
00:54:03 Component: OMERO.py 5.21.1.dev0
00:54:03 Component: OMERO.server 5.6.3-574-3465a6037d-ice36-b513
00:54:03
00:54:03 Server: icegridnode running
00:54:03 Server: Blitz-0 active (pid = 88927, enabled)
00:54:03 Server: Indexer-0 activating (enabled)
00:54:03 Server: OMERO.Glacier2 active (pid = 88959, enabled)
00:54:03 Server: OMERO.IceStorm active (pid = 88986, enabled)
00:54:03 Server: Processor-0 activating (enabled)
00:54:03 Server: Tables-0 activating (enabled)
00:54:03
00:54:03 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:54:03 Log files: Blitz-0.log 23.8 KB errors=0 warnings=1
00:54:03 Log files: DropBox.log n/a
00:54:03 Log files: FileServer.log n/a
00:54:03 Log files: Indexer-0.log 114 B
00:54:03 Log files: MonitorServer.log n/a
00:54:03 Log files: Processor-0.log 281 B
00:54:03 Log files: Tables-0.log 281 B
00:54:03 Log files: TestDropBox.log n/a
00:54:03 Log files: master.err empty
00:54:03 Log files: master.out 30.5 KB
00:54:03 Log files: Total size 0.06 MB
00:54:03
00:54:03
00:54:03 Environment:OMERO_HOME=(unset)
00:54:03 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:54:03 Environment:OMERO_NODE=(unset)
00:54:03 Environment:OMERO_MASTER=(unset)
00:54:03 Environment:OMERO_USERDIR=(unset)
00:54:03 Environment:OMERO_TMPDIR=(unset)
00:54:03 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
00:54:03 Environment:PYTHONPATH=(unset)
00:54:03 Environment:ICE_HOME=/opt/ice-3.6.5
00:54:03 Environment:LD_LIBRARY_PATH=(unset)
00:54:03 Environment:DYLD_LIBRARY_PATH=(unset)
00:54:03
00:54:03 OMERO SSL port:4064
00:54:03 OMERO TCP port:4063
00:54:03 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:54:03 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:54:03
00:54:03 JVM settings: Blitz-${index} -Xmx7200m
00:54:03 JVM settings: Indexer-${index} -Xmx4800m
00:54:03 JVM settings: PixelData-${index} -Xmx7200m
00:54:03 JVM settings: Repository-${index} -Xmx4800m
00:54:03
00:54:03 Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 2 September 2025 46dcb843af7712e63c6488a9aeba31b6d61873e6
00:54:03 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 2 September 2025 46dcb843af7712e63c6488a9aeba31b6d61873e6
00:54:03 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 2 September 2025 46dcb843af7712e63c6488a9aeba31b6d61873e6
00:54:03 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 2 September 2025 da187e0e1439983a311a4199ef7819f76e1ce038
00:54:03 Jar: lib/server/ome-common.jar OME Common Java 6.1.1-SNAPSHOT 2 September 2025 da187e0e1439983a311a4199ef7819f76e1ce038
00:54:03 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 2 September 2025 da187e0e1439983a311a4199ef7819f76e1ce038
00:54:03 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 2 September 2025 da187e0e1439983a311a4199ef7819f76e1ce038
00:54:03 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 2 September 2025 da187e0e1439983a311a4199ef7819f76e1ce038
00:54:03 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 2 September 2025 da187e0e1439983a311a4199ef7819f76e1ce038
00:54:03 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:54:03 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT 8653db8471e10046545e71b30cc12389080062ad
00:54:03 + deactivate
00:54:03 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:54:03 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:54:03 + export PATH
00:54:03 + unset _OLD_VIRTUAL_PATH
00:54:03 + '[' -n '' ']'
00:54:03 + hash -r
00:54:03 + '[' -n '' ']'
00:54:03 + unset VIRTUAL_ENV
00:54:03 + unset VIRTUAL_ENV_PROMPT
00:54:03 + '[' '!' '' = nondestructive ']'
00:54:03 + unset -f deactivate
00:54:03 Finished: SUCCESS
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