00:47:46 Started by upstream project "Trigger" build number 497
00:47:46 originally caused by:
00:47:46 Started by timer
00:47:46 Running as SYSTEM
00:47:46 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:47:46 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13254900263368716710.sh
00:47:46 + source /home/settings.env
00:47:46 ++ OMERO_DB_HOST=pg
00:47:46 ++ OMERO_DB_USER=postgres
00:47:46 ++ OMERO_DB_PASS=
00:47:46 ++ OMERO_ROOT_PASS=omero
00:47:46 ++ OMERO_DATA_DIR=/OMERO
00:47:46 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:47:46 + OMERO_DB_NAME=OMERO-server
00:47:46 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:47:46 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:46 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:46 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:47:46 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:47:46 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:47:46 ++ deactivate nondestructive
00:47:46 ++ '[' -n '' ']'
00:47:46 ++ '[' -n '' ']'
00:47:46 ++ hash -r
00:47:46 ++ '[' -n '' ']'
00:47:46 ++ unset VIRTUAL_ENV
00:47:46 ++ unset VIRTUAL_ENV_PROMPT
00:47:46 ++ '[' '!' nondestructive = nondestructive ']'
00:47:46 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:47:46 ++ export VIRTUAL_ENV
00:47:46 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:47:46 ++ 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
00:47:46 ++ export PATH
00:47:46 ++ '[' -n '' ']'
00:47:46 ++ '[' -z '' ']'
00:47:46 ++ _OLD_VIRTUAL_PS1=
00:47:46 ++ PS1='(.venv3) '
00:47:46 ++ export PS1
00:47:46 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:47:46 ++ export VIRTUAL_ENV_PROMPT
00:47:46 ++ hash -r
00:47:46 + omero admin stop
00:47:48 Waiting on shutdown. Use CTRL-C to exit
00:47:48 .+ sleep 5
00:48:03 + deactivate
00:48:03 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:48:03 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:03 + export PATH
00:48:03 + unset _OLD_VIRTUAL_PATH
00:48:03 + '[' -n '' ']'
00:48:03 + hash -r
00:48:03 + '[' -n '' ']'
00:48:03 + unset VIRTUAL_ENV
00:48:03 + unset VIRTUAL_ENV_PROMPT
00:48:03 + '[' '!' '' = nondestructive ']'
00:48:03 + unset -f deactivate
00:48:03 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:48:05 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:48:08 + '[' false = true ']'
00:48:08 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:48:08 Skipping PURGE_DATA:CleanDbAndRepo
00:48:08 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.3-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-5.20.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.29.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:48:10 Copied 1 artifact from "OMERO-build" build number 428
00:48:10 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 420
00:48:10 Copied 2 artifacts from "OMERO-build-build" build number 447
00:48:10 [OMERO-server] $ /bin/bash -xe /tmp/jenkins6815515381346167922.sh
00:48:10 + source /home/settings.env
00:48:10 ++ OMERO_DB_HOST=pg
00:48:10 ++ OMERO_DB_USER=postgres
00:48:10 ++ OMERO_DB_PASS=
00:48:10 ++ OMERO_ROOT_PASS=omero
00:48:10 ++ OMERO_DATA_DIR=/OMERO
00:48:10 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:48:10 + OMERO_DB_NAME=OMERO-server
00:48:10 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:48:10 + mkdir -p /home/omero/omero-server-data
00:48:10 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:48:10 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:10 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:10 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:10 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:10 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:10 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:10 ++ ls OMERO.server-5.6.3-552-09ed98ed70-ice36-b428.zip
00:48:10 + ZIP=OMERO.server-5.6.3-552-09ed98ed70-ice36-b428.zip
00:48:10 + '[' '!' -z '' ']'
00:48:10 + DIST=OMERO.server-5.6.3-552-09ed98ed70-ice36-b428
00:48:10 + unzip OMERO.server-5.6.3-552-09ed98ed70-ice36-b428.zip
00:48:10 Archive: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428.zip
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/blitz/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/grid/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/profiles/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/error/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/grid/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/luts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/luts/janelia/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/luts/matplotlib/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/luts/ncsa_paledit/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/luts/seaborn/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/luts/wcif/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/analysis_scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/annotation_scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/export_scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/figure_scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/import_scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/scripts/omero/util_scripts/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/server/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/share/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/share/licenses/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/misc/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__1/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__10/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__11/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__2/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__3/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__4/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__5/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__6/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__7/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__8/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3A__9/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3__4/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3__5/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3__6/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO3__7/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO4.1__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO4.2__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO4.2__0/t/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO4.3__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO4.4__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO4__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.0__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.1__1/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.2__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.3__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4DEV__1/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4DEV__2/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4DEV__3/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4__0/
00:48:10 creating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/var/
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/LICENSE.txt
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/backup.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/blitz/mail-senders.example
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/blitz/mail-server.example
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/build.properties
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/env.bat
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/env.sh
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/hibernate.properties
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/ice.config
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/logback-cli.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/logback-indexing-cli.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/logback-indexing.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/logback.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/mime.types
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/node1.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/node2.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/omero.properties
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/profiles/psql
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/rollover.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/Windows.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/error/maintainance.html
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/grid/README
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/grid/default.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/grid/templates.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/grid/windefault.xml
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/ice.config
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/internal.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/master.cfg
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/templates/robot.template
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/etc/testdropbox.config
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/history.rst
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/OMEZarrReader.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/accessors-smart.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/activation.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/aggdesigner-algorithm.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/aircompressor.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/antlr.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/aopalliance.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/apiguardian-api.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/asm.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/avatica-core.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/avatica-metrics.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/aws-java-sdk-core.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/aws-java-sdk-kms.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/aws-java-sdk-s3.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/base.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-anim.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-awt-util.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-bridge.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-codec.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-constants.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-css.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-dom.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-ext.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-gvt.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-i18n.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-parser.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-script.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-shared-resources.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-svg-dom.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-svggen.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-transcoder.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-util.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/batik-xml.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/btm.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/calcite-core.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/calcite-linq4j.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/cdm-core.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/checker-qual.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/commons-beanutils.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/commons-codec.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/commons-collections.jar
00:48:10 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/lib/client/commons-collections4.jar
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00:48:12 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4__0/psql-header.sql
00:48:12 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4__0/schema.sql
00:48:12 inflating: OMERO.server-5.6.3-552-09ed98ed70-ice36-b428/sql/psql/OMERO5.4__0/views.sql
00:48:12 + rm -f OMERO.server-5.6.3-552-09ed98ed70-ice36-b428.zip
00:48:12 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-552-09ed98ed70-ice36-b428 /home/omero/workspace/OMERO-server/OMERO.server
00:48:12 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server/ https://artifacts.glencoesoftware.com:443/artifactory/omero-plus/com/glencoesoftware/omero/omero-zarr-pixel-buffer/0.4.1/omero-zarr-pixel-buffer-0.4.1.jar
00:48:12 --2025-05-29 00:48:12-- https://artifacts.glencoesoftware.com/artifactory/omero-plus/com/glencoesoftware/omero/omero-zarr-pixel-buffer/0.4.1/omero-zarr-pixel-buffer-0.4.1.jar
00:48:13 Resolving artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)... 67.205.169.144, 2604:a880:400:d0::19b7:6001
00:48:13 Connecting to artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)|67.205.169.144|:443... connected.
00:48:13 HTTP request sent, awaiting response... 200 OK
00:48:13 Length: 26159 (26K) [application/java-archive]
00:48:13 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’
00:48:13
00:48:13 0K .......... .......... ..... 100% 129M=0s
00:48:13
00:48:13 2025-05-29 00:48:13 (129 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’ saved [26159/26159]
00:48:13
00:48:13 + 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
00:48:13 --2025-05-29 00:48:13-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:48:14 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:14 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:14 HTTP request sent, awaiting response... 200 OK
00:48:14 Length: 889211 (868K) [application/java-archive]
00:48:14 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:48:14
00:48:14 0K .......... .......... .......... .......... .......... 5% 3.98M 0s
00:48:14 50K .......... .......... .......... .......... .......... 11% 9.91M 0s
00:48:14 100K .......... .......... .......... .......... .......... 17% 7.06M 0s
00:48:14 150K .......... .......... .......... .......... .......... 23% 24.9M 0s
00:48:14 200K .......... .......... .......... .......... .......... 28% 8.10M 0s
00:48:14 250K .......... .......... .......... .......... .......... 34% 39.2M 0s
00:48:14 300K .......... .......... .......... .......... .......... 40% 22.3M 0s
00:48:14 350K .......... .......... .......... .......... .......... 46% 28.5M 0s
00:48:14 400K .......... .......... .......... .......... .......... 51% 111M 0s
00:48:14 450K .......... .......... .......... .......... .......... 57% 9.46M 0s
00:48:14 500K .......... .......... .......... .......... .......... 63% 21.0M 0s
00:48:14 550K .......... .......... .......... .......... .......... 69% 37.2M 0s
00:48:14 600K .......... .......... .......... .......... .......... 74% 148M 0s
00:48:14 650K .......... .......... .......... .......... .......... 80% 30.1M 0s
00:48:14 700K .......... .......... .......... .......... .......... 86% 9.59M 0s
00:48:14 750K .......... .......... .......... .......... .......... 92% 20.0M 0s
00:48:14 800K .......... .......... .......... .......... .......... 97% 42.7M 0s
00:48:14 850K .......... ........ 100% 62.7M=0.06s
00:48:14
00:48:14 2025-05-29 00:48:14 (14.8 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:48:14
00:48:14 + 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
00:48:14 --2025-05-29 00:48:14-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:48:14 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:14 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:14 HTTP request sent, awaiting response... 200 OK
00:48:14 Length: 73309 (72K) [application/java-archive]
00:48:14 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:48:14
00:48:14 0K .......... .......... .......... .......... .......... 69% 3.75M 0s
00:48:14 50K .......... .......... . 100% 25.9M=0.01s
00:48:14
00:48:14 2025-05-29 00:48:14 (5.06 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:48:14
00:48:14 + 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
00:48:14 --2025-05-29 00:48:14-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:48:14 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:14 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:14 HTTP request sent, awaiting response... 200 OK
00:48:14 Length: 63303 (62K) [application/java-archive]
00:48:14 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:48:14
00:48:14 0K .......... .......... .......... .......... .......... 80% 4.19M 0s
00:48:14 50K .......... . 100% 11.0M=0.01s
00:48:14
00:48:14 2025-05-29 00:48:14 (4.75 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:48:14
00:48:14 + 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
00:48:14 --2025-05-29 00:48:14-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:48:14 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:48:14 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:48:14 HTTP request sent, awaiting response... 200 OK
00:48:14 Length: 1271272 (1.2M) [application/java-archive]
00:48:14 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:48:14
00:48:14 0K .......... .......... .......... .......... .......... 4% 4.16M 0s
00:48:14 50K .......... .......... .......... .......... .......... 8% 5.30M 0s
00:48:14 100K .......... .......... .......... .......... .......... 12% 20.7M 0s
00:48:14 150K .......... .......... .......... .......... .......... 16% 25.4M 0s
00:48:14 200K .......... .......... .......... .......... .......... 20% 8.05M 0s
00:48:14 250K .......... .......... .......... .......... .......... 24% 31.9M 0s
00:48:14 300K .......... .......... .......... .......... .......... 28% 47.3M 0s
00:48:14 350K .......... .......... .......... .......... .......... 32% 26.5M 0s
00:48:14 400K .......... .......... .......... .......... .......... 36% 32.1M 0s
00:48:14 450K .......... .......... .......... .......... .......... 40% 8.57M 0s
00:48:14 500K .......... .......... .......... .......... .......... 44% 36.3M 0s
00:48:14 550K .......... .......... .......... .......... .......... 48% 109M 0s
00:48:14 600K .......... .......... .......... .......... .......... 52% 31.6M 0s
00:48:14 650K .......... .......... .......... .......... .......... 56% 27.8M 0s
00:48:14 700K .......... .......... .......... .......... .......... 60% 9.28M 0s
00:48:14 750K .......... .......... .......... .......... .......... 64% 28.6M 0s
00:48:14 800K .......... .......... .......... .......... .......... 68% 149M 0s
00:48:14 850K .......... .......... .......... .......... .......... 72% 31.3M 0s
00:48:14 900K .......... .......... .......... .......... .......... 76% 26.6M 0s
00:48:14 950K .......... .......... .......... .......... .......... 80% 9.97M 0s
00:48:14 1000K .......... .......... .......... .......... .......... 84% 70.4M 0s
00:48:14 1050K .......... .......... .......... .......... .......... 88% 31.5M 0s
00:48:14 1100K .......... .......... .......... .......... .......... 92% 32.2M 0s
00:48:14 1150K .......... .......... .......... .......... .......... 96% 25.0M 0s
00:48:14 1200K .......... .......... .......... .......... . 100% 184M=0.07s
00:48:14
00:48:14 2025-05-29 00:48:14 (17.4 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:48:14
00:48:14 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:48:14 ++ deactivate nondestructive
00:48:14 ++ '[' -n '' ']'
00:48:14 ++ '[' -n '' ']'
00:48:14 ++ hash -r
00:48:14 ++ '[' -n '' ']'
00:48:14 ++ unset VIRTUAL_ENV
00:48:14 ++ unset VIRTUAL_ENV_PROMPT
00:48:14 ++ '[' '!' nondestructive = nondestructive ']'
00:48:14 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:48:14 ++ export VIRTUAL_ENV
00:48:14 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:14 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:14 ++ export PATH
00:48:14 ++ '[' -n '' ']'
00:48:14 ++ '[' -z '' ']'
00:48:14 ++ _OLD_VIRTUAL_PS1=
00:48:14 ++ PS1='(.venv3) '
00:48:14 ++ export PS1
00:48:14 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:48:14 ++ export VIRTUAL_ENV_PROMPT
00:48:14 ++ hash -r
00:48:14 + pip install -U pip
00:48:15 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:48:15 Collecting pip
00:48:15 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
00:48:15 Installing collected packages: pip
00:48:15 Attempting uninstall: pip
00:48:15 Found existing installation: pip 22.3.1
00:48:15 Uninstalling pip-22.3.1:
00:48:15 Successfully uninstalled pip-22.3.1
00:48:16 Successfully installed pip-25.1.1
00:48:16 WARNING: There was an error checking the latest version of pip.
00:48:16 + 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
00:48:17 Collecting zeroc-ice==3.6.5
00:48:17 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)
00:48:19 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 23.5 MB/s eta 0:00:00
00:48:19 Installing collected packages: zeroc-ice
00:48:20 Successfully installed zeroc-ice-3.6.5
00:48:20 + pip install markdown
00:48:20 Collecting markdown
00:48:20 Using cached markdown-3.8-py3-none-any.whl.metadata (5.1 kB)
00:48:20 Using cached markdown-3.8-py3-none-any.whl (106 kB)
00:48:20 Installing collected packages: markdown
00:48:20 Successfully installed markdown-3.8
00:48:20 + pip install reportlab
00:48:21 Collecting reportlab
00:48:21 Using cached reportlab-4.4.1-py3-none-any.whl.metadata (1.8 kB)
00:48:21 Collecting pillow>=9.0.0 (from reportlab)
00:48:21 Using cached pillow-11.2.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (8.9 kB)
00:48:21 Collecting chardet (from reportlab)
00:48:21 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
00:48:21 Using cached reportlab-4.4.1-py3-none-any.whl (2.0 MB)
00:48:21 Using cached pillow-11.2.1-cp311-cp311-manylinux_2_28_x86_64.whl (4.6 MB)
00:48:21 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
00:48:21 Installing collected packages: pillow, chardet, reportlab
00:48:22
00:48:22 Successfully installed chardet-5.2.0 pillow-11.2.1 reportlab-4.4.1
00:48:22 + pip install omego
00:48:23 Collecting omego
00:48:23 Using cached omego-0.7.0-py3-none-any.whl
00:48:23 Collecting future (from omego)
00:48:23 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:48:23 Collecting yaclifw>=0.1.1 (from omego)
00:48:23 Using cached yaclifw-0.2.0-py3-none-any.whl
00:48:23 Collecting six (from yaclifw>=0.1.1->omego)
00:48:23 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:48:23 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:48:23 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:48:23 Installing collected packages: six, future, yaclifw, omego
00:48:23
00:48:23 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:48:23 + pip install tables
00:48:24 Collecting tables
00:48:24 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:48:24 Collecting numpy>=1.20.0 (from tables)
00:48:24 Using cached numpy-2.2.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
00:48:24 Collecting numexpr>=2.6.2 (from tables)
00:48:24 Using cached numexpr-2.10.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
00:48:24 Collecting packaging (from tables)
00:48:24 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:48:24 Collecting py-cpuinfo (from tables)
00:48:24 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:48:24 Collecting blosc2>=2.3.0 (from tables)
00:48:24 Using cached blosc2-3.3.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.9 kB)
00:48:24 Collecting typing-extensions>=4.4.0 (from tables)
00:48:24 Using cached typing_extensions-4.13.2-py3-none-any.whl.metadata (3.0 kB)
00:48:24 Collecting ndindex (from blosc2>=2.3.0->tables)
00:48:24 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:48:24 Collecting msgpack (from blosc2>=2.3.0->tables)
00:48:24 Using cached msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:48:24 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:48:24 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
00:48:24 Collecting requests (from blosc2>=2.3.0->tables)
00:48:24 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
00:48:24 Collecting charset-normalizer<4,>=2 (from requests->blosc2>=2.3.0->tables)
00:48:24 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
00:48:24 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:48:24 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:48:24 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:48:24 Using cached urllib3-2.4.0-py3-none-any.whl.metadata (6.5 kB)
00:48:24 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:48:24 Using cached certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB)
00:48:24 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:48:24 Using cached blosc2-3.3.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
00:48:24 Using cached numexpr-2.10.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (398 kB)
00:48:24 Using cached numpy-2.2.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.8 MB)
00:48:24 Using cached typing_extensions-4.13.2-py3-none-any.whl (45 kB)
00:48:24 Using cached msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (403 kB)
00:48:24 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:48:24 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:48:24 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
00:48:24 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:48:24 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
00:48:24 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
00:48:24 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:48:24 Using cached urllib3-2.4.0-py3-none-any.whl (128 kB)
00:48:24 Using cached certifi-2025.4.26-py3-none-any.whl (159 kB)
00:48:25 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, charset-normalizer, certifi, requests, numexpr, blosc2, tables
00:48:28
00:48:28 Successfully installed blosc2-3.3.4 certifi-2025.4.26 charset-normalizer-3.4.2 idna-3.10 msgpack-1.1.0 ndindex-1.10.0 numexpr-2.10.2 numpy-2.2.6 packaging-25.0 platformdirs-4.3.8 py-cpuinfo-9.0.0 requests-2.32.3 tables-3.10.2 typing-extensions-4.13.2 urllib3-2.4.0
00:48:28 + pip install jinja2
00:48:28 Collecting jinja2
00:48:28 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:48:28 Collecting MarkupSafe>=2.0 (from jinja2)
00:48:28 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:48:29 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:48:29 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
00:48:29 Installing collected packages: MarkupSafe, jinja2
00:48:29
00:48:29 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
00:48:29 + pip install omero-py
00:48:29 Collecting omero-py
00:48:29 Using cached omero_py-5.20.0-py3-none-any.whl.metadata (6.5 kB)
00:48:29 Collecting urllib3<2 (from omero-py)
00:48:29 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:48:29 Collecting appdirs (from omero-py)
00:48:29 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:48:29 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:48:29 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.2.6)
00:48:29 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.2.1)
00:48:29 Collecting PyYAML (from omero-py)
00:48:29 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:48:29 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:48:29 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.3)
00:48:29 Collecting portalocker (from omero-py)
00:48:29 Using cached portalocker-3.1.1-py3-none-any.whl.metadata (8.6 kB)
00:48:29 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
00:48:29 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
00:48:29 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.4.26)
00:48:29 Using cached omero_py-5.20.0-py3-none-any.whl (2.8 MB)
00:48:29 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:48:29 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:48:29 Using cached portalocker-3.1.1-py3-none-any.whl (19 kB)
00:48:29 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
00:48:29 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, omero-py
00:48:29 Attempting uninstall: urllib3
00:48:29 Found existing installation: urllib3 2.4.0
00:48:29 Uninstalling urllib3-2.4.0:
00:48:29 Successfully uninstalled urllib3-2.4.0
00:48:31
00:48:31 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 omero-py-5.20.0 portalocker-3.1.1 urllib3-1.26.20
00:48:31 + pip install git+https://github.com/dominikl/omero-cli-zarr.git@extinfo#egg=omero-cli-zarr
00:48:32 Collecting omero-cli-zarr
00:48:32 Cloning https://github.com/dominikl/omero-cli-zarr.git (to revision extinfo) to /tmp/pip-install-j0yiezd8/omero-cli-zarr_8a2afd19d1234435be4ed02d9d8424b1
00:48:32 Running command git clone --filter=blob:none --quiet https://github.com/dominikl/omero-cli-zarr.git /tmp/pip-install-j0yiezd8/omero-cli-zarr_8a2afd19d1234435be4ed02d9d8424b1
00:48:33 Running command git checkout -b extinfo --track origin/extinfo
00:48:33 Switched to a new branch 'extinfo'
00:48:33 branch 'extinfo' set up to track 'origin/extinfo'.
00:48:33 Resolved https://github.com/dominikl/omero-cli-zarr.git to commit 59cc4a191547284fab4f6e16d1f228c10b661821
00:48:33 Installing build dependencies: started
00:48:34 Installing build dependencies: finished with status 'done'
00:48:34 Getting requirements to build wheel: started
00:48:34 Getting requirements to build wheel: finished with status 'done'
00:48:34 Installing backend dependencies: started
00:48:35 Installing backend dependencies: finished with status 'done'
00:48:35 Preparing metadata (pyproject.toml): started
00:48:35 Preparing metadata (pyproject.toml): finished with status 'done'
00:48:35 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.20.0)
00:48:35 Collecting ome-zarr>=0.5.0 (from omero-cli-zarr)
00:48:35 Using cached ome_zarr-0.11.1-py3-none-any.whl.metadata (2.9 kB)
00:48:35 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.5.0->omero-cli-zarr) (2.2.6)
00:48:35 Collecting dask (from ome-zarr>=0.5.0->omero-cli-zarr)
00:48:35 Using cached dask-2025.5.1-py3-none-any.whl.metadata (3.8 kB)
00:48:35 Collecting zarr<3,>=2.8.1 (from ome-zarr>=0.5.0->omero-cli-zarr)
00:48:35 Using cached zarr-2.18.7-py3-none-any.whl.metadata (5.8 kB)
00:48:35 Collecting fsspec!=2021.07.0,!=2023.9.0,>=0.8 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:35 Using cached fsspec-2025.5.1-py3-none-any.whl.metadata (11 kB)
00:48:36 Collecting aiohttp<4 (from ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Downloading aiohttp-3.12.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.6 kB)
00:48:36 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.5.0->omero-cli-zarr) (2.32.3)
00:48:36 Collecting scikit-image (from ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Using cached scikit_image-0.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
00:48:36 Collecting toolz (from ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Using cached toolz-1.0.0-py3-none-any.whl.metadata (5.1 kB)
00:48:36 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
00:48:36 Collecting aiosignal>=1.1.2 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Using cached aiosignal-1.3.2-py2.py3-none-any.whl.metadata (3.8 kB)
00:48:36 Collecting attrs>=17.3.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB)
00:48:36 Collecting frozenlist>=1.1.1 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:36 Using cached frozenlist-1.6.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (16 kB)
00:48:37 Collecting multidict<7.0,>=4.5 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached multidict-6.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.3 kB)
00:48:37 Collecting propcache>=0.2.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached propcache-0.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (10 kB)
00:48:37 Collecting yarl<2.0,>=1.17.0 (from aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached yarl-1.20.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (72 kB)
00:48:37 Requirement already satisfied: idna>=2.0 in ./.venv3/lib64/python3.11/site-packages (from yarl<2.0,>=1.17.0->aiohttp<4->ome-zarr>=0.5.0->omero-cli-zarr) (3.10)
00:48:37 Collecting asciitree (from zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached asciitree-0.3.3-py3-none-any.whl
00:48:37 Collecting fasteners (from zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached fasteners-0.19-py3-none-any.whl.metadata (4.9 kB)
00:48:37 Collecting numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0 (from zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached numcodecs-0.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB)
00:48:37 Collecting deprecated (from numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0->zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB)
00:48:37 Collecting s3fs (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached s3fs-2025.5.1-py3-none-any.whl.metadata (1.9 kB)
00:48:37 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.26.20)
00:48:37 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
00:48:37 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.0.0)
00:48:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (11.2.1)
00:48:37 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (6.0.2)
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00:48:37 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (3.1.1)
00:48:37 Collecting click>=8.1 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB)
00:48:37 Collecting cloudpickle>=3.0.0 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached cloudpickle-3.1.1-py3-none-any.whl.metadata (7.1 kB)
00:48:37 Requirement already satisfied: packaging>=20.0 in ./.venv3/lib64/python3.11/site-packages (from dask->ome-zarr>=0.5.0->omero-cli-zarr) (25.0)
00:48:37 Collecting partd>=1.4.0 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
00:48:37 Collecting importlib_metadata>=4.13.0 (from dask->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached importlib_metadata-8.7.0-py3-none-any.whl.metadata (4.8 kB)
00:48:37 Collecting zipp>=3.20 (from importlib_metadata>=4.13.0->dask->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached zipp-3.22.0-py3-none-any.whl.metadata (3.6 kB)
00:48:37 Collecting locket (from partd>=1.4.0->dask->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:37 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
00:48:38 Collecting wrapt<2,>=1.10 (from deprecated->numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0->zarr<3,>=2.8.1->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 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)
00:48:38 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.5.0->omero-cli-zarr) (3.4.2)
00:48:38 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.5.0->omero-cli-zarr) (2025.4.26)
00:48:38 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached aiobotocore-2.22.0-py3-none-any.whl.metadata (24 kB)
00:48:38 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
00:48:38 Collecting botocore<1.37.4,>=1.37.2 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached botocore-1.37.3-py3-none-any.whl.metadata (5.7 kB)
00:48:38 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:48:38 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
00:48:38 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->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.5.0->omero-cli-zarr) (1.17.0)
00:48:38 Collecting scipy>=1.11.4 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached scipy-1.15.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
00:48:38 Collecting networkx>=3.0 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
00:48:38 Collecting imageio!=2.35.0,>=2.33 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB)
00:48:38 Collecting tifffile>=2022.8.12 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached tifffile-2025.5.26-py3-none-any.whl.metadata (32 kB)
00:48:38 Collecting lazy-loader>=0.4 (from scikit-image->ome-zarr>=0.5.0->omero-cli-zarr)
00:48:38 Using cached lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB)
00:48:38 Using cached ome_zarr-0.11.1-py3-none-any.whl (40 kB)
00:48:39 Downloading aiohttp-3.12.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB)
00:48:39 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.7/1.7 MB 21.3 MB/s eta 0:00:00
00:48:39 Using cached multidict-6.4.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (223 kB)
00:48:39 Using cached yarl-1.20.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (358 kB)
00:48:39 Using cached zarr-2.18.7-py3-none-any.whl (211 kB)
00:48:39 Using cached numcodecs-0.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.9 MB)
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00:48:39 Using cached aiosignal-1.3.2-py2.py3-none-any.whl (7.6 kB)
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00:48:39 Using cached frozenlist-1.6.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (313 kB)
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00:48:39 Using cached fasteners-0.19-py3-none-any.whl (18 kB)
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00:48:39 Using cached scikit_image-0.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.8 MB)
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00:48:39 Using cached tifffile-2025.5.26-py3-none-any.whl (230 kB)
00:48:39 Building wheels for collected packages: omero-cli-zarr
00:48:39 Building wheel for omero-cli-zarr (pyproject.toml): started
00:48:39 Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
00:48:39 Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.0.2.dev451+g59cc4a1-py3-none-any.whl size=30997 sha256=c431c33fc8193e211b6eedb91879f9252579e8f1ca4dddffea53e2280ca84318
00:48:39 Stored in directory: /tmp/pip-ephem-wheel-cache-gb1s40nu/wheels/dd/b9/0c/0415f7fe907b9498563db54fc83efe934b62c0a5e710ef7b23
00:48:39 Successfully built omero-cli-zarr
00:48:39 Installing collected packages: asciitree, zipp, wrapt, toolz, tifffile, scipy, python-dateutil, propcache, networkx, multidict, locket, lazy-loader, jmespath, imageio, fsspec, frozenlist, fasteners, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, yarl, scikit-image, partd, importlib_metadata, deprecated, botocore, aiosignal, numcodecs, dask, aiohttp, zarr, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
00:48:49
00:48:49 Successfully installed aiobotocore-2.22.0 aiohappyeyeballs-2.6.1 aiohttp-3.12.3 aioitertools-0.12.0 aiosignal-1.3.2 asciitree-0.3.3 attrs-25.3.0 botocore-1.37.3 click-8.2.1 cloudpickle-3.1.1 dask-2025.5.1 deprecated-1.2.18 fasteners-0.19 frozenlist-1.6.0 fsspec-2025.5.1 imageio-2.37.0 importlib_metadata-8.7.0 jmespath-1.0.1 lazy-loader-0.4 locket-1.0.0 multidict-6.4.4 networkx-3.4.2 numcodecs-0.15.1 ome-zarr-0.11.1 omero-cli-zarr-0.0.2.dev451+g59cc4a1 partd-1.4.2 propcache-0.3.1 python-dateutil-2.9.0.post0 s3fs-2025.5.1 scikit-image-0.25.2 scipy-1.15.3 tifffile-2025.5.26 toolz-1.0.0 wrapt-1.17.2 yarl-1.20.0 zarr-2.18.7 zipp-3.22.0
00:48:49 + 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-42pg3ahq/omero-metadata_d34c323bbaa54993806449646a95a8e3
00:48:50 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-42pg3ahq/omero-metadata_d34c323bbaa54993806449646a95a8e3
00:48:51 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 5bf2d008f1e3bd780c803fb7e48eac081d75f925
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
00:48:52 Preparing metadata (pyproject.toml): finished with status 'done'
00:48:52 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.20.0)
00:48:52 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
00:48:52 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:48:52 Collecting pandas (from omero-metadata)
00:48:52 Using cached pandas-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
00:48:52 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:48:52 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:48:52 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:48:52 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.2.6)
00:48:52 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (11.2.1)
00:48:52 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)
00:48:52 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
00:48:52 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.1.1)
00:48:52 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
00:48:52 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:48:52 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:48:52 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:48:52 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:48:52 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:48:52 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)
00:48:52 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)
00:48:52 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)
00:48:52 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.4.26)
00:48:52 Using cached pandas-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
00:48:52 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:48:52 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:48:52 Building wheels for collected packages: omero-metadata
00:48:52 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=b57dcbf32cf87f1a6e634d81796a3ff14818e8f459622b78852497d45b8328c8
00:48:53 Stored in directory: /tmp/pip-ephem-wheel-cache-mnon0_ep/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-2.2.3 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-75h87jqd/omero-cli-render_cb03d9b1321a4f509783d67281a1473a
00:48:58 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-75h87jqd/omero-cli-render_cb03d9b1321a4f509783d67281a1473a
00:49:01 Running command git checkout -b merge_ci --track origin/merge_ci
00:49:01 Switched to a new branch 'merge_ci'
00:49:01 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:49:01 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit cf89046175ccbeb579aee2c29c06c778989f7732
00:49:01 Installing build dependencies: started
00:49:02 Installing build dependencies: finished with status 'done'
00:49:02 Getting requirements to build wheel: started
00:49:02 Getting requirements to build wheel: finished with status 'done'
00:49:02 Preparing metadata (pyproject.toml): started
00:49:03 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:03 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
00:49:03 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.20.0)
00:49:03 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:49:03 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:49:03 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:49:03 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.2.6)
00:49:03 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.2.1)
00:49:03 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)
00:49:03 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
00:49:03 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.1.1)
00:49:03 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)
00:49:03 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)
00:49:03 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.4.26)
00:49:03 Building wheels for collected packages: omero-cli-render
00:49:03 Building wheel for omero-cli-render (pyproject.toml): started
00:49:03 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:49:03 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=bb6a1f7b0bfc3fd66549ccb8cef7e78f691737e72150bbae2360c4926c6d2171
00:49:03 Stored in directory: /tmp/pip-ephem-wheel-cache-pxypnwz0/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:49:03 Successfully built omero-cli-render
00:49:03 Installing collected packages: omero-cli-render
00:49:03 Successfully installed omero-cli-render-0.8.2.dev0
00:49:03 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:49:03 Collecting omero-cli-duplicate
00:49:03 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-_4w8bhz_/omero-cli-duplicate_e673127b2d5942778b1544150c20bac4
00:49:03 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-_4w8bhz_/omero-cli-duplicate_e673127b2d5942778b1544150c20bac4
00:49:04 Running command git checkout -b merge_ci --track origin/merge_ci
00:49:05 Switched to a new branch 'merge_ci'
00:49:05 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:49:05 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit c363264a07fe7b8e9596f41fb4e38278f9893e25
00:49:05 Installing build dependencies: started
00:49:05 Installing build dependencies: finished with status 'done'
00:49:05 Getting requirements to build wheel: started
00:49:06 Getting requirements to build wheel: finished with status 'done'
00:49:06 Preparing metadata (pyproject.toml): started
00:49:06 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:06 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.20.0)
00:49:06 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:49:06 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:49:06 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:49:06 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.2.6)
00:49:06 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.2.1)
00:49:06 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:49:06 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)
00:49:06 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
00:49:06 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.1.1)
00:49:06 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)
00:49:06 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)
00:49:06 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.4.26)
00:49:06 Building wheels for collected packages: omero-cli-duplicate
00:49:06 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:49:06 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:49:06 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=a3891fcb87aa6e75a3364d9e50290ac190276911049c3801c7e09ba55175fc18
00:49:06 Stored in directory: /tmp/pip-ephem-wheel-cache-9g08m2g9/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:49:06 Successfully built omero-cli-duplicate
00:49:06 Installing collected packages: omero-cli-duplicate
00:49:06 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:49:06 + pip install omero-certificates
00:49:07 Collecting omero-certificates
00:49:07 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:49:07 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.20.0)
00:49:07 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:49:07 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:49:07 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:49:07 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.2.6)
00:49:07 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (11.2.1)
00:49:07 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:49:07 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)
00:49:07 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
00:49:07 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.1.1)
00:49:07 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)
00:49:07 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)
00:49:07 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.4.26)
00:49:07 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:49:07 Installing collected packages: omero-certificates
00:49:07 Successfully installed omero-certificates-0.4.0
00:49:07 + for x in *.tar.gz
00:49:07 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:49:08 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:49:08 Installing build dependencies: started
00:49:08 Installing build dependencies: finished with status 'done'
00:49:08 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) (5.20.0)
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) (2.2.6)
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) (11.2.1)
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) (2.32.3)
00:49:09 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.1.1)
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) (2025.4.26)
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=819c4a9548f74a1e136575fb3341297be9bc8d4bda6a0f66f1e3aa530d5eef23
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=668d25cfeb3a08ed3d9eddca20331144497f27633e5d881b1da922fdbbf98327
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
00:49:13 Successfully installed omero_marshal-0.9.1.dev0
00:49:13 + for x in *.tar.gz
00:49:13 + pip install -U omero_py-5.20.1.dev0.tar.gz
00:49:13 Processing ./omero_py-5.20.1.dev0.tar.gz
00:49:13 Installing build dependencies: started
00:49:14 Installing build dependencies: finished with status 'done'
00:49:14 Getting requirements to build wheel: started
00:49:15 Getting requirements to build wheel: finished with status 'done'
00:49:15 Preparing metadata (pyproject.toml): started
00:49:15 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:15 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (1.26.20)
00:49:15 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (1.4.4)
00:49:15 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (1.0.0)
00:49:15 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (2.2.6)
00:49:15 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (11.2.1)
00:49:15 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (6.0.2)
00:49:15 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (3.6.5)
00:49:15 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (2.32.3)
00:49:15 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (3.1.1)
00:49:15 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.20.1.dev0) (3.4.2)
00:49:15 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.20.1.dev0) (3.10)
00:49:15 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.20.1.dev0) (2025.4.26)
00:49:15 Building wheels for collected packages: omero-py
00:49:15 Building wheel for omero-py (pyproject.toml): started
00:49:16 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:49:16 Created wheel for omero-py: filename=omero_py-5.20.1.dev0-py3-none-any.whl size=2783385 sha256=db03f149af128bdadc35013e5e726a767a8ac96daa962c03d633b6b156a5253c
00:49:16 Stored in directory: /home/omero/.cache/pip/wheels/32/f0/8b/0c9b8cf4f8a22d20fdbdb6d870eee959c7bb16ef86f85fd19c
00:49:16 Successfully built omero-py
00:49:16 Installing collected packages: omero-py
00:49:16 Attempting uninstall: omero-py
00:49:16 Found existing installation: omero-py 5.20.0
00:49:16 Uninstalling omero-py-5.20.0:
00:49:17 Successfully uninstalled omero-py-5.20.0
00:49:20 Successfully installed omero-py-5.20.1.dev0
00:49:20 + for x in *.tar.gz
00:49:20 + pip install -U omero_scripts-5.9.1.dev0.tar.gz
00:49:20 Processing ./omero_scripts-5.9.1.dev0.tar.gz
00:49:20 Installing build dependencies: started
00:49:21 Installing build dependencies: finished with status 'done'
00:49:21 Getting requirements to build wheel: started
00:49:21 Getting requirements to build wheel: finished with status 'done'
00:49:21 Preparing metadata (pyproject.toml): started
00:49:22 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:22 Building wheels for collected packages: omero-scripts
00:49:22 Building wheel for omero-scripts (pyproject.toml): started
00:49:22 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:49:22 Created wheel for omero-scripts: filename=omero_scripts-5.9.1.dev0-py3-none-any.whl size=136848 sha256=c483783a7e8e0e10f6661621c5aced5d087b9395940ab5d2a5813259ff860bac
00:49:22 Stored in directory: /home/omero/.cache/pip/wheels/5d/64/64/66c19773daf66dee2b16f9ebd49fde08680f277d4fff67beed
00:49:22 Successfully built omero-scripts
00:49:22 Installing collected packages: omero-scripts
00:49:22 Successfully installed omero-scripts-5.9.1.dev0
00:49:22 + for x in *.tar.gz
00:49:22 + pip install -U omero_web-5.29.1.dev0.tar.gz
00:49:23 Processing ./omero_web-5.29.1.dev0.tar.gz
00:49:23 Installing build dependencies: started
00:49:24 Installing build dependencies: finished with status 'done'
00:49:24 Getting requirements to build wheel: started
00:49:24 Getting requirements to build wheel: finished with status 'done'
00:49:24 Preparing metadata (pyproject.toml): started
00:49:25 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:25 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (5.20.1.dev0)
00:49:25 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.1.dev0)
00:49:25 Using cached concurrent_log_handler-0.9.26-py3-none-any.whl.metadata (19 kB)
00:49:25 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.1.dev0)
00:49:25 Using cached django-4.2.21-py3-none-any.whl.metadata (4.2 kB)
00:49:25 Collecting django-pipeline (from omero-web==5.29.1.dev0)
00:49:25 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
00:49:25 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.1.dev0)
00:49:25 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:49:25 Collecting django-csp (from omero-web==5.29.1.dev0)
00:49:25 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:49:25 Collecting whitenoise>=5.3.0 (from omero-web==5.29.1.dev0)
00:49:25 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
00:49:25 Collecting gunicorn>=19.3 (from omero-web==5.29.1.dev0)
00:49:25 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:49:25 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (0.9.1.dev0)
00:49:25 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (11.2.1)
00:49:25 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (2025.2)
00:49:25 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (3.1.1)
00:49:25 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (25.0)
00:49:25 Collecting importlib-resources (from omero-web==5.29.1.dev0)
00:49:25 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:49:25 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.1.dev0)
00:49:25 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
00:49:25 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.1.dev0)
00:49:25 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:49:25 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (1.26.20)
00:49:25 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (1.4.4)
00:49:25 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (1.0.0)
00:49:25 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (2.2.6)
00:49:25 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (6.0.2)
00:49:25 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==5.29.1.dev0) (3.6.5)
00:49:25 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (2.32.3)
00:49:25 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.1.dev0) (65.5.1)
00:49:25 Collecting wheel (from django-pipeline->omero-web==5.29.1.dev0)
00:49:25 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:49:25 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.1.dev0) (3.4.2)
00:49:25 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.1.dev0) (3.10)
00:49:25 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.1.dev0) (2025.4.26)
00:49:25 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:49:25 Using cached django-4.2.21-py3-none-any.whl (8.0 MB)
00:49:25 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
00:49:25 Using cached concurrent_log_handler-0.9.26-py3-none-any.whl (28 kB)
00:49:25 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:49:25 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:49:25 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
00:49:25 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:49:25 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
00:49:25 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:49:25 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:49:25 Building wheels for collected packages: omero-web
00:49:25 Building wheel for omero-web (pyproject.toml): started
00:49:27 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:49:27 Created wheel for omero-web: filename=omero_web-5.29.1.dev0-py3-none-any.whl size=2817989 sha256=52e8de52680ab5800c8c6cdf1d9e6d73c1ce1b8f0e12b0b4dc5603d68dfc3da6
00:49:27 Stored in directory: /home/omero/.cache/pip/wheels/b6/72/73/a29488e9ae7a2242fcfdc532a2c6f9884a34cc378eb261962a
00:49:27 Successfully built omero-web
00:49:27 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:49:30
00:49:30 Successfully installed Django-4.2.21 asgiref-3.8.1 concurrent-log-handler-0.9.26 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-5.29.1.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.9.0
00:49:30 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:49:30 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:49:30 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:49:30 --2025-05-29 00:49:30-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:49:30 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.111.133, ...
00:49:30 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
00:49:30 HTTP request sent, awaiting response... 200 OK
00:49:30 Length: 122144 (119K) [text/plain]
00:49:30 Saving to: ‘Figure_To_Pdf.py’
00:49:30
00:49:30 0K .......... .......... .......... .......... .......... 41% 4.06M 0s
00:49:30 50K .......... .......... .......... .......... .......... 83% 11.5M 0s
00:49:30 100K .......... ......... 100% 3.91M=0.02s
00:49:30
00:49:30 2025-05-29 00:49:30 (5.53 MB/s) - ‘Figure_To_Pdf.py’ saved [122144/122144]
00:49:30
00:49:30 + chmod 755 Figure_To_Pdf.py
00:49:30 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:49:30 + omero config set omero.db.name OMERO-server
00:49:32 + omero config set omero.db.host pg
00:49:33 + omero config set omero.db.user postgres
00:49:35 + omero config set omero.data.dir /home/omero/omero-server-data
00:49:37 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:49:38 + omero config set omero.db.poolsize 25
00:49:40 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:49:42 + omero config set omero.security.trustStorePassword changeit
00:49:43 + omero config set omero.mail.config true
00:49:45 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:49:47 + omero config set omero.mail.host smtp.dundee.ac.uk
00:49:48 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:49:50 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:49:52 + omero certificates
00:49:53 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:49:53 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:49:53 + '[' false = true ']'
00:49:53 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:49:53 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:49:53 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG dbcommand => upgrade
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG dbhost => localhost
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG dbname => OMERO-server
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG dbpass => omero
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG dbuser => omero
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG rootpass => omero
00:49:53 2025-05-29 00:49:53,919 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:49:53 2025-05-29 00:49:53,919 [omego.extern] INFO Executing : omero version
00:49:55 OMERO.py version:
00:49:55 OMERO.server version:
00:49:55 5.6.3-552-09ed98ed70-ice36-b428
00:49:55 5.20.1.dev0
00:49:55 2025-05-29 00:49:55,690 [omego.extern] INFO Completed [1.771 s]
00:49:55 2025-05-29 00:49:55,691 [omego.extern] DEBUG Using omero CLI from omero
00:49:55 2025-05-29 00:49:55,691 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:49:55 2025-05-29 00:49:55,691 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:55 2025-05-29 00:49:55,691 [omego.extern] INFO Executing : omero config get --show-password
00:49:57 2025-05-29 00:49:57,317 [omego.extern] INFO Completed [1.626 s]
00:49:57 2025-05-29 00:49:57,317 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:57 2025-05-29 00:49:57,317 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:49:57 2025-05-29 00:49:57,323 [omego.extern] INFO Completed [0.006 s]
00:49:57 2025-05-29 00:49:57,323 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.8\n'
00:49:57 2025-05-29 00:49:57,323 [ omego.db] INFO psql version: psql (PostgreSQL) 16.8
00:49:57
00:49:57 2025-05-29 00:49:57,323 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:57 2025-05-29 00:49:57,323 [omego.extern] INFO Executing : omero config get --show-password
00:49:58 2025-05-29 00:49:58,943 [omego.extern] INFO Completed [1.619 s]
00:49:58 2025-05-29 00:49:58,943 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:58 2025-05-29 00:49:58,943 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:49:58 2025-05-29 00:49:58,952 [omego.extern] INFO Completed [0.009 s]
00:49:58 2025-05-29 00:49:58,952 [ 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'
00:49:58 2025-05-29 00:49:58,952 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:49:58 2025-05-29 00:49:58,952 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:58 2025-05-29 00:49:58,952 [omego.extern] INFO Executing : omero config get --show-password
00:50:00 2025-05-29 00:50:00,616 [omego.extern] INFO Completed [1.663 s]
00:50:00 2025-05-29 00:50:00,616 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:50:00 2025-05-29 00:50:00,616 [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
00:50:00 2025-05-29 00:50:00,627 [omego.extern] INFO Completed [0.011 s]
00:50:00 2025-05-29 00:50:00,627 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:50:00 2025-05-29 00:50:00,627 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:50:00 2025-05-29 00:50:00,628 [ omego.db] INFO Database is already at OMERO5.4__0
00:50:00 + export LANG=en_US.UTF-8
00:50:00 + LANG=en_US.UTF-8
00:50:00 + export LANGUAGE=en_US:en
00:50:00 + LANGUAGE=en_US:en
00:50:00 + export LC_ALL=en_US.UTF-8
00:50:00 + LC_ALL=en_US.UTF-8
00:50:00 + BUILD_ID=DONT_KILL_ME
00:50:00 + omero admin start
00:50:05 No descriptor given. Using etc/grid/default.xml
00:50:13 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:50:13 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:50:13 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:50:13 Waiting on startup. Use CTRL-C to exit
00:50:13 + omero admin waitup
00:50:15 Waiting on startup. Use CTRL-C to exit
00:50:15 + omero admin diagnostics
00:50:16 WARNING:omero.util.UpgradeCheck:UPGRADE AVAILABLE:<html>
00:50:16 <head><title>503 Service Temporarily Unavailable</title></head>
00:50:16 <body>
00:50:16 <center><h1>503 Service Temporarily Unavailable</h1></center>
00:50:16 <hr><center>nginx/1.28.0</center>
00:50:16 </body>
00:50:16 </html>
00:50:16
00:50:16
00:50:16 ================================================================================
00:50:16 OMERO Diagnostics (admin)
00:50:16 ================================================================================
00:50:16
00:50:16
00:50:16 Commands: java -version 11.0.25 (/usr/bin/java)
00:50:16 Commands: python -V 3.11.9 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:50:16 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:50:16 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:50:16 Commands: psql --version 16.8 (/usr/bin/psql)
00:50:16 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:50:16
00:50:16 Component: OMERO.py 5.20.1.dev0
00:50:16 Component: OMERO.server 5.6.3-552-09ed98ed70-ice36-b428
00:50:16
00:50:16 Server: icegridnode running
00:50:16 Server: Blitz-0 active (pid = 18667, enabled)
00:50:16 Server: Indexer-0 activating (enabled)
00:50:16 Server: OMERO.Glacier2 active (pid = 18694, enabled)
00:50:16 Server: OMERO.IceStorm active (pid = 18711, enabled)
00:50:16 Server: Processor-0 activating (enabled)
00:50:16 Server: Tables-0 activating (enabled)
00:50:16
00:50:16 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:50:16 Log files: Blitz-0.log 24.0 KB errors=1 warnings=0
00:50:16 Log files: DropBox.log n/a
00:50:16 Log files: FileServer.log n/a
00:50:16 Log files: Indexer-0.log 114 B
00:50:16 Log files: MonitorServer.log n/a
00:50:16 Log files: Processor-0.log 281 B
00:50:16 Log files: Tables-0.log 281 B
00:50:16 Log files: TestDropBox.log n/a
00:50:16 Log files: master.err empty
00:50:16 Log files: master.out 30.5 KB
00:50:16 Log files: Total size 0.06 MB
00:50:16
00:50:16
00:50:16 Environment:OMERO_HOME=(unset)
00:50:16 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:50:16 Environment:OMERO_NODE=(unset)
00:50:16 Environment:OMERO_MASTER=(unset)
00:50:16 Environment:OMERO_USERDIR=(unset)
00:50:16 Environment:OMERO_TMPDIR=(unset)
00:50:16 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
00:50:16 Environment:PYTHONPATH=(unset)
00:50:16 Environment:ICE_HOME=/opt/ice-3.6.5
00:50:16 Environment:LD_LIBRARY_PATH=(unset)
00:50:16 Environment:DYLD_LIBRARY_PATH=(unset)
00:50:16
00:50:16 OMERO SSL port:4064
00:50:16 OMERO TCP port:4063
00:50:16 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:50:16 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:50:16
00:50:16 JVM settings: Blitz-${index} -Xmx7200m
00:50:16 JVM settings: Indexer-${index} -Xmx4800m
00:50:16 JVM settings: PixelData-${index} -Xmx7200m
00:50:16 JVM settings: Repository-${index} -Xmx4800m
00:50:16
00:50:16 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 29 May 2025 0be315e8ddc5450d06e91acef3b533a2b61fa23e
00:50:16 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 29 May 2025 0be315e8ddc5450d06e91acef3b533a2b61fa23e
00:50:16 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 29 May 2025 0be315e8ddc5450d06e91acef3b533a2b61fa23e
00:50:16 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.1-SNAPSHOT 29 May 2025 028e4376e32a8d9d05378d3f2ae0e635306e08a3
00:50:16 Jar: lib/server/ome-common.jar OME Common Java 6.0.26-SNAPSHOT 29 May 2025 028e4376e32a8d9d05378d3f2ae0e635306e08a3
00:50:16 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 29 May 2025 028e4376e32a8d9d05378d3f2ae0e635306e08a3
00:50:16 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4-SNAPSHOT 29 May 2025 028e4376e32a8d9d05378d3f2ae0e635306e08a3
00:50:16 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 29 May 2025 028e4376e32a8d9d05378d3f2ae0e635306e08a3
00:50:16 Jar: lib/server/ome-xml.jar OME XML library 6.5.0-SNAPSHOT 29 May 2025 028e4376e32a8d9d05378d3f2ae0e635306e08a3
00:50:17 Jar: lib/server/omero-blitz.jar jar 5.8.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-common.jar jar 5.7.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-gateway.jar jar 5.10.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-model.jar jar 5.7.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-renderer.jar jar 5.6.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-romio.jar jar 5.8.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-server.jar jar 5.7.3-SNAPSHOT
00:50:17 Jar: lib/server/omero-zarr-pixel-buffer-0.4.1.jar OMERO Zarr Pixel Buffer 0.4.1 7c2d45bab0b51137dada7abda144282d6dcc76e1
00:50:17 + deactivate
00:50:17 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:50:17 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:17 + export PATH
00:50:17 + unset _OLD_VIRTUAL_PATH
00:50:17 + '[' -n '' ']'
00:50:17 + hash -r
00:50:17 + '[' -n '' ']'
00:50:17 + unset VIRTUAL_ENV
00:50:17 + unset VIRTUAL_ENV_PROMPT
00:50:17 + '[' '!' '' = nondestructive ']'
00:50:17 + unset -f deactivate
00:50:17 Finished: SUCCESS
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