00:48:35 Started by upstream project "Trigger" build number 651
00:48:35 originally caused by:
00:48:35 Started by timer
00:48:35 Running as SYSTEM
00:48:35 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:48:35 [OMERO-server] $ /bin/bash -xe /tmp/jenkins14679225487756136008.sh
00:48:35 + source /home/settings.env
00:48:35 ++ OMERO_DB_HOST=pg
00:48:35 ++ OMERO_DB_USER=postgres
00:48:35 ++ OMERO_DB_PASS=
00:48:35 ++ OMERO_ROOT_PASS=omero
00:48:35 ++ OMERO_DATA_DIR=/OMERO
00:48:35 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:48:35 + OMERO_DB_NAME=OMERO-server
00:48:35 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:48:35 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:35 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:35 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:48:35 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:48:35 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:48:35 ++ deactivate nondestructive
00:48:35 ++ '[' -n '' ']'
00:48:35 ++ '[' -n '' ']'
00:48:35 ++ hash -r
00:48:35 ++ '[' -n '' ']'
00:48:35 ++ unset VIRTUAL_ENV
00:48:35 ++ unset VIRTUAL_ENV_PROMPT
00:48:35 ++ '[' '!' nondestructive = nondestructive ']'
00:48:35 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:48:35 ++ export VIRTUAL_ENV
00:48:35 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:35 ++ 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
00:48:35 ++ export PATH
00:48:35 ++ '[' -n '' ']'
00:48:35 ++ '[' -z '' ']'
00:48:35 ++ _OLD_VIRTUAL_PS1=
00:48:35 ++ PS1='(.venv3) '
00:48:35 ++ export PS1
00:48:35 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:48:35 ++ export VIRTUAL_ENV_PROMPT
00:48:35 ++ hash -r
00:48:35 + omero admin stop
00:48:36 Waiting on shutdown. Use CTRL-C to exit
00:48:36 .+ sleep 5
00:48:51 + deactivate
00:48:51 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:48:51 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:51 + export PATH
00:48:51 + unset _OLD_VIRTUAL_PATH
00:48:51 + '[' -n '' ']'
00:48:51 + hash -r
00:48:51 + '[' -n '' ']'
00:48:51 + unset VIRTUAL_ENV
00:48:51 + unset VIRTUAL_ENV_PROMPT
00:48:51 + '[' '!' '' = nondestructive ']'
00:48:51 + unset -f deactivate
00:48:51 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:48:52 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:48:55 + '[' false = true ']'
00:48:55 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:48:55 Skipping PURGE_DATA:CleanDbAndRepo
00:48:55 + 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-5.21.3.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
00:48:57 Copied 1 artifact from "OMERO-build" build number 547
00:48:57 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 544
00:48:57 Copied 2 artifacts from "OMERO-build-build" build number 578
00:48:57 Copied 1 artifact from "OMERO-zarr-pixel-buffer-build" build number 79
00:48:57 [OMERO-server] $ /bin/bash -xe /tmp/jenkins12984878065598574749.sh
00:48:57 + source /home/settings.env
00:48:57 ++ OMERO_DB_HOST=pg
00:48:57 ++ OMERO_DB_USER=postgres
00:48:57 ++ OMERO_DB_PASS=
00:48:57 ++ OMERO_ROOT_PASS=omero
00:48:57 ++ OMERO_DATA_DIR=/OMERO
00:48:57 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:48:57 + OMERO_DB_NAME=OMERO-server
00:48:57 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:48:57 + mkdir -p /home/omero/omero-server-data
00:48:57 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:48:57 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:57 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:57 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:57 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:57 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:57 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:57 ++ ls OMERO.server-5.6.3-576-6847162daa-ice36-b547.zip
00:48:57 + ZIP=OMERO.server-5.6.3-576-6847162daa-ice36-b547.zip
00:48:57 + '[' '!' -z '' ']'
00:48:57 + DIST=OMERO.server-5.6.3-576-6847162daa-ice36-b547
00:48:57 + unzip OMERO.server-5.6.3-576-6847162daa-ice36-b547.zip
00:48:57 Archive: OMERO.server-5.6.3-576-6847162daa-ice36-b547.zip
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/blitz/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/grid/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/profiles/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/error/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/grid/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/luts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/luts/janelia/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/luts/matplotlib/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/luts/ncsa_paledit/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/luts/seaborn/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/luts/wcif/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/analysis_scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/annotation_scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/export_scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/figure_scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/import_scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/scripts/omero/util_scripts/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/server/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/share/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/share/licenses/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/misc/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__1/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__10/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__11/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__2/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__3/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__4/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__5/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__6/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__7/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__8/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3A__9/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3__4/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3__5/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3__6/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO3__7/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO4.1__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO4.2__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO4.2__0/t/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO4.3__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO4.4__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO4__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.0__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.1__1/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.2__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.3__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4DEV__1/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4DEV__2/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4DEV__3/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4__0/
00:48:57 creating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/var/
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/LICENSE.txt
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/backup.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/blitz/mail-senders.example
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/blitz/mail-server.example
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/build.properties
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/env.bat
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/env.sh
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/hibernate.properties
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/ice.config
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/logback-cli.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/logback-indexing-cli.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/logback-indexing.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/logback.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/mime.types
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/node1.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/node2.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/omero.properties
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/profiles/psql
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/rollover.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/Windows.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/error/maintainance.html
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/grid/README
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/grid/default.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/grid/templates.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/grid/windefault.xml
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/ice.config
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/internal.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/master.cfg
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/templates/robot.template
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/etc/testdropbox.config
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/history.rst
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/OMEZarrReader.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/accessors-smart.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/activation.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/aggdesigner-algorithm.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/aircompressor.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/antlr.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/aopalliance.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/apiguardian-api.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/asm.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/avatica-core.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/avatica-metrics.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/aws-java-sdk-core.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/aws-java-sdk-kms.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/aws-java-sdk-s3.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/base.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-anim.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-awt-util.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-bridge.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-codec.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-constants.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-css.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-dom.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-ext.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-gvt.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-i18n.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-parser.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-script.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-shared-resources.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-svg-dom.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-svggen.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-transcoder.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-util.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/batik-xml.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/btm.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/calcite-core.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/calcite-linq4j.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/cdm-core.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/checker-qual.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/commons-beanutils.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/commons-codec.jar
00:48:57 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/lib/client/commons-collections.jar
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00:48:59 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4__0/psql-footer.sql
00:48:59 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4__0/psql-header.sql
00:48:59 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4__0/schema.sql
00:48:59 inflating: OMERO.server-5.6.3-576-6847162daa-ice36-b547/sql/psql/OMERO5.4__0/views.sql
00:48:59 + rm -f OMERO.server-5.6.3-576-6847162daa-ice36-b547.zip
00:48:59 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-576-6847162daa-ice36-b547 /home/omero/workspace/OMERO-server/OMERO.server
00:48:59 ++ ls omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:48:59 + JAR=omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:48:59 ++ basename omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:48:59 + JAR_NAME=omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:48:59 + mv /home/omero/workspace/OMERO-server/omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar
00:48:59 + 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
00:48:59 --2025-10-13 00:48:59-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:48:59 Resolving repo1.maven.org (repo1.maven.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
00:48:59 Connecting to repo1.maven.org (repo1.maven.org)|104.18.18.12|:443... connected.
00:49:00 HTTP request sent, awaiting response... 200 OK
00:49:00 Length: 889211 (868K) [application/java-archive]
00:49:00 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:49:00
00:49:00 0K .......... .......... .......... .......... .......... 5% 32.0M 0s
00:49:00 50K .......... .......... .......... .......... .......... 11% 5.48M 0s
00:49:00 100K .......... .......... .......... .......... .......... 17% 5.59M 0s
00:49:00 150K .......... .......... .......... .......... .......... 23% 187M 0s
00:49:00 200K .......... .......... .......... .......... .......... 28% 99.0M 0s
00:49:00 250K .......... .......... .......... .......... .......... 34% 161M 0s
00:49:00 300K .......... .......... .......... .......... .......... 40% 90.9M 0s
00:49:00 350K .......... .......... .......... .......... .......... 46% 6.67M 0s
00:49:00 400K .......... .......... .......... .......... .......... 51% 120M 0s
00:49:00 450K .......... .......... .......... .......... .......... 57% 75.6M 0s
00:49:00 500K .......... .......... .......... .......... .......... 63% 106M 0s
00:49:00 550K .......... .......... .......... .......... .......... 69% 191M 0s
00:49:00 600K .......... .......... .......... .......... .......... 74% 6.48M 0s
00:49:00 650K .......... .......... .......... .......... .......... 80% 256M 0s
00:49:00 700K .......... .......... .......... .......... .......... 86% 79.8M 0s
00:49:00 750K .......... .......... .......... .......... .......... 92% 98.4M 0s
00:49:00 800K .......... .......... .......... .......... .......... 97% 150M 0s
00:49:00 850K .......... ........ 100% 385M=0.04s
00:49:00
00:49:00 2025-10-13 00:49:00 (21.7 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:49:00
00:49:00 + 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
00:49:00 --2025-10-13 00:49:00-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:49:00 Resolving repo1.maven.org (repo1.maven.org)... 104.18.19.12, 104.18.18.12, 2606:4700::6812:120c, ...
00:49:00 Connecting to repo1.maven.org (repo1.maven.org)|104.18.19.12|:443... connected.
00:49:00 HTTP request sent, awaiting response... 200 OK
00:49:00 Length: 73309 (72K) [application/java-archive]
00:49:00 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:49:00
00:49:00 0K .......... .......... .......... .......... .......... 69% 34.5M 0s
00:49:00 50K .......... .......... . 100% 2.72M=0.009s
00:49:00
00:49:00 2025-10-13 00:49:00 (7.63 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:49:00
00:49:00 + 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
00:49:00 --2025-10-13 00:49:00-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:49:00 Resolving repo1.maven.org (repo1.maven.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:130c, ...
00:49:00 Connecting to repo1.maven.org (repo1.maven.org)|104.18.18.12|:443... connected.
00:49:00 HTTP request sent, awaiting response... 200 OK
00:49:00 Length: 63303 (62K) [application/java-archive]
00:49:00 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:49:00
00:49:00 0K .......... .......... .......... .......... .......... 80% 30.3M 0s
00:49:00 50K .......... . 100% 167M=0.002s
00:49:00
00:49:00 2025-10-13 00:49:00 (35.9 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:49:00
00:49:00 + 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
00:49:00 --2025-10-13 00:49:00-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:49:00 Resolving repo1.maven.org (repo1.maven.org)... 104.18.18.12, 104.18.19.12, 2606:4700::6812:120c, ...
00:49:00 Connecting to repo1.maven.org (repo1.maven.org)|104.18.18.12|:443... connected.
00:49:00 HTTP request sent, awaiting response... 200 OK
00:49:00 Length: 1271272 (1.2M) [application/java-archive]
00:49:00 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:49:00
00:49:00 0K .......... .......... .......... .......... .......... 4% 33.8M 0s
00:49:00 50K .......... .......... .......... .......... .......... 8% 5.43M 0s
00:49:00 100K .......... .......... .......... .......... .......... 12% 5.99M 0s
00:49:00 150K .......... .......... .......... .......... .......... 16% 62.9M 0s
00:49:00 200K .......... .......... .......... .......... .......... 20% 170M 0s
00:49:00 250K .......... .......... .......... .......... .......... 24% 102M 0s
00:49:00 300K .......... .......... .......... .......... .......... 28% 6.61M 0s
00:49:00 350K .......... .......... .......... .......... .......... 32% 196M 0s
00:49:00 400K .......... .......... .......... .......... .......... 36% 59.6M 0s
00:49:00 450K .......... .......... .......... .......... .......... 40% 158M 0s
00:49:00 500K .......... .......... .......... .......... .......... 44% 94.3M 0s
00:49:00 550K .......... .......... .......... .......... .......... 48% 6.73M 0s
00:49:00 600K .......... .......... .......... .......... .......... 52% 202M 0s
00:49:00 650K .......... .......... .......... .......... .......... 56% 56.6M 0s
00:49:00 700K .......... .......... .......... .......... .......... 60% 177M 0s
00:49:00 750K .......... .......... .......... .......... .......... 64% 111M 0s
00:49:00 800K .......... .......... .......... .......... .......... 68% 6.59M 0s
00:49:00 850K .......... .......... .......... .......... .......... 72% 230M 0s
00:49:00 900K .......... .......... .......... .......... .......... 76% 63.8M 0s
00:49:00 950K .......... .......... .......... .......... .......... 80% 174M 0s
00:49:00 1000K .......... .......... .......... .......... .......... 84% 92.2M 0s
00:49:00 1050K .......... .......... .......... .......... .......... 88% 7.51M 0s
00:49:00 1100K .......... .......... .......... .......... .......... 92% 48.0M 0s
00:49:00 1150K .......... .......... .......... .......... .......... 96% 64.6M 0s
00:49:00 1200K .......... .......... .......... .......... . 100% 151M=0.06s
00:49:00
00:49:00 2025-10-13 00:49:00 (21.6 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:49:00
00:49:00 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:49:00 ++ deactivate nondestructive
00:49:00 ++ '[' -n '' ']'
00:49:00 ++ '[' -n '' ']'
00:49:00 ++ hash -r
00:49:00 ++ '[' -n '' ']'
00:49:00 ++ unset VIRTUAL_ENV
00:49:00 ++ unset VIRTUAL_ENV_PROMPT
00:49:00 ++ '[' '!' nondestructive = nondestructive ']'
00:49:00 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:49:00 ++ export VIRTUAL_ENV
00:49:00 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:49:00 ++ 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
00:49:00 ++ export PATH
00:49:00 ++ '[' -n '' ']'
00:49:00 ++ '[' -z '' ']'
00:49:00 ++ _OLD_VIRTUAL_PS1=
00:49:00 ++ PS1='(.venv3) '
00:49:00 ++ export PS1
00:49:00 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:49:00 ++ export VIRTUAL_ENV_PROMPT
00:49:00 ++ hash -r
00:49:00 + pip install -U pip
00:49:01 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:49:03 Collecting pip
00:49:03 Using cached pip-25.2-py3-none-any.whl (1.8 MB)
00:49:03 Installing collected packages: pip
00:49:03 Attempting uninstall: pip
00:49:03 Found existing installation: pip 22.3.1
00:49:03 Uninstalling pip-22.3.1:
00:49:03 Successfully uninstalled pip-22.3.1
00:49:04 Successfully installed pip-25.2
00:49:04 WARNING: There was an error checking the latest version of pip.
00:49:04 + 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
00:49:05 Collecting zeroc-ice==3.6.5
00:49:05 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)
00:49:07 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 23.3 MB/s 0:00:01
00:49:07 Installing collected packages: zeroc-ice
00:49:08 Successfully installed zeroc-ice-3.6.5
00:49:08 + pip install markdown
00:49:08 Collecting markdown
00:49:08 Using cached markdown-3.9-py3-none-any.whl.metadata (5.1 kB)
00:49:08 Using cached markdown-3.9-py3-none-any.whl (107 kB)
00:49:08 Installing collected packages: markdown
00:49:08 Successfully installed markdown-3.9
00:49:08 + pip install reportlab
00:49:09 Collecting reportlab
00:49:09 Using cached reportlab-4.4.4-py3-none-any.whl.metadata (1.7 kB)
00:49:09 Collecting pillow>=9.0.0 (from reportlab)
00:49:09 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:49:09 Collecting charset-normalizer (from reportlab)
00:49:09 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)
00:49:09 Using cached reportlab-4.4.4-py3-none-any.whl (2.0 MB)
00:49:09 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:49:09 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)
00:49:09 Installing collected packages: pillow, charset-normalizer, reportlab
00:49:10
00:49:10 Successfully installed charset-normalizer-3.4.3 pillow-11.3.0 reportlab-4.4.4
00:49:10 + pip install pyarrow
00:49:10 Collecting pyarrow
00:49:10 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB)
00:49:10 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB)
00:49:11 Installing collected packages: pyarrow
00:49:12 Successfully installed pyarrow-21.0.0
00:49:12 + pip install omego
00:49:12 Collecting omego
00:49:12 Using cached omego-0.7.0-py3-none-any.whl
00:49:12 Collecting future (from omego)
00:49:12 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:49:13 Collecting yaclifw>=0.1.1 (from omego)
00:49:13 Using cached yaclifw-0.2.0-py3-none-any.whl
00:49:13 Collecting six (from yaclifw>=0.1.1->omego)
00:49:13 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:49:13 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:49:13 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:49:13 Installing collected packages: six, future, yaclifw, omego
00:49:13
00:49:13 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:49:13 + pip install tables
00:49:13 Collecting tables
00:49:13 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:49:14 Collecting numpy>=1.20.0 (from tables)
00:49:14 Using cached numpy-2.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
00:49:14 Collecting numexpr>=2.6.2 (from tables)
00:49:14 Using cached numexpr-2.13.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:49:14 Collecting packaging (from tables)
00:49:14 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:49:14 Collecting py-cpuinfo (from tables)
00:49:14 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:49:14 Collecting blosc2>=2.3.0 (from tables)
00:49:14 Using cached blosc2-3.10.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.1 kB)
00:49:14 Collecting typing-extensions>=4.4.0 (from tables)
00:49:14 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
00:49:14 Collecting ndindex (from blosc2>=2.3.0->tables)
00:49:14 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB)
00:49:14 Collecting msgpack (from blosc2>=2.3.0->tables)
00:49:14 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
00:49:14 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:49:14 Using cached platformdirs-4.5.0-py3-none-any.whl.metadata (12 kB)
00:49:14 Collecting requests (from blosc2>=2.3.0->tables)
00:49:14 Using cached requests-2.32.5-py3-none-any.whl.metadata (4.9 kB)
00:49:14 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.3)
00:49:14 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:49:14 Downloading idna-3.11-py3-none-any.whl.metadata (8.4 kB)
00:49:14 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:49:14 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB)
00:49:14 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:49:14 Using cached certifi-2025.10.5-py3-none-any.whl.metadata (2.5 kB)
00:49:14 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:49:14 Using cached blosc2-3.10.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.5 MB)
00:49:14 Using cached numexpr-2.13.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (441 kB)
00:49:14 Using cached numpy-2.3.3-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
00:49:14 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
00:49:14 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB)
00:49:14 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB)
00:49:14 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:49:14 Using cached platformdirs-4.5.0-py3-none-any.whl (18 kB)
00:49:14 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:49:14 Using cached requests-2.32.5-py3-none-any.whl (64 kB)
00:49:14 Downloading idna-3.11-py3-none-any.whl (71 kB)
00:49:14 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB)
00:49:14 Using cached certifi-2025.10.5-py3-none-any.whl (163 kB)
00:49:15 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
00:49:18
00:49:18 Successfully installed blosc2-3.10.0 certifi-2025.10.5 idna-3.11 msgpack-1.1.2 ndindex-1.10.0 numexpr-2.13.1 numpy-2.3.3 packaging-25.0 platformdirs-4.5.0 py-cpuinfo-9.0.0 requests-2.32.5 tables-3.10.2 typing-extensions-4.15.0 urllib3-2.5.0
00:49:18 + pip install jinja2
00:49:18 Collecting jinja2
00:49:18 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:49:18 Collecting MarkupSafe>=2.0 (from jinja2)
00:49:18 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
00:49:18 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:49:18 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
00:49:18 Installing collected packages: MarkupSafe, jinja2
00:49:18
00:49:18 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
00:49:19 + pip install zarr
00:49:19 Collecting zarr
00:49:19 Using cached zarr-3.1.3-py3-none-any.whl.metadata (10 kB)
00:49:19 Collecting donfig>=0.8 (from zarr)
00:49:19 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
00:49:19 Collecting numcodecs>=0.14 (from numcodecs[crc32c]>=0.14->zarr)
00:49:19 Using cached numcodecs-0.16.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.3 kB)
00:49:19 Requirement already satisfied: numpy>=1.26 in ./.venv3/lib64/python3.11/site-packages (from zarr) (2.3.3)
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00:49:20 Collecting pyyaml (from donfig>=0.8->zarr)
00:49:20 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
00:49:20 Collecting crc32c>=2.7 (from numcodecs[crc32c]>=0.14->zarr)
00:49:20 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)
00:49:20 Using cached zarr-3.1.3-py3-none-any.whl (276 kB)
00:49:20 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
00:49:20 Using cached numcodecs-0.16.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.9 MB)
00:49:20 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)
00:49:20 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
00:49:20 Installing collected packages: pyyaml, numcodecs, crc32c, donfig, zarr
00:49:21
00:49:21 Successfully installed crc32c-2.7.1 donfig-0.8.1.post1 numcodecs-0.16.3 pyyaml-6.0.3 zarr-3.1.3
00:49:21 + pip install fsspec requests aiohttp s3fs
00:49:21 Collecting fsspec
00:49:21 Using cached fsspec-2025.9.0-py3-none-any.whl.metadata (10 kB)
00:49:21 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (2.32.5)
00:49:22 Collecting aiohttp
00:49:22 Using cached aiohttp-3.13.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
00:49:22 Collecting s3fs
00:49:22 Using cached s3fs-2025.9.0-py3-none-any.whl.metadata (1.4 kB)
00:49:22 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests) (3.4.3)
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00:49:22 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp)
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00:49:22 Collecting aiosignal>=1.4.0 (from aiohttp)
00:49:22 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
00:49:22 Collecting attrs>=17.3.0 (from aiohttp)
00:49:22 Using cached attrs-25.4.0-py3-none-any.whl.metadata (10 kB)
00:49:22 Collecting frozenlist>=1.1.1 (from aiohttp)
00:49:22 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (20 kB)
00:49:23 Collecting multidict<7.0,>=4.5 (from aiohttp)
00:49:23 Using cached multidict-6.7.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
00:49:23 Collecting propcache>=0.2.0 (from aiohttp)
00:49:23 Using cached propcache-0.4.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)
00:49:23 Collecting yarl<2.0,>=1.17.0 (from aiohttp)
00:49:23 Using cached yarl-1.22.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (75 kB)
00:49:23 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs)
00:49:23 Using cached aiobotocore-2.25.0-py3-none-any.whl.metadata (25 kB)
00:49:23 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:49:23 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB)
00:49:24 Collecting botocore<1.40.50,>=1.40.46 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:49:24 Using cached botocore-1.40.49-py3-none-any.whl.metadata (5.7 kB)
00:49:24 Collecting python-dateutil<3.0.0,>=2.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:49:24 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:49:24 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:49:24 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB)
00:49:24 Collecting wrapt<2.0.0,>=1.10.10 (from aiobotocore<3.0.0,>=2.5.4->s3fs)
00:49:24 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)
00:49:24 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)
00:49:24 Requirement already satisfied: typing-extensions>=4.2 in ./.venv3/lib64/python3.11/site-packages (from aiosignal>=1.4.0->aiohttp) (4.15.0)
00:49:24 Using cached fsspec-2025.9.0-py3-none-any.whl (199 kB)
00:49:24 Using cached aiohttp-3.13.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.7 MB)
00:49:24 Using cached multidict-6.7.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
00:49:24 Using cached yarl-1.22.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (365 kB)
00:49:24 Using cached s3fs-2025.9.0-py3-none-any.whl (30 kB)
00:49:24 Using cached aiobotocore-2.25.0-py3-none-any.whl (86 kB)
00:49:24 Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB)
00:49:24 Using cached botocore-1.40.49-py3-none-any.whl (14.1 MB)
00:49:24 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB)
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00:49:24 Using cached wrapt-1.17.3-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (82 kB)
00:49:24 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
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00:49:24 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (231 kB)
00:49:24 Using cached propcache-0.4.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (210 kB)
00:49:24 Installing collected packages: wrapt, python-dateutil, propcache, multidict, jmespath, fsspec, frozenlist, attrs, aioitertools, aiohappyeyeballs, yarl, botocore, aiosignal, aiohttp, aiobotocore, s3fs
00:49:25
00:49:25 Successfully installed aiobotocore-2.25.0 aiohappyeyeballs-2.6.1 aiohttp-3.13.0 aioitertools-0.12.0 aiosignal-1.4.0 attrs-25.4.0 botocore-1.40.49 frozenlist-1.8.0 fsspec-2025.9.0 jmespath-1.0.1 multidict-6.7.0 propcache-0.4.1 python-dateutil-2.9.0.post0 s3fs-2025.9.0 wrapt-1.17.3 yarl-1.22.0
00:49:25 + pip install omero-py
00:49:26 Collecting omero-py
00:49:26 Using cached omero_py-5.21.2-py3-none-any.whl.metadata (6.5 kB)
00:49:26 Collecting appdirs (from omero-py)
00:49:26 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:49:26 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:49:26 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.3)
00:49:26 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0)
00:49:26 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.3)
00:49:26 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:49:26 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.5)
00:49:26 Collecting portalocker (from omero-py)
00:49:26 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
00:49:26 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.3)
00:49:26 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.11)
00:49:26 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.5.0)
00:49:26 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.10.5)
00:49:26 Using cached omero_py-5.21.2-py3-none-any.whl (2.8 MB)
00:49:26 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:49:26 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
00:49:26 Installing collected packages: appdirs, portalocker, omero-py
00:49:28
00:49:28 Successfully installed appdirs-1.4.4 omero-py-5.21.2 portalocker-3.2.0
00:49:28 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:49:28 Collecting omero-metadata
00:49:28 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-a07x8vw0/omero-metadata_db8d5a23cf4a40e18f36e822e5a2908e
00:49:28 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-a07x8vw0/omero-metadata_db8d5a23cf4a40e18f36e822e5a2908e
00:49:29 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit afb620d43ae56dd1a7f077c343c795440baa9f89
00:49:29 Installing build dependencies: started
00:49:30 Installing build dependencies: finished with status 'done'
00:49:30 Getting requirements to build wheel: started
00:49:30 Getting requirements to build wheel: finished with status 'done'
00:49:30 Preparing metadata (pyproject.toml): started
00:49:30 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:30 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.2)
00:49:30 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
00:49:30 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:49:32 Collecting pandas (from omero-metadata)
00:49:32 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
00:49:32 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:49:32 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:49:32 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.3)
00:49:32 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)
00:49:32 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)
00:49:32 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.5)
00:49:32 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
00:49:32 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
00:49:32 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0)
00:49:32 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:49:32 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:49:32 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:49:32 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:49:32 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)
00:49:32 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)
00:49:32 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.11)
00:49:32 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.5.0)
00:49:32 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.10.5)
00:49:32 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB)
00:49:32 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:49:32 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:49:32 Building wheels for collected packages: omero-metadata
00:49:32 Building wheel for omero-metadata (pyproject.toml): started
00:49:33 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:49:33 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=28e00843e2ec6b2470456a28e55cc2b1bfe488d312e8125bf1e74376428a4e3a
00:49:33 Stored in directory: /tmp/pip-ephem-wheel-cache-u3wsj2l0/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:49:33 Successfully built omero-metadata
00:49:33 Installing collected packages: pytz, tzdata, pandas, omero-metadata
00:49:39
00:49:39 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.3 pytz-2025.2 tzdata-2025.2
00:49:39 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:49:39 Collecting omero-cli-render
00:49:39 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-ghtpyx8e/omero-cli-render_b1441cd1cce74279b6339141684f1765
00:49:39 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-ghtpyx8e/omero-cli-render_b1441cd1cce74279b6339141684f1765
00:49:40 Running command git checkout -b merge_ci --track origin/merge_ci
00:49:41 Switched to a new branch 'merge_ci'
00:49:41 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:49:41 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 63bc63e4858b94569d2515b09bdfe45a17dbd686
00:49:41 Installing build dependencies: started
00:49:41 Installing build dependencies: finished with status 'done'
00:49:41 Getting requirements to build wheel: started
00:49:42 Getting requirements to build wheel: finished with status 'done'
00:49:42 Preparing metadata (pyproject.toml): started
00:49:42 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
00:49:42 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.2)
00:49:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:49:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:49:42 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.3)
00:49:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.3.0)
00:49:42 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)
00:49:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.5)
00:49:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
00:49:42 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)
00:49:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.11)
00:49:42 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.5.0)
00:49:42 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.10.5)
00:49:42 Building wheels for collected packages: omero-cli-render
00:49:42 Building wheel for omero-cli-render (pyproject.toml): started
00:49:42 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:49:42 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=150541a4faed4c970427ceb170a137cc433b4e1222431816a66446c2f182ec71
00:49:42 Stored in directory: /tmp/pip-ephem-wheel-cache-cq2ic623/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:49:42 Successfully built omero-cli-render
00:49:42 Installing collected packages: omero-cli-render
00:49:42 Successfully installed omero-cli-render-0.8.2.dev0
00:49:42 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:49:43 Collecting omero-cli-duplicate
00:49:43 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-6f4nmdki/omero-cli-duplicate_779317460b834e2999003c209912272a
00:49:43 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-6f4nmdki/omero-cli-duplicate_779317460b834e2999003c209912272a
00:49:44 Running command git checkout -b merge_ci --track origin/merge_ci
00:49:44 Switched to a new branch 'merge_ci'
00:49:44 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:49:44 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit efebde715e43b58f45d02afa8b1b6c60d8b27e4c
00:49:44 Installing build dependencies: started
00:49:45 Installing build dependencies: finished with status 'done'
00:49:45 Getting requirements to build wheel: started
00:49:45 Getting requirements to build wheel: finished with status 'done'
00:49:45 Preparing metadata (pyproject.toml): started
00:49:45 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:45 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.2)
00:49:45 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:49:45 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:49:45 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.3)
00:49:45 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.3.0)
00:49:45 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
00:49:45 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)
00:49:45 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.5)
00:49:45 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
00:49:45 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)
00:49:45 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.11)
00:49:45 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.5.0)
00:49:45 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.10.5)
00:49:45 Building wheels for collected packages: omero-cli-duplicate
00:49:45 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:49:45 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:49:45 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=d451a2a57710d785e89151431d0a57e4487b0e799e1517432c7b43a0334497cc
00:49:45 Stored in directory: /tmp/pip-ephem-wheel-cache-xqst3vpc/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:49:45 Successfully built omero-cli-duplicate
00:49:46 Installing collected packages: omero-cli-duplicate
00:49:46 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:49:46 + pip install omero-certificates
00:49:47 Collecting omero-certificates
00:49:47 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:49:47 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.2)
00:49:47 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:49:47 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:49:47 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.3)
00:49:47 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (11.3.0)
00:49:47 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
00:49:47 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
00:49:47 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.5)
00:49:47 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
00:49:47 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)
00:49:47 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.11)
00:49:47 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.5.0)
00:49:47 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.10.5)
00:49:47 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:49:47 Installing collected packages: omero-certificates
00:49:47 Successfully installed omero-certificates-0.4.0
00:49:47 + for x in *.tar.gz
00:49:47 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:49:47 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:49:47 Installing build dependencies: started
00:49:48 Installing build dependencies: finished with status 'done'
00:49:48 Getting requirements to build wheel: started
00:49:48 Getting requirements to build wheel: finished with status 'done'
00:49:48 Preparing metadata (pyproject.toml): started
00:49:49 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:49 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.2)
00:49:49 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:49:49 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:49:49 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.3)
00:49:49 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.3.0)
00:49:49 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
00:49:49 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)
00:49:49 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.5)
00:49:49 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
00:49:49 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)
00:49:49 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.11)
00:49:49 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.5.0)
00:49:49 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.10.5)
00:49:49 Building wheels for collected packages: omero-dropbox
00:49:49 Building wheel for omero-dropbox (pyproject.toml): started
00:49:49 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:49:49 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=e8e5350149b49cccce6d1258938732002cc16d4c3c1f84fcbe147173fa0ba427
00:49:49 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:49:49 Successfully built omero-dropbox
00:49:49 Installing collected packages: omero-dropbox
00:49:49 Successfully installed omero-dropbox-5.7.1.dev0
00:49:49 + for x in *.tar.gz
00:49:49 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:49:49 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:49:49 Installing build dependencies: started
00:49:50 Installing build dependencies: finished with status 'done'
00:49:50 Getting requirements to build wheel: started
00:49:50 Getting requirements to build wheel: finished with status 'done'
00:49:50 Preparing metadata (pyproject.toml): started
00:49:51 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:51 Building wheels for collected packages: omero_marshal
00:49:51 Building wheel for omero_marshal (pyproject.toml): started
00:49:51 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:49:51 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88121 sha256=3862225f3a927787636d65d0a513104501c2742e01c31da07a5794ae6b45a322
00:49:51 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:49:51 Successfully built omero_marshal
00:49:51 Installing collected packages: omero_marshal
00:49:51 Successfully installed omero_marshal-0.9.1.dev0
00:49:51 + for x in *.tar.gz
00:49:51 + pip install -U omero_py-5.21.3.dev0.tar.gz
00:49:52 Processing ./omero_py-5.21.3.dev0.tar.gz
00:49:52 Installing build dependencies: started
00:49:53 Installing build dependencies: finished with status 'done'
00:49:53 Getting requirements to build wheel: started
00:49:53 Getting requirements to build wheel: finished with status 'done'
00:49:53 Preparing metadata (pyproject.toml): started
00:49:53 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:53 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (1.4.4)
00:49:53 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (1.0.0)
00:49:53 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (2.3.3)
00:49:53 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (11.3.0)
00:49:53 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (6.0.3)
00:49:53 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (3.6.5)
00:49:53 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (2.32.5)
00:49:53 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.3.dev0) (3.2.0)
00:49:53 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (3.4.3)
00:49:53 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (3.11)
00:49:53 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (2.5.0)
00:49:53 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.3.dev0) (2025.10.5)
00:49:53 Building wheels for collected packages: omero-py
00:49:53 Building wheel for omero-py (pyproject.toml): started
00:49:54 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:49:54 Created wheel for omero-py: filename=omero_py-5.21.3.dev0-py3-none-any.whl size=2785643 sha256=8f2a4cde7c5c8daddc970c680aa830137b8bf21dd450f90484c7c4f003c8c572
00:49:54 Stored in directory: /home/omero/.cache/pip/wheels/b2/c3/69/7f46e8715cbcb96e4ea5a88612191cc747a1c318af7c8f681c
00:49:54 Successfully built omero-py
00:49:54 Installing collected packages: omero-py
00:49:54 Attempting uninstall: omero-py
00:49:54 Found existing installation: omero-py 5.21.2
00:49:54 Uninstalling omero-py-5.21.2:
00:49:55 Successfully uninstalled omero-py-5.21.2
00:49:57 Successfully installed omero-py-5.21.3.dev0
00:49:57 + for x in *.tar.gz
00:49:57 + pip install -U omero_scripts-5.9.2.dev0.tar.gz
00:49:57 Processing ./omero_scripts-5.9.2.dev0.tar.gz
00:49:57 Installing build dependencies: started
00:49:58 Installing build dependencies: finished with status 'done'
00:49:58 Getting requirements to build wheel: started
00:49:58 Getting requirements to build wheel: finished with status 'done'
00:49:58 Preparing metadata (pyproject.toml): started
00:49:58 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:58 Building wheels for collected packages: omero-scripts
00:49:58 Building wheel for omero-scripts (pyproject.toml): started
00:49:59 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:49:59 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=1a46b0a52de7e501918e30a08338658dc3a5bf8964c375a05d396e0d3701fb8a
00:49:59 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850
00:49:59 Successfully built omero-scripts
00:49:59 Installing collected packages: omero-scripts
00:49:59 Successfully installed omero-scripts-5.9.2.dev0
00:49:59 + for x in *.tar.gz
00:49:59 + pip install -U omero_web-5.29.3.dev0.tar.gz
00:49:59 Processing ./omero_web-5.29.3.dev0.tar.gz
00:50:00 Installing build dependencies: started
00:50:01 Installing build dependencies: finished with status 'done'
00:50:01 Getting requirements to build wheel: started
00:50:01 Getting requirements to build wheel: finished with status 'done'
00:50:01 Preparing metadata (pyproject.toml): started
00:50:01 Preparing metadata (pyproject.toml): finished with status 'done'
00:50:01 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (5.21.3.dev0)
00:50:01 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.3.dev0)
00:50:01 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB)
00:50:01 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.3.dev0)
00:50:01 Using cached django-4.2.25-py3-none-any.whl.metadata (4.2 kB)
00:50:01 Collecting django-pipeline (from omero-web==5.29.3.dev0)
00:50:01 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
00:50:02 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.3.dev0)
00:50:02 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:50:02 Collecting django-csp (from omero-web==5.29.3.dev0)
00:50:02 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:50:02 Collecting whitenoise>=5.3.0 (from omero-web==5.29.3.dev0)
00:50:02 Using cached whitenoise-6.11.0-py3-none-any.whl.metadata (3.7 kB)
00:50:02 Collecting gunicorn>=19.3 (from omero-web==5.29.3.dev0)
00:50:02 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:50:02 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)
00:50:02 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (11.3.0)
00:50:02 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (2025.2)
00:50:02 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (3.2.0)
00:50:02 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.3.dev0) (25.0)
00:50:02 Collecting importlib-resources (from omero-web==5.29.3.dev0)
00:50:02 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:50:02 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:50:02 Using cached asgiref-3.10.0-py3-none-any.whl.metadata (9.3 kB)
00:50:02 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.3.dev0)
00:50:02 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:50:02 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)
00:50:02 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)
00:50:02 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.3.3)
00:50:02 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.3.dev0) (6.0.3)
00:50:02 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)
00:50:02 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)
00:50:02 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.3.dev0) (65.5.1)
00:50:02 Collecting wheel (from django-pipeline->omero-web==5.29.3.dev0)
00:50:02 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:50:02 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)
00:50:02 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) (3.11)
00:50:02 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (2.5.0)
00:50:02 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.3.dev0) (2025.10.5)
00:50:02 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:50:02 Using cached django-4.2.25-py3-none-any.whl (8.0 MB)
00:50:02 Using cached asgiref-3.10.0-py3-none-any.whl (24 kB)
00:50:02 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB)
00:50:02 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:50:02 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:50:02 Using cached whitenoise-6.11.0-py3-none-any.whl (20 kB)
00:50:02 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:50:02 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
00:50:02 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:50:02 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:50:02 Building wheels for collected packages: omero-web
00:50:02 Building wheel for omero-web (pyproject.toml): started
00:50:03 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:50:03 Created wheel for omero-web: filename=omero_web-5.29.3.dev0-py3-none-any.whl size=2818265 sha256=372faeb4cb1d632b04586f4923f41d8cba111b6daf47f120d000f245b2b16fb1
00:50:03 Stored in directory: /home/omero/.cache/pip/wheels/22/5c/22/7feca3b3e1a26ce9fb6b16848ce79640a0079788b3a7d5450b
00:50:03 Successfully built omero-web
00:50:03 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:50:06
00:50:06 Successfully installed Django-4.2.25 asgiref-3.10.0 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.1.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.3.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.11.0
00:50:06 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:50:06 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:50:06 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:50:06 --2025-10-13 00:50:06-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:50:06 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.109.133, 185.199.111.133, ...
00:50:06 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
00:50:06 HTTP request sent, awaiting response... 200 OK
00:50:06 Length: 125361 (122K) [text/plain]
00:50:06 Saving to: ‘Figure_To_Pdf.py’
00:50:06
00:50:06 0K .......... .......... .......... .......... .......... 40% 3.90M 0s
00:50:06 50K .......... .......... .......... .......... .......... 81% 13.4M 0s
00:50:06 100K .......... .......... .. 100% 4.38M=0.02s
00:50:06
00:50:06 2025-10-13 00:50:06 (5.64 MB/s) - ‘Figure_To_Pdf.py’ saved [125361/125361]
00:50:06
00:50:06 + chmod 755 Figure_To_Pdf.py
00:50:06 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:50:06 + omero config set omero.db.name OMERO-server
00:50:07 + omero config set omero.db.host pg
00:50:09 + omero config set omero.db.user postgres
00:50:10 + omero config set omero.data.dir /home/omero/omero-server-data
00:50:11 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:50:12 + omero config set omero.db.poolsize 25
00:50:13 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:50:15 + omero config set omero.security.trustStorePassword changeit
00:50:16 + omero config set omero.mail.config true
00:50:17 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:50:18 + omero config set omero.mail.host smtp.dundee.ac.uk
00:50:19 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:50:21 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:50:22 + omero certificates
00:50:23 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:50:23 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:50:23 + '[' false = true ']'
00:50:23 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:50:23 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:50:23 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:50:23 2025-10-13 00:50:23,804 [ omego.db] DEBUG dbcommand => upgrade
00:50:23 2025-10-13 00:50:23,804 [ omego.db] DEBUG dbhost => localhost
00:50:23 2025-10-13 00:50:23,804 [ omego.db] DEBUG dbname => OMERO-server
00:50:23 2025-10-13 00:50:23,804 [ omego.db] DEBUG dbpass => omero
00:50:23 2025-10-13 00:50:23,805 [ omego.db] DEBUG dbuser => omero
00:50:23 2025-10-13 00:50:23,805 [ omego.db] DEBUG rootpass => omero
00:50:23 2025-10-13 00:50:23,805 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:50:23 2025-10-13 00:50:23,805 [omego.extern] INFO Executing : omero version
00:50:24 OMERO.py version:
00:50:24 OMERO.server version:
00:50:24 5.6.3-576-6847162daa-ice36-b547
00:50:24 5.21.3.dev0
00:50:25 2025-10-13 00:50:25,082 [omego.extern] INFO Completed [1.277 s]
00:50:25 2025-10-13 00:50:25,082 [omego.extern] DEBUG Using omero CLI from omero
00:50:25 2025-10-13 00:50:25,082 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:50:25 2025-10-13 00:50:25,082 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:50:25 2025-10-13 00:50:25,082 [omego.extern] INFO Executing : omero config get --show-password
00:50:26 2025-10-13 00:50:26,286 [omego.extern] INFO Completed [1.204 s]
00:50:26 2025-10-13 00:50:26,286 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:50:26 2025-10-13 00:50:26,286 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:50:26 2025-10-13 00:50:26,292 [omego.extern] INFO Completed [0.005 s]
00:50:26 2025-10-13 00:50:26,292 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n'
00:50:26 2025-10-13 00:50:26,292 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9
00:50:26
00:50:26 2025-10-13 00:50:26,292 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:50:26 2025-10-13 00:50:26,292 [omego.extern] INFO Executing : omero config get --show-password
00:50:27 2025-10-13 00:50:27,503 [omego.extern] INFO Completed [1.212 s]
00:50:27 2025-10-13 00:50:27,504 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:50:27 2025-10-13 00:50:27,504 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:50:27 2025-10-13 00:50:27,512 [omego.extern] INFO Completed [0.009 s]
00:50:27 2025-10-13 00:50:27,512 [ 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'
00:50:27 2025-10-13 00:50:27,512 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:50:27 2025-10-13 00:50:27,512 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:50:27 2025-10-13 00:50:27,512 [omego.extern] INFO Executing : omero config get --show-password
00:50:28 2025-10-13 00:50:28,714 [omego.extern] INFO Completed [1.202 s]
00:50:28 2025-10-13 00:50:28,714 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:50:28 2025-10-13 00:50:28,715 [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
00:50:28 2025-10-13 00:50:28,724 [omego.extern] INFO Completed [0.010 s]
00:50:28 2025-10-13 00:50:28,725 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:50:28 2025-10-13 00:50:28,725 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:50:28 2025-10-13 00:50:28,726 [ omego.db] INFO Database is already at OMERO5.4__0
00:50:28 + export LANG=en_US.UTF-8
00:50:28 + LANG=en_US.UTF-8
00:50:28 + export LANGUAGE=en_US:en
00:50:28 + LANGUAGE=en_US:en
00:50:28 + export LC_ALL=en_US.UTF-8
00:50:28 + LC_ALL=en_US.UTF-8
00:50:28 + BUILD_ID=DONT_KILL_ME
00:50:28 + omero admin start
00:50:33 No descriptor given. Using etc/grid/default.xml
00:50:41 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:50:41 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:50:41 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:50:41 Waiting on startup. Use CTRL-C to exit
00:50:41 + omero admin waitup
00:50:42 Waiting on startup. Use CTRL-C to exit
00:50:42 + omero admin diagnostics
00:50:44
00:50:44 ================================================================================
00:50:44 OMERO Diagnostics (admin)
00:50:44 ================================================================================
00:50:44
00:50:44 Commands: java -version 11.0.25 (/usr/bin/java)
00:50:45 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:50:45 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:50:45 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:50:45 Commands: psql --version 16.9 (/usr/bin/psql)
00:50:45 Commands: openssl version 3.2.24 (/usr/bin/openssl)
00:50:45
00:50:45 Component: OMERO.py 5.21.3.dev0
00:50:45 Component: OMERO.server 5.6.3-576-6847162daa-ice36-b547
00:50:45
00:50:45 Server: icegridnode running
00:50:45 Server: Blitz-0 active (pid = 69904, enabled)
00:50:45 Server: Indexer-0 activating (enabled)
00:50:45 Server: OMERO.Glacier2 active (pid = 69934, enabled)
00:50:45 Server: OMERO.IceStorm active (pid = 69941, enabled)
00:50:45 Server: Processor-0 activating (enabled)
00:50:45 Server: Tables-0 activating (enabled)
00:50:45
00:50:45 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:50:45 Log files: Blitz-0.log 25.6 KB errors=0 warnings=1
00:50:45 Log files: DropBox.log n/a
00:50:45 Log files: FileServer.log n/a
00:50:45 Log files: Indexer-0.log 238 B
00:50:45 Log files: MonitorServer.log n/a
00:50:45 Log files: Processor-0.log 471 B
00:50:45 Log files: Tables-0.log 720 B
00:50:45 Log files: TestDropBox.log n/a
00:50:45 Log files: master.err empty
00:50:45 Log files: master.out 30.5 KB
00:50:45 Log files: Total size 0.06 MB
00:50:45
00:50:45
00:50:45 Environment:OMERO_HOME=(unset)
00:50:45 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:50:45 Environment:OMERO_NODE=(unset)
00:50:45 Environment:OMERO_MASTER=(unset)
00:50:45 Environment:OMERO_USERDIR=(unset)
00:50:45 Environment:OMERO_TMPDIR=(unset)
00:50:45 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
00:50:45 Environment:PYTHONPATH=(unset)
00:50:45 Environment:ICE_HOME=/opt/ice-3.6.5
00:50:45 Environment:LD_LIBRARY_PATH=(unset)
00:50:45 Environment:DYLD_LIBRARY_PATH=(unset)
00:50:45
00:50:45 OMERO SSL port:4064
00:50:45 OMERO TCP port:4063
00:50:45 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:50:45 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:50:45
00:50:45 JVM settings: Blitz-${index} -Xmx7200m
00:50:45 JVM settings: Indexer-${index} -Xmx4800m
00:50:45 JVM settings: PixelData-${index} -Xmx7200m
00:50:45 JVM settings: Repository-${index} -Xmx4800m
00:50:45
00:50:45 Jar: lib/server/formats-api.jar Bio-Formats API 8.4.0-SNAPSHOT 13 October 2025 acd9673f01eb94169e9c2eb184d7c6c00298aa5f
00:50:45 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.4.0-SNAPSHOT 13 October 2025 acd9673f01eb94169e9c2eb184d7c6c00298aa5f
00:50:45 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.4.0-SNAPSHOT 13 October 2025 acd9673f01eb94169e9c2eb184d7c6c00298aa5f
00:50:45 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 13 October 2025 c3cb2a633a687891139021f2cb707f410d51785d
00:50:45 Jar: lib/server/ome-common.jar OME Common Java 6.1.1-SNAPSHOT 13 October 2025 c3cb2a633a687891139021f2cb707f410d51785d
00:50:45 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 13 October 2025 c3cb2a633a687891139021f2cb707f410d51785d
00:50:45 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 13 October 2025 c3cb2a633a687891139021f2cb707f410d51785d
00:50:45 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 13 October 2025 c3cb2a633a687891139021f2cb707f410d51785d
00:50:45 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 13 October 2025 c3cb2a633a687891139021f2cb707f410d51785d
00:50:45 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT
00:50:45 Jar: lib/server/omero-zarr-pixel-buffer-0.6.0-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.6.0-SNAPSHOT e62fdd4f8856e513c9c0e92bc4d2a931ef261755
00:50:45 + deactivate
00:50:45 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:50:45 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:45 + export PATH
00:50:45 + unset _OLD_VIRTUAL_PATH
00:50:45 + '[' -n '' ']'
00:50:45 + hash -r
00:50:45 + '[' -n '' ']'
00:50:45 + unset VIRTUAL_ENV
00:50:45 + unset VIRTUAL_ENV_PROMPT
00:50:45 + '[' '!' '' = nondestructive ']'
00:50:45 + unset -f deactivate
00:50:45 Finished: SUCCESS
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