00:44:49 Started by upstream project "Trigger" build number 563 00:44:49 originally caused by: 00:44:49 Started by timer 00:44:49 Running as SYSTEM 00:44:50 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server 00:44:51 [OMERO-server] $ /bin/bash -xe /tmp/jenkins8769373300787695138.sh 00:44:51 + source /home/settings.env 00:44:51 ++ OMERO_DB_HOST=pg 00:44:51 ++ OMERO_DB_USER=postgres 00:44:51 ++ OMERO_DB_PASS= 00:44:51 ++ OMERO_ROOT_PASS=omero 00:44:51 ++ OMERO_DATA_DIR=/OMERO 00:44:51 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR 00:44:51 + OMERO_DB_NAME=OMERO-server 00:44:51 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server 00:44:51 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:44:51 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:44:51 + OMERO_DATA_DIR=/home/omero/omero-server-data 00:44:51 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']' 00:44:51 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate 00:44:51 ++ deactivate nondestructive 00:44:51 ++ '[' -n '' ']' 00:44:51 ++ '[' -n '' ']' 00:44:51 ++ hash -r 00:44:51 ++ '[' -n '' ']' 00:44:51 ++ unset VIRTUAL_ENV 00:44:51 ++ unset VIRTUAL_ENV_PROMPT 00:44:51 ++ '[' '!' nondestructive = nondestructive ']' 00:44:51 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3 00:44:51 ++ export VIRTUAL_ENV 00:44:51 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:44:51 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:44:51 ++ export PATH 00:44:51 ++ '[' -n '' ']' 00:44:51 ++ '[' -z '' ']' 00:44:51 ++ _OLD_VIRTUAL_PS1= 00:44:51 ++ PS1='(.venv3) ' 00:44:51 ++ export PS1 00:44:51 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' 00:44:51 ++ export VIRTUAL_ENV_PROMPT 00:44:51 ++ hash -r 00:44:51 + omero admin stop 00:45:25 Server not running 00:45:25 + echo not running 00:45:25 not running 00:45:25 + sleep 5 00:45:30 + deactivate 00:45:30 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' 00:45:30 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:45:30 + export PATH 00:45:30 + unset _OLD_VIRTUAL_PATH 00:45:30 + '[' -n '' ']' 00:45:30 + hash -r 00:45:30 + '[' -n '' ']' 00:45:30 + unset VIRTUAL_ENV 00:45:30 + unset VIRTUAL_ENV_PROMPT 00:45:30 + '[' '!' '' = nondestructive ']' 00:45:30 + unset -f deactivate 00:45:30 + rm -rf /home/omero/workspace/OMERO-server/.venv3 00:45:32 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3 00:45:37 + '[' false = true ']' 00:45:37 + echo 'Skipping PURGE_DATA:CleanDbAndRepo' 00:45:37 Skipping PURGE_DATA:CleanDbAndRepo 00:45:37 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.4-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.21.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.29.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT-with-dependencies.jar /home/omero/workspace/OMERO-server/version.properties 00:45:39 Copied 1 artifact from "OMERO-build" build number 476 00:45:39 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 469 00:45:39 Copied 2 artifacts from "OMERO-build-build" build number 499 00:45:40 Copied 2 artifacts from "OMERO-zarr-pixel-buffer-build" build number 9 00:45:40 [OMERO-server] $ /bin/bash -xe /tmp/jenkins12084076507102789926.sh 00:45:40 + source /home/settings.env 00:45:40 ++ OMERO_DB_HOST=pg 00:45:40 ++ OMERO_DB_USER=postgres 00:45:40 ++ OMERO_DB_PASS= 00:45:40 ++ OMERO_ROOT_PASS=omero 00:45:40 ++ OMERO_DATA_DIR=/OMERO 00:45:40 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR 00:45:40 + OMERO_DB_NAME=OMERO-server 00:45:40 + OMERO_DATA_DIR=/home/omero/omero-server-data 00:45:40 + mkdir -p /home/omero/omero-server-data 00:45:40 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server 00:45:40 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:45:40 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:45:40 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip 00:45:40 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip 00:45:40 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties 00:45:40 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties 00:45:40 ++ ls OMERO.server-5.6.3-572-e40f7383aa-ice36-b476.zip 00:45:40 + ZIP=OMERO.server-5.6.3-572-e40f7383aa-ice36-b476.zip 00:45:40 + '[' '!' -z '' ']' 00:45:40 + DIST=OMERO.server-5.6.3-572-e40f7383aa-ice36-b476 00:45:40 + unzip OMERO.server-5.6.3-572-e40f7383aa-ice36-b476.zip 00:45:41 Archive: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476.zip 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/blitz/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/grid/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/profiles/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/error/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/grid/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/luts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/luts/janelia/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/luts/matplotlib/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/luts/ncsa_paledit/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/luts/seaborn/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/luts/wcif/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/analysis_scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/annotation_scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/export_scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/figure_scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/import_scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/scripts/omero/util_scripts/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/server/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/share/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/share/licenses/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/misc/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__1/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__10/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__11/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__2/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__3/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__4/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__5/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__6/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__7/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__8/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__9/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__4/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__5/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__6/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__7/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.1__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.2__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.2__0/t/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.3__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.4__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.0__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.1__1/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.2__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4DEV__1/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4DEV__2/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4DEV__3/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/ 00:45:41 creating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/var/ 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/LICENSE.txt 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/backup.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/blitz/mail-senders.example 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/blitz/mail-server.example 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/build.properties 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/env.bat 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/env.sh 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/hibernate.properties 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/ice.config 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/logback-cli.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/logback-indexing-cli.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/logback-indexing.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/logback.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/mime.types 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/node1.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/node2.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/omero.properties 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/profiles/psql 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/rollover.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/Windows.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/error/maintainance.html 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/grid/README 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/grid/default.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/grid/templates.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/grid/windefault.xml 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/ice.config 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/internal.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/master.cfg 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/templates/robot.template 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/etc/testdropbox.config 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/history.rst 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/OMEZarrReader.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/accessors-smart.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/activation.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/aggdesigner-algorithm.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/aircompressor.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/antlr.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/aopalliance.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/apiguardian-api.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/asm.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/avatica-core.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/avatica-metrics.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/aws-java-sdk-core.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/aws-java-sdk-kms.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/aws-java-sdk-s3.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/base.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-anim.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-awt-util.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-bridge.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-codec.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-constants.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-css.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-dom.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-ext.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-gvt.jar 00:45:41 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/lib/client/batik-i18n.jar 00:45:41 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OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/misc/current.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/misc/enums.py 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__1/OMERO3__7.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__10/OMERO3A__9.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__11/OMERO3A__10.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__11/OMERO3A__5.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__2/OMERO3A__1.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__3/OMERO3A__2.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__3/OMERO3__5.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__4/OMERO3A__3.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__4/OMERO3__5.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__5/OMERO3A__4.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__6/OMERO3A__5.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__7/OMERO3A__6.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__8/OMERO3A__6.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3A__9/OMERO3A__8.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__4/OMERO3__1.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__5/OMERO3__4.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__6/OMERO3__5.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO3__7/OMERO3__6.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.1__0/OMERO4__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.2__0/OMERO4.1__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.3__0/OMERO4.2__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.4__0/OMERO4.1__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4.4__0/OMERO4.3__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO4__0/OMERO3A__11.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.0__0/OMERO4.4__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.1__1/OMERO5.0__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.1__1/OMERO5.1__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.2__0/OMERO5.1__1.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/OMERO5.2__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/delete-ns-orphans.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/OMERO5.3__0.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/OMERO5.3__1.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/psql-footer.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/psql-header.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/schema.sql 00:45:43 inflating: OMERO.server-5.6.3-572-e40f7383aa-ice36-b476/sql/psql/OMERO5.4__0/views.sql 00:45:43 + rm -f OMERO.server-5.6.3-572-e40f7383aa-ice36-b476.zip 00:45:43 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-572-e40f7383aa-ice36-b476 /home/omero/workspace/OMERO-server/OMERO.server 00:45:43 ++ ls omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar omero-zarr-pixel-buffer-0.5.1-SNAPSHOT-with-dependencies.jar 00:45:43 + JAR='omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:45:43 omero-zarr-pixel-buffer-0.5.1-SNAPSHOT-with-dependencies.jar' 00:45:43 ++ basename omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar omero-zarr-pixel-buffer-0.5.1-SNAPSHOT-with-dependencies.jar 00:45:43 + JAR_NAME=omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:45:43 + mv /home/omero/workspace/OMERO-server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar /home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar 00:45:43 + 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 00:45:43 --2025-07-23 00:45:43-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar 00:45:44 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:45:44 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:45:44 HTTP request sent, awaiting response... 200 OK 00:45:44 Length: 889211 (868K) [application/java-archive] 00:45:44 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ 00:45:44 00:45:44 0K .......... .......... .......... .......... .......... 5% 3.84M 0s 00:45:44 50K .......... .......... .......... .......... .......... 11% 5.83M 0s 00:45:44 100K .......... .......... .......... .......... .......... 17% 22.0M 0s 00:45:44 150K .......... .......... .......... .......... .......... 23% 23.5M 0s 00:45:44 200K .......... .......... .......... .......... .......... 28% 8.02M 0s 00:45:44 250K .......... .......... .......... .......... .......... 34% 35.2M 0s 00:45:44 300K .......... .......... .......... .......... .......... 40% 43.7M 0s 00:45:44 350K .......... .......... .......... .......... .......... 46% 26.8M 0s 00:45:44 400K .......... .......... .......... .......... .......... 51% 30.0M 0s 00:45:44 450K .......... .......... .......... .......... .......... 57% 8.95M 0s 00:45:44 500K .......... .......... .......... .......... .......... 63% 33.9M 0s 00:45:44 550K .......... .......... .......... .......... .......... 69% 31.7M 0s 00:45:44 600K .......... .......... .......... .......... .......... 74% 56.6M 0s 00:45:44 650K .......... .......... .......... .......... .......... 80% 36.9M 0s 00:45:44 700K .......... .......... .......... .......... .......... 86% 8.71M 0s 00:45:44 750K .......... .......... .......... .......... .......... 92% 36.2M 0s 00:45:44 800K .......... .......... .......... .......... .......... 97% 32.6M 0s 00:45:44 850K .......... ........ 100% 54.1M=0.06s 00:45:44 00:45:44 2025-07-23 00:45:44 (14.9 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211] 00:45:44 00:45:44 + 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 00:45:44 --2025-07-23 00:45:44-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar 00:45:44 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:45:44 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:45:44 HTTP request sent, awaiting response... 200 OK 00:45:44 Length: 73309 (72K) [application/java-archive] 00:45:44 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ 00:45:44 00:45:44 0K .......... .......... .......... .......... .......... 69% 3.88M 0s 00:45:44 50K .......... .......... . 100% 25.9M=0.01s 00:45:44 00:45:44 2025-07-23 00:45:44 (5.22 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309] 00:45:44 00:45:44 + 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 00:45:44 --2025-07-23 00:45:44-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar 00:45:44 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:45:44 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:45:44 HTTP request sent, awaiting response... 200 OK 00:45:44 Length: 63303 (62K) [application/java-archive] 00:45:44 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ 00:45:44 00:45:44 0K .......... .......... .......... .......... .......... 80% 4.05M 0s 00:45:44 50K .......... . 100% 11.7M=0.01s 00:45:44 00:45:44 2025-07-23 00:45:44 (4.63 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303] 00:45:44 00:45:44 + 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 00:45:44 --2025-07-23 00:45:44-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar 00:45:45 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209 00:45:45 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected. 00:45:45 HTTP request sent, awaiting response... 200 OK 00:45:45 Length: 1271272 (1.2M) [application/java-archive] 00:45:45 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ 00:45:45 00:45:45 0K .......... .......... .......... .......... .......... 4% 3.87M 0s 00:45:45 50K .......... .......... .......... .......... .......... 8% 9.08M 0s 00:45:45 100K .......... .......... .......... .......... .......... 12% 7.92M 0s 00:45:45 150K .......... .......... .......... .......... .......... 16% 28.4M 0s 00:45:45 200K .......... .......... .......... .......... .......... 20% 7.59M 0s 00:45:45 250K .......... .......... .......... .......... .......... 24% 33.2M 0s 00:45:45 300K .......... .......... .......... .......... .......... 28% 27.8M 0s 00:45:45 350K .......... .......... .......... .......... .......... 32% 83.2M 0s 00:45:45 400K .......... .......... .......... .......... .......... 36% 17.0M 0s 00:45:45 450K .......... .......... .......... .......... .......... 40% 11.0M 0s 00:45:45 500K .......... .......... .......... .......... .......... 44% 27.2M 0s 00:45:45 550K .......... .......... .......... .......... .......... 48% 116M 0s 00:45:45 600K .......... .......... .......... .......... .......... 52% 38.7M 0s 00:45:45 650K .......... .......... .......... .......... .......... 56% 16.0M 0s 00:45:45 700K .......... .......... .......... .......... .......... 60% 11.0M 0s 00:45:45 750K .......... .......... .......... .......... .......... 64% 33.5M 0s 00:45:45 800K .......... .......... .......... .......... .......... 68% 37.6M 0s 00:45:45 850K .......... .......... .......... .......... .......... 72% 142M 0s 00:45:45 900K .......... .......... .......... .......... .......... 76% 15.6M 0s 00:45:45 950K .......... .......... .......... .......... .......... 80% 11.3M 0s 00:45:45 1000K .......... .......... .......... .......... .......... 84% 35.9M 0s 00:45:45 1050K .......... .......... .......... .......... .......... 88% 83.0M 0s 00:45:45 1100K .......... .......... .......... .......... .......... 92% 38.1M 0s 00:45:45 1150K .......... .......... .......... .......... .......... 96% 15.9M 0s 00:45:45 1200K .......... .......... .......... .......... . 100% 13.3M=0.07s 00:45:45 00:45:45 2025-07-23 00:45:45 (16.3 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272] 00:45:45 00:45:45 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate 00:45:45 ++ deactivate nondestructive 00:45:45 ++ '[' -n '' ']' 00:45:45 ++ '[' -n '' ']' 00:45:45 ++ hash -r 00:45:45 ++ '[' -n '' ']' 00:45:45 ++ unset VIRTUAL_ENV 00:45:45 ++ unset VIRTUAL_ENV_PROMPT 00:45:45 ++ '[' '!' nondestructive = nondestructive ']' 00:45:45 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3 00:45:45 ++ export VIRTUAL_ENV 00:45:45 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:45:45 ++ 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 00:45:45 ++ export PATH 00:45:45 ++ '[' -n '' ']' 00:45:45 ++ '[' -z '' ']' 00:45:45 ++ _OLD_VIRTUAL_PS1= 00:45:45 ++ PS1='(.venv3) ' 00:45:45 ++ export PS1 00:45:45 ++ VIRTUAL_ENV_PROMPT='(.venv3) ' 00:45:45 ++ export VIRTUAL_ENV_PROMPT 00:45:45 ++ hash -r 00:45:45 + pip install -U pip 00:45:45 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1) 00:45:46 Collecting pip 00:45:46 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB) 00:45:46 Installing collected packages: pip 00:45:46 Attempting uninstall: pip 00:45:46 Found existing installation: pip 22.3.1 00:45:46 Uninstalling pip-22.3.1: 00:45:46 Successfully uninstalled pip-22.3.1 00:45:47 Successfully installed pip-25.1.1 00:45:47 WARNING: There was an error checking the latest version of pip. 00:45:47 + 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 00:45:48 Collecting zeroc-ice==3.6.5 00:45:48 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) 00:45:50 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 23.3 MB/s eta 0:00:00 00:45:50 Installing collected packages: zeroc-ice 00:45:50 Successfully installed zeroc-ice-3.6.5 00:45:51 + pip install markdown 00:45:51 Collecting markdown 00:45:51 Using cached markdown-3.8.2-py3-none-any.whl.metadata (5.1 kB) 00:45:51 Using cached markdown-3.8.2-py3-none-any.whl (106 kB) 00:45:51 Installing collected packages: markdown 00:45:51 Successfully installed markdown-3.8.2 00:45:51 + pip install reportlab 00:45:52 Collecting reportlab 00:45:52 Using cached reportlab-4.4.2-py3-none-any.whl.metadata (1.8 kB) 00:45:52 Collecting pillow>=9.0.0 (from reportlab) 00:45:52 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) 00:45:52 Collecting charset-normalizer (from reportlab) 00:45:52 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB) 00:45:52 Using cached reportlab-4.4.2-py3-none-any.whl (2.0 MB) 00:45:52 Using cached pillow-11.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB) 00:45:52 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB) 00:45:52 Installing collected packages: pillow, charset-normalizer, reportlab 00:45:53 00:45:53 Successfully installed charset-normalizer-3.4.2 pillow-11.3.0 reportlab-4.4.2 00:45:53 + pip install pyarrow 00:45:54 Collecting pyarrow 00:45:54 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.3 kB) 00:45:54 Using cached pyarrow-21.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (42.8 MB) 00:45:54 Installing collected packages: pyarrow 00:45:56 Successfully installed pyarrow-21.0.0 00:45:56 + pip install omego 00:45:56 Collecting omego 00:45:56 Using cached omego-0.7.0-py3-none-any.whl 00:45:56 Collecting future (from omego) 00:45:56 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) 00:45:56 Collecting yaclifw>=0.1.1 (from omego) 00:45:56 Using cached yaclifw-0.2.0-py3-none-any.whl 00:45:56 Collecting six (from yaclifw>=0.1.1->omego) 00:45:56 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) 00:45:56 Using cached future-1.0.0-py3-none-any.whl (491 kB) 00:45:57 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) 00:45:57 Installing collected packages: six, future, yaclifw, omego 00:45:57 00:45:57 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0 00:45:57 + pip install tables 00:45:57 Collecting tables 00:45:57 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB) 00:45:58 Collecting numpy>=1.20.0 (from tables) 00:45:58 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (62 kB) 00:45:58 Collecting numexpr>=2.6.2 (from tables) 00:45:58 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) 00:45:58 Collecting packaging (from tables) 00:45:58 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB) 00:45:58 Collecting py-cpuinfo (from tables) 00:45:58 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes) 00:45:58 Collecting blosc2>=2.3.0 (from tables) 00:45:58 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (7.0 kB) 00:45:58 Collecting typing-extensions>=4.4.0 (from tables) 00:45:58 Using cached typing_extensions-4.14.1-py3-none-any.whl.metadata (3.0 kB) 00:45:59 Collecting ndindex (from blosc2>=2.3.0->tables) 00:45:59 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.6 kB) 00:45:59 Collecting msgpack (from blosc2>=2.3.0->tables) 00:45:59 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB) 00:45:59 Collecting platformdirs (from blosc2>=2.3.0->tables) 00:45:59 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB) 00:45:59 Collecting requests (from blosc2>=2.3.0->tables) 00:45:59 Using cached requests-2.32.4-py3-none-any.whl.metadata (4.9 kB) 00:45:59 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.2) 00:45:59 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables) 00:45:59 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) 00:45:59 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables) 00:45:59 Using cached urllib3-2.5.0-py3-none-any.whl.metadata (6.5 kB) 00:45:59 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables) 00:45:59 Using cached certifi-2025.7.14-py3-none-any.whl.metadata (2.4 kB) 00:45:59 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB) 00:46:00 Using cached blosc2-3.6.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (4.4 MB) 00:46:00 Using cached numexpr-2.11.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (401 kB) 00:46:00 Using cached numpy-2.3.1-cp311-cp311-manylinux_2_28_x86_64.whl (16.9 MB) 00:46:00 Using cached typing_extensions-4.14.1-py3-none-any.whl (43 kB) 00:46:00 Using cached msgpack-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (429 kB) 00:46:00 Using cached ndindex-1.10.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (528 kB) 00:46:00 Using cached packaging-25.0-py3-none-any.whl (66 kB) 00:46:00 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB) 00:46:00 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB) 00:46:00 Using cached requests-2.32.4-py3-none-any.whl (64 kB) 00:46:00 Using cached idna-3.10-py3-none-any.whl (70 kB) 00:46:01 Using cached urllib3-2.5.0-py3-none-any.whl (129 kB) 00:46:01 Using cached certifi-2025.7.14-py3-none-any.whl (162 kB) 00:46:01 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables 00:46:04 00:46:04 Successfully installed blosc2-3.6.1 certifi-2025.7.14 idna-3.10 msgpack-1.1.1 ndindex-1.10.0 numexpr-2.11.0 numpy-2.3.1 packaging-25.0 platformdirs-4.3.8 py-cpuinfo-9.0.0 requests-2.32.4 tables-3.10.2 typing-extensions-4.14.1 urllib3-2.5.0 00:46:04 + pip install jinja2 00:46:05 Collecting jinja2 00:46:05 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB) 00:46:05 Collecting MarkupSafe>=2.0 (from jinja2) 00:46:05 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB) 00:46:05 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB) 00:46:05 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB) 00:46:05 Installing collected packages: MarkupSafe, jinja2 00:46:05 00:46:05 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6 00:46:05 + pip install ome-zarr 00:46:06 Collecting ome-zarr 00:46:06 Using cached ome_zarr-0.11.1-py3-none-any.whl.metadata (2.9 kB) 00:46:06 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr) (2.3.1) 00:46:06 Collecting dask (from ome-zarr) 00:46:06 Using cached dask-2025.7.0-py3-none-any.whl.metadata (3.8 kB) 00:46:06 Collecting zarr<3,>=2.8.1 (from ome-zarr) 00:46:06 Using cached zarr-2.18.7-py3-none-any.whl.metadata (5.8 kB) 00:46:06 Collecting fsspec!=2021.07.0,!=2023.9.0,>=0.8 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr) 00:46:06 Using cached fsspec-2025.7.0-py3-none-any.whl.metadata (12 kB) 00:46:07 Collecting aiohttp<4 (from ome-zarr) 00:46:07 Using cached aiohttp-3.12.14-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.6 kB) 00:46:07 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr) (2.32.4) 00:46:07 Collecting scikit-image (from ome-zarr) 00:46:07 Using cached scikit_image-0.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB) 00:46:07 Collecting toolz (from ome-zarr) 00:46:07 Using cached toolz-1.0.0-py3-none-any.whl.metadata (5.1 kB) 00:46:08 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp<4->ome-zarr) 00:46:08 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB) 00:46:08 Collecting aiosignal>=1.4.0 (from aiohttp<4->ome-zarr) 00:46:08 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB) 00:46:08 Collecting attrs>=17.3.0 (from aiohttp<4->ome-zarr) 00:46:08 Using cached attrs-25.3.0-py3-none-any.whl.metadata (10 kB) 00:46:08 Collecting frozenlist>=1.1.1 (from aiohttp<4->ome-zarr) 00:46:08 Using cached frozenlist-1.7.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB) 00:46:08 Collecting multidict<7.0,>=4.5 (from aiohttp<4->ome-zarr) 00:46:08 Using cached multidict-6.6.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB) 00:46:09 Collecting propcache>=0.2.0 (from aiohttp<4->ome-zarr) 00:46:09 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB) 00:46:09 Collecting yarl<2.0,>=1.17.0 (from aiohttp<4->ome-zarr) 00:46:09 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (73 kB) 00:46:09 Requirement already satisfied: idna>=2.0 in ./.venv3/lib64/python3.11/site-packages (from yarl<2.0,>=1.17.0->aiohttp<4->ome-zarr) (3.10) 00:46:09 Collecting asciitree (from zarr<3,>=2.8.1->ome-zarr) 00:46:09 Using cached asciitree-0.3.3-py3-none-any.whl 00:46:09 Collecting fasteners (from zarr<3,>=2.8.1->ome-zarr) 00:46:09 Using cached fasteners-0.19-py3-none-any.whl.metadata (4.9 kB) 00:46:09 Collecting numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0 (from zarr<3,>=2.8.1->ome-zarr) 00:46:09 Using cached numcodecs-0.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.9 kB) 00:46:09 Collecting deprecated (from numcodecs!=0.14.0,!=0.14.1,<0.16,>=0.10.0->zarr<3,>=2.8.1->ome-zarr) 00:46:09 Using cached Deprecated-1.2.18-py2.py3-none-any.whl.metadata (5.7 kB) 00:46:09 Requirement already satisfied: typing-extensions>=4.2 in ./.venv3/lib64/python3.11/site-packages (from aiosignal>=1.4.0->aiohttp<4->ome-zarr) (4.14.1) 00:46:10 Collecting s3fs (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr) 00:46:10 Using cached s3fs-2025.7.0-py3-none-any.whl.metadata (1.4 kB) 00:46:10 Collecting click>=8.1 (from dask->ome-zarr) 00:46:10 Using cached click-8.2.1-py3-none-any.whl.metadata (2.5 kB) 00:46:10 Collecting cloudpickle>=3.0.0 (from dask->ome-zarr) 00:46:10 Using cached cloudpickle-3.1.1-py3-none-any.whl.metadata (7.1 kB) 00:46:10 Requirement already satisfied: packaging>=20.0 in ./.venv3/lib64/python3.11/site-packages (from dask->ome-zarr) (25.0) 00:46:10 Collecting partd>=1.4.0 (from dask->ome-zarr) 00:46:10 Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB) 00:46:10 Collecting pyyaml>=5.3.1 (from dask->ome-zarr) 00:46:10 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) 00:46:10 Collecting importlib_metadata>=4.13.0 (from dask->ome-zarr) 00:46:10 Using cached importlib_metadata-8.7.0-py3-none-any.whl.metadata (4.8 kB) 00:46:10 Collecting zipp>=3.20 (from importlib_metadata>=4.13.0->dask->ome-zarr) 00:46:10 Using cached zipp-3.23.0-py3-none-any.whl.metadata (3.6 kB) 00:46:10 Collecting locket (from partd>=1.4.0->dask->ome-zarr) 00:46:10 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB) 00:46:10 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) 00:46:10 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) 00:46:10 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr) (3.4.2) 00:46:10 Requirement already satisfied: urllib3<3,>=1.21.1 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr) (2.5.0) 00:46:10 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr) (2025.7.14) 00:46:10 Collecting aiobotocore<3.0.0,>=2.5.4 (from s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr) 00:46:10 Using cached aiobotocore-2.23.1-py3-none-any.whl.metadata (25 kB) 00:46:10 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) 00:46:10 Using cached aioitertools-0.12.0-py3-none-any.whl.metadata (3.8 kB) 00:46:11 Collecting botocore<1.38.47,>=1.38.40 (from aiobotocore<3.0.0,>=2.5.4->s3fs->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr) 00:46:11 Using cached botocore-1.38.46-py3-none-any.whl.metadata (5.7 kB) 00:46:11 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) 00:46:11 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) 00:46:11 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) 00:46:11 Using cached jmespath-1.0.1-py3-none-any.whl.metadata (7.6 kB) 00:46:11 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) (1.17.0) 00:46:11 Collecting scipy>=1.11.4 (from scikit-image->ome-zarr) 00:46:11 Using cached scipy-1.16.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (61 kB) 00:46:12 Collecting networkx>=3.0 (from scikit-image->ome-zarr) 00:46:12 Using cached networkx-3.5-py3-none-any.whl.metadata (6.3 kB) 00:46:12 Requirement already satisfied: pillow>=10.1 in ./.venv3/lib64/python3.11/site-packages (from scikit-image->ome-zarr) (11.3.0) 00:46:12 Collecting imageio!=2.35.0,>=2.33 (from scikit-image->ome-zarr) 00:46:12 Using cached imageio-2.37.0-py3-none-any.whl.metadata (5.2 kB) 00:46:12 Collecting tifffile>=2022.8.12 (from scikit-image->ome-zarr) 00:46:12 Using cached tifffile-2025.6.11-py3-none-any.whl.metadata (32 kB) 00:46:12 Collecting lazy-loader>=0.4 (from scikit-image->ome-zarr) 00:46:12 Using cached lazy_loader-0.4-py3-none-any.whl.metadata (7.6 kB) 00:46:12 Using cached ome_zarr-0.11.1-py3-none-any.whl (40 kB) 00:46:12 Using cached aiohttp-3.12.14-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (1.7 MB) 00:46:12 Using cached multidict-6.6.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB) 00:46:12 Using cached yarl-1.20.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (348 kB) 00:46:12 Using cached zarr-2.18.7-py3-none-any.whl (211 kB) 00:46:12 Using cached numcodecs-0.15.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.9 MB) 00:46:12 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB) 00:46:12 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB) 00:46:12 Using cached attrs-25.3.0-py3-none-any.whl (63 kB) 00:46:12 Using cached frozenlist-1.7.0-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (235 kB) 00:46:12 Using cached fsspec-2025.7.0-py3-none-any.whl (199 kB) 00:46:12 Using cached propcache-0.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (213 kB) 00:46:12 Using cached dask-2025.7.0-py3-none-any.whl (1.5 MB) 00:46:13 Using cached click-8.2.1-py3-none-any.whl (102 kB) 00:46:13 Using cached cloudpickle-3.1.1-py3-none-any.whl (20 kB) 00:46:13 Using cached importlib_metadata-8.7.0-py3-none-any.whl (27 kB) 00:46:13 Using cached partd-1.4.2-py3-none-any.whl (18 kB) 00:46:13 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB) 00:46:13 Using cached toolz-1.0.0-py3-none-any.whl (56 kB) 00:46:13 Using cached zipp-3.23.0-py3-none-any.whl (10 kB) 00:46:13 Using cached Deprecated-1.2.18-py2.py3-none-any.whl (10.0 kB) 00:46:13 Using cached wrapt-1.17.2-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (83 kB) 00:46:13 Using cached fasteners-0.19-py3-none-any.whl (18 kB) 00:46:13 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB) 00:46:13 Using cached s3fs-2025.7.0-py3-none-any.whl (30 kB) 00:46:13 Using cached aiobotocore-2.23.1-py3-none-any.whl (84 kB) 00:46:13 Using cached aioitertools-0.12.0-py3-none-any.whl (24 kB) 00:46:13 Using cached botocore-1.38.46-py3-none-any.whl (13.7 MB) 00:46:13 Using cached jmespath-1.0.1-py3-none-any.whl (20 kB) 00:46:13 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 00:46:14 Using cached scikit_image-0.25.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (14.8 MB) 00:46:14 Using cached imageio-2.37.0-py3-none-any.whl (315 kB) 00:46:14 Using cached lazy_loader-0.4-py3-none-any.whl (12 kB) 00:46:14 Using cached networkx-3.5-py3-none-any.whl (2.0 MB) 00:46:14 Using cached scipy-1.16.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (35.3 MB) 00:46:14 Using cached tifffile-2025.6.11-py3-none-any.whl (230 kB) 00:46:15 Installing collected packages: asciitree, zipp, wrapt, toolz, tifffile, scipy, pyyaml, 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 00:46:26 00:46:26 Successfully installed aiobotocore-2.23.1 aiohappyeyeballs-2.6.1 aiohttp-3.12.14 aioitertools-0.12.0 aiosignal-1.4.0 asciitree-0.3.3 attrs-25.3.0 botocore-1.38.46 click-8.2.1 cloudpickle-3.1.1 dask-2025.7.0 deprecated-1.2.18 fasteners-0.19 frozenlist-1.7.0 fsspec-2025.7.0 imageio-2.37.0 importlib_metadata-8.7.0 jmespath-1.0.1 lazy-loader-0.4 locket-1.0.0 multidict-6.6.3 networkx-3.5 numcodecs-0.15.1 ome-zarr-0.11.1 partd-1.4.2 propcache-0.3.2 python-dateutil-2.9.0.post0 pyyaml-6.0.2 s3fs-2025.7.0 scikit-image-0.25.2 scipy-1.16.0 tifffile-2025.6.11 toolz-1.0.0 wrapt-1.17.2 yarl-1.20.1 zarr-2.18.7 zipp-3.23.0 00:46:26 + pip install omero-rois 00:46:27 Collecting omero-rois 00:46:27 Using cached omero_rois-0.3.0-py3-none-any.whl.metadata (2.4 kB) 00:46:27 Collecting omero-py>=5.6.0 (from omero-rois) 00:46:27 Using cached omero_py-5.21.0-py3-none-any.whl.metadata (6.5 kB) 00:46:27 Collecting urllib3<2 (from omero-py>=5.6.0->omero-rois) 00:46:27 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) 00:46:27 Collecting appdirs (from omero-py>=5.6.0->omero-rois) 00:46:27 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) 00:46:27 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-rois) (1.0.0) 00:46:27 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-rois) (2.3.1) 00:46:27 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-rois) (11.3.0) 00:46:27 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-rois) (6.0.2) 00:46:27 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-rois) (3.6.5) 00:46:27 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-rois) (2.32.4) 00:46:27 Collecting portalocker (from omero-py>=5.6.0->omero-rois) 00:46:27 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB) 00:46:27 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-rois) (3.4.2) 00:46:27 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-rois) (3.10) 00:46:27 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-rois) (2025.7.14) 00:46:27 Using cached omero_rois-0.3.0-py3-none-any.whl (11 kB) 00:46:27 Using cached omero_py-5.21.0-py3-none-any.whl (2.8 MB) 00:46:27 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) 00:46:27 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) 00:46:27 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB) 00:46:28 Installing collected packages: appdirs, urllib3, portalocker, omero-py, omero-rois 00:46:28 Attempting uninstall: urllib3 00:46:28 Found existing installation: urllib3 2.5.0 00:46:28 Uninstalling urllib3-2.5.0: 00:46:28 Successfully uninstalled urllib3-2.5.0 00:46:30 00:46:30 Successfully installed appdirs-1.4.4 omero-py-5.21.0 omero-rois-0.3.0 portalocker-3.2.0 urllib3-1.26.20 00:46:30 + pip install boto3 00:46:30 Collecting boto3 00:46:30 Downloading boto3-1.39.11-py3-none-any.whl.metadata (6.7 kB) 00:46:31 Collecting botocore<1.40.0,>=1.39.11 (from boto3) 00:46:31 Downloading botocore-1.39.11-py3-none-any.whl.metadata (5.7 kB) 00:46:31 Requirement already satisfied: jmespath<2.0.0,>=0.7.1 in ./.venv3/lib64/python3.11/site-packages (from boto3) (1.0.1) 00:46:31 Collecting s3transfer<0.14.0,>=0.13.0 (from boto3) 00:46:31 Using cached s3transfer-0.13.1-py3-none-any.whl.metadata (1.7 kB) 00:46:31 Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.40.0,>=1.39.11->boto3) (2.9.0.post0) 00:46:31 Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.40.0,>=1.39.11->boto3) (1.26.20) 00:46:31 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->botocore<1.40.0,>=1.39.11->boto3) (1.17.0) 00:46:31 Downloading boto3-1.39.11-py3-none-any.whl (139 kB) 00:46:31 Downloading botocore-1.39.11-py3-none-any.whl (13.9 MB) 00:46:32 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 13.9/13.9 MB 23.1 MB/s eta 0:00:00 00:46:32 Using cached s3transfer-0.13.1-py3-none-any.whl (85 kB) 00:46:32 Installing collected packages: botocore, s3transfer, boto3 00:46:32 Attempting uninstall: botocore 00:46:32 Found existing installation: botocore 1.38.46 00:46:32 Uninstalling botocore-1.38.46: 00:46:32 Successfully uninstalled botocore-1.38.46 00:46:33 00:46:33 ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. 00:46:33 aiobotocore 2.23.1 requires botocore<1.38.47,>=1.38.40, but you have botocore 1.39.11 which is incompatible. 00:46:33 Successfully installed boto3-1.39.11 botocore-1.39.11 s3transfer-0.13.1 00:46:33 + pip install smart-open 00:46:34 Collecting smart-open 00:46:34 Using cached smart_open-7.3.0.post1-py3-none-any.whl.metadata (24 kB) 00:46:34 Requirement already satisfied: wrapt in ./.venv3/lib64/python3.11/site-packages (from smart-open) (1.17.2) 00:46:34 Using cached smart_open-7.3.0.post1-py3-none-any.whl (61 kB) 00:46:34 Installing collected packages: smart-open 00:46:34 Successfully installed smart-open-7.3.0.post1 00:46:34 + pip install omero-py 00:46:34 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (5.21.0) 00:46:34 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.26.20) 00:46:34 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.4.4) 00:46:34 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0) 00:46:34 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.3.1) 00:46:34 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.3.0) 00:46:34 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py) (6.0.2) 00:46:34 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5) 00:46:34 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.4) 00:46:34 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.2.0) 00:46:34 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2) 00:46:34 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10) 00:46:34 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.7.14) 00:46:35 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata 00:46:35 Collecting omero-metadata 00:46:35 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-x1u_gy8k/omero-metadata_b7c4469cf35142a5b1b85a4fa4b6c66e 00:46:35 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-x1u_gy8k/omero-metadata_b7c4469cf35142a5b1b85a4fa4b6c66e 00:46:37 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit be4dc51ea9aa1cc7bc4461d956b768b85a2d078c 00:46:37 Installing build dependencies: started 00:46:39 Installing build dependencies: finished with status 'done' 00:46:39 Getting requirements to build wheel: started 00:46:39 Getting requirements to build wheel: finished with status 'done' 00:46:39 Preparing metadata (pyproject.toml): started 00:46:39 Preparing metadata (pyproject.toml): finished with status 'done' 00:46:39 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.21.0) 00:46:39 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2) 00:46:39 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6) 00:46:40 Collecting pandas (from omero-metadata) 00:46:40 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB) 00:46:40 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20) 00:46:40 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4) 00:46:40 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0) 00:46:40 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.3.1) 00:46:40 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) 00:46:40 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) 00:46:40 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.4) 00:46:40 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0) 00:46:40 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2) 00:46:40 Requirement already satisfied: python-dateutil>=2.8.2 in ./.venv3/lib64/python3.11/site-packages (from pandas->omero-metadata) (2.9.0.post0) 00:46:41 Collecting pytz>=2020.1 (from pandas->omero-metadata) 00:46:41 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) 00:46:41 Collecting tzdata>=2022.7 (from pandas->omero-metadata) 00:46:41 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB) 00:46:41 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) 00:46:41 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) 00:46:41 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) 00:46:41 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.7.14) 00:46:41 Using cached pandas-2.3.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.4 MB) 00:46:41 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB) 00:46:41 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB) 00:46:41 Building wheels for collected packages: omero-metadata 00:46:41 Building wheel for omero-metadata (pyproject.toml): started 00:46:42 Building wheel for omero-metadata (pyproject.toml): finished with status 'done' 00:46:42 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39282 sha256=caf400f5b23e7dc21930e6e9a2de50833da756d0bfb7b7e7e9fb521d889c1707 00:46:42 Stored in directory: /tmp/pip-ephem-wheel-cache-g45fg0s2/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b 00:46:42 Successfully built omero-metadata 00:46:42 Installing collected packages: pytz, tzdata, pandas, omero-metadata 00:46:47 00:46:47 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.3.1 pytz-2025.2 tzdata-2025.2 00:46:47 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render 00:46:47 Collecting omero-cli-render 00:46:47 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-i9j_z895/omero-cli-render_dbca16e90c234983971a100fcd0ba0e3 00:46:47 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-i9j_z895/omero-cli-render_dbca16e90c234983971a100fcd0ba0e3 00:46:48 Running command git checkout -b merge_ci --track origin/merge_ci 00:46:48 Switched to a new branch 'merge_ci' 00:46:48 branch 'merge_ci' set up to track 'origin/merge_ci'. 00:46:48 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit fcbfc9f7c1da50fbfa8c820fe5b8c70894b24476 00:46:48 Installing build dependencies: started 00:46:49 Installing build dependencies: finished with status 'done' 00:46:49 Getting requirements to build wheel: started 00:46:49 Getting requirements to build wheel: finished with status 'done' 00:46:49 Preparing metadata (pyproject.toml): started 00:46:50 Preparing metadata (pyproject.toml): finished with status 'done' 00:46:50 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2) 00:46:50 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.21.0) 00:46:50 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20) 00:46:50 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4) 00:46:50 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0) 00:46:50 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.3.1) 00:46:50 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) 00:46:50 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) 00:46:50 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.4) 00:46:50 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0) 00:46:50 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) 00:46:50 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) 00:46:50 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.7.14) 00:46:50 Building wheels for collected packages: omero-cli-render 00:46:50 Building wheel for omero-cli-render (pyproject.toml): started 00:46:50 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done' 00:46:50 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=ce0863e3a305789495bc17558bedaabb97ee73578c32f1c3b4731951f848ceaf 00:46:50 Stored in directory: /tmp/pip-ephem-wheel-cache-rpxwbk8r/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee 00:46:50 Successfully built omero-cli-render 00:46:50 Installing collected packages: omero-cli-render 00:46:50 Successfully installed omero-cli-render-0.8.2.dev0 00:46:50 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate 00:46:50 Collecting omero-cli-duplicate 00:46:50 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-2j6qxgsq/omero-cli-duplicate_f9469532ce844769bcd7279fe13cb830 00:46:50 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-2j6qxgsq/omero-cli-duplicate_f9469532ce844769bcd7279fe13cb830 00:46:51 Running command git checkout -b merge_ci --track origin/merge_ci 00:46:52 Switched to a new branch 'merge_ci' 00:46:52 branch 'merge_ci' set up to track 'origin/merge_ci'. 00:46:52 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit c2fededc344afb952d4bd27b37202e9ab72e114c 00:46:52 Installing build dependencies: started 00:46:52 Installing build dependencies: finished with status 'done' 00:46:52 Getting requirements to build wheel: started 00:46:53 Getting requirements to build wheel: finished with status 'done' 00:46:53 Preparing metadata (pyproject.toml): started 00:46:53 Preparing metadata (pyproject.toml): finished with status 'done' 00:46:53 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.21.0) 00:46:53 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20) 00:46:53 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4) 00:46:53 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0) 00:46:53 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.3.1) 00:46:53 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) 00:46:53 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2) 00:46:53 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) 00:46:53 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.4) 00:46:53 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0) 00:46:53 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) 00:46:53 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) 00:46:53 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.7.14) 00:46:53 Building wheels for collected packages: omero-cli-duplicate 00:46:53 Building wheel for omero-cli-duplicate (pyproject.toml): started 00:46:53 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done' 00:46:53 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11541 sha256=f98a98c07058093314c4ae7271b586be3a7c24e68da31aad208b495928c2ad9b 00:46:53 Stored in directory: /tmp/pip-ephem-wheel-cache-eeko09jv/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46 00:46:53 Successfully built omero-cli-duplicate 00:46:53 Installing collected packages: omero-cli-duplicate 00:46:53 Successfully installed omero-cli-duplicate-0.4.1.dev0 00:46:54 + pip install omero-certificates 00:46:54 Collecting omero-certificates 00:46:54 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB) 00:46:54 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.21.0) 00:46:54 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20) 00:46:54 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4) 00:46:54 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0) 00:46:54 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.3.1) 00:46:54 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) 00:46:54 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2) 00:46:54 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5) 00:46:54 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.4) 00:46:54 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0) 00:46:54 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) 00:46:54 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) 00:46:54 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.7.14) 00:46:54 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB) 00:46:54 Installing collected packages: omero-certificates 00:46:54 Successfully installed omero-certificates-0.4.0 00:46:54 + for x in *.tar.gz 00:46:54 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz 00:46:55 Processing ./omero_dropbox-5.7.1.dev0.tar.gz 00:46:55 Installing build dependencies: started 00:46:56 Installing build dependencies: finished with status 'done' 00:46:56 Getting requirements to build wheel: started 00:46:56 Getting requirements to build wheel: finished with status 'done' 00:46:56 Preparing metadata (pyproject.toml): started 00:46:56 Preparing metadata (pyproject.toml): finished with status 'done' 00:46:56 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.21.0) 00:46:56 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20) 00:46:56 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4) 00:46:56 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0) 00:46:56 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.3.1) 00:46:56 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) 00:46:56 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2) 00:46:56 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) 00:46:56 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.4) 00:46:56 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0) 00:46:56 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) 00:46:56 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) 00:46:56 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.7.14) 00:46:56 Building wheels for collected packages: omero-dropbox 00:46:56 Building wheel for omero-dropbox (pyproject.toml): started 00:46:57 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done' 00:46:57 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49138 sha256=3488197894b45d625f1ce2b810aed9411fc0778245e12a09ed6181cd7646070d 00:46:57 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92 00:46:57 Successfully built omero-dropbox 00:46:57 Installing collected packages: omero-dropbox 00:46:57 Successfully installed omero-dropbox-5.7.1.dev0 00:46:57 + for x in *.tar.gz 00:46:57 + pip install -U omero_marshal-0.9.1.dev0.tar.gz 00:46:57 Processing ./omero_marshal-0.9.1.dev0.tar.gz 00:46:57 Installing build dependencies: started 00:46:58 Installing build dependencies: finished with status 'done' 00:46:58 Getting requirements to build wheel: started 00:46:59 Getting requirements to build wheel: finished with status 'done' 00:46:59 Preparing metadata (pyproject.toml): started 00:46:59 Preparing metadata (pyproject.toml): finished with status 'done' 00:46:59 Building wheels for collected packages: omero_marshal 00:46:59 Building wheel for omero_marshal (pyproject.toml): started 00:46:59 Building wheel for omero_marshal (pyproject.toml): finished with status 'done' 00:46:59 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88126 sha256=52d95e9039b49bb020df06089f75a36fe6f1bd679471cab31a4c91b5eba22c49 00:46:59 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18 00:46:59 Successfully built omero_marshal 00:46:59 Installing collected packages: omero_marshal 00:46:59 Successfully installed omero_marshal-0.9.1.dev0 00:46:59 + for x in *.tar.gz 00:46:59 + pip install -U omero_py-5.21.1.dev0.tar.gz 00:47:00 Processing ./omero_py-5.21.1.dev0.tar.gz 00:47:00 Installing build dependencies: started 00:47:01 Installing build dependencies: finished with status 'done' 00:47:01 Getting requirements to build wheel: started 00:47:01 Getting requirements to build wheel: finished with status 'done' 00:47:01 Preparing metadata (pyproject.toml): started 00:47:02 Preparing metadata (pyproject.toml): finished with status 'done' 00:47:02 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.26.20) 00:47:02 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.4.4) 00:47:02 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (1.0.0) 00:47:02 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.3.1) 00:47:02 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (11.3.0) 00:47:02 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (6.0.2) 00:47:02 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.6.5) 00:47:02 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (2.32.4) 00:47:02 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.21.1.dev0) (3.2.0) 00:47:02 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.4.2) 00:47:02 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (3.10) 00:47:02 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.21.1.dev0) (2025.7.14) 00:47:02 Building wheels for collected packages: omero-py 00:47:02 Building wheel for omero-py (pyproject.toml): started 00:47:03 Building wheel for omero-py (pyproject.toml): finished with status 'done' 00:47:03 Created wheel for omero-py: filename=omero_py-5.21.1.dev0-py3-none-any.whl size=2783541 sha256=203b7021c9ea78f4a8afef1e657fd2330ca4dbc3f36f7d7ed64c9905349107ba 00:47:03 Stored in directory: /home/omero/.cache/pip/wheels/32/8a/68/256ffa196397e2ec55e537fc96a9b9c4178b3eab623cd87f3d 00:47:03 Successfully built omero-py 00:47:03 Installing collected packages: omero-py 00:47:03 Attempting uninstall: omero-py 00:47:03 Found existing installation: omero-py 5.21.0 00:47:03 Uninstalling omero-py-5.21.0: 00:47:04 Successfully uninstalled omero-py-5.21.0 00:47:05 Successfully installed omero-py-5.21.1.dev0 00:47:06 + for x in *.tar.gz 00:47:06 + pip install -U omero_scripts-5.9.2.dev0.tar.gz 00:47:06 Processing ./omero_scripts-5.9.2.dev0.tar.gz 00:47:06 Installing build dependencies: started 00:47:07 Installing build dependencies: finished with status 'done' 00:47:07 Getting requirements to build wheel: started 00:47:07 Getting requirements to build wheel: finished with status 'done' 00:47:07 Preparing metadata (pyproject.toml): started 00:47:07 Preparing metadata (pyproject.toml): finished with status 'done' 00:47:07 Building wheels for collected packages: omero-scripts 00:47:07 Building wheel for omero-scripts (pyproject.toml): started 00:47:08 Building wheel for omero-scripts (pyproject.toml): finished with status 'done' 00:47:08 Created wheel for omero-scripts: filename=omero_scripts-5.9.2.dev0-py3-none-any.whl size=136847 sha256=8df99f743e1f520f11e76336171b70eef6961b3cbbee6ee888768e25fe7aa22b 00:47:08 Stored in directory: /home/omero/.cache/pip/wheels/e3/db/94/c7ed73401c8459f3935212f514ee953d11b520ca8c20333850 00:47:08 Successfully built omero-scripts 00:47:08 Installing collected packages: omero-scripts 00:47:08 Successfully installed omero-scripts-5.9.2.dev0 00:47:08 + for x in *.tar.gz 00:47:08 + pip install -U omero_web-5.29.2.dev0.tar.gz 00:47:08 Processing ./omero_web-5.29.2.dev0.tar.gz 00:47:09 Installing build dependencies: started 00:47:10 Installing build dependencies: finished with status 'done' 00:47:10 Getting requirements to build wheel: started 00:47:10 Getting requirements to build wheel: finished with status 'done' 00:47:10 Preparing metadata (pyproject.toml): started 00:47:10 Preparing metadata (pyproject.toml): finished with status 'done' 00:47:10 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (5.21.1.dev0) 00:47:11 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.2.dev0) 00:47:11 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl.metadata (23 kB) 00:47:11 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.2.dev0) 00:47:11 Using cached django-4.2.23-py3-none-any.whl.metadata (4.2 kB) 00:47:12 Collecting django-pipeline (from omero-web==5.29.2.dev0) 00:47:12 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB) 00:47:12 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.2.dev0) 00:47:12 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB) 00:47:12 Collecting django-csp (from omero-web==5.29.2.dev0) 00:47:12 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB) 00:47:13 Collecting whitenoise>=5.3.0 (from omero-web==5.29.2.dev0) 00:47:13 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB) 00:47:13 Collecting gunicorn>=19.3 (from omero-web==5.29.2.dev0) 00:47:13 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB) 00:47:13 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (0.9.1.dev0) 00:47:13 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (11.3.0) 00:47:13 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (2025.2) 00:47:13 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (3.2.0) 00:47:13 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.2.dev0) (25.0) 00:47:13 Collecting importlib-resources (from omero-web==5.29.2.dev0) 00:47:13 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB) 00:47:13 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0) 00:47:13 Using cached asgiref-3.9.1-py3-none-any.whl.metadata (9.3 kB) 00:47:13 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.2.dev0) 00:47:13 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB) 00:47:13 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.26.20) 00:47:13 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.4.4) 00:47:13 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (1.0.0) 00:47:13 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.3.1) 00:47:13 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (6.0.2) 00:47:13 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.6.5) 00:47:13 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.2.dev0) (2.32.4) 00:47:13 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.2.dev0) (65.5.1) 00:47:13 Collecting wheel (from django-pipeline->omero-web==5.29.2.dev0) 00:47:13 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB) 00:47:13 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.4.2) 00:47:13 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (3.10) 00:47:13 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.2.dev0) (2025.7.14) 00:47:13 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB) 00:47:13 Using cached django-4.2.23-py3-none-any.whl (8.0 MB) 00:47:13 Using cached asgiref-3.9.1-py3-none-any.whl (23 kB) 00:47:13 Using cached concurrent_log_handler-0.9.28-py3-none-any.whl (28 kB) 00:47:14 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB) 00:47:14 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB) 00:47:14 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB) 00:47:14 Using cached django_csp-4.0-py3-none-any.whl (25 kB) 00:47:14 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB) 00:47:14 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB) 00:47:14 Using cached wheel-0.45.1-py3-none-any.whl (72 kB) 00:47:14 Building wheels for collected packages: omero-web 00:47:14 Building wheel for omero-web (pyproject.toml): started 00:47:15 Building wheel for omero-web (pyproject.toml): finished with status 'done' 00:47:15 Created wheel for omero-web: filename=omero_web-5.29.2.dev0-py3-none-any.whl size=2817943 sha256=cd23c2377b45f6725f66f1bf3f19daacf8207c10d241bff8140d311c91594c40 00:47:15 Stored in directory: /home/omero/.cache/pip/wheels/8b/82/d4/64ba3d9f4efaa51110316831003d98aee03867a3665750278c 00:47:15 Successfully built omero-web 00:47:16 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web 00:47:21 00:47:21 Successfully installed Django-4.2.23 asgiref-3.9.1 concurrent-log-handler-0.9.28 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.0.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.2.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.9.0 00:47:21 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py 00:47:21 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file. 00:47:21 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled. 00:47:21 --2025-07-23 00:47:21-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py 00:47:21 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.109.133, 185.199.108.133, ... 00:47:21 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected. 00:47:21 HTTP request sent, awaiting response... 200 OK 00:47:21 Length: 125072 (122K) [text/plain] 00:47:21 Saving to: ‘Figure_To_Pdf.py’ 00:47:21 00:47:21 0K .......... .......... .......... .......... .......... 40% 3.92M 0s 00:47:21 50K .......... .......... .......... .......... .......... 81% 13.4M 0s 00:47:21 100K .......... .......... .. 100% 4.32M=0.02s 00:47:21 00:47:21 2025-07-23 00:47:21 (5.65 MB/s) - ‘Figure_To_Pdf.py’ saved [125072/125072] 00:47:21 00:47:21 + chmod 755 Figure_To_Pdf.py 00:47:21 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts 00:47:21 + omero config set omero.db.name OMERO-server 00:47:22 + omero config set omero.db.host pg 00:47:24 + omero config set omero.db.user postgres 00:47:25 + omero config set omero.data.dir /home/omero/omero-server-data 00:47:26 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time% 00:47:27 + omero config set omero.db.poolsize 25 00:47:29 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts 00:47:30 + omero config set omero.security.trustStorePassword changeit 00:47:31 + omero config set omero.mail.config true 00:47:32 + omero config set omero.mail.from qa@openmicroscopy.org.uk 00:47:34 + omero config set omero.mail.host smtp.dundee.ac.uk 00:47:35 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0 00:47:36 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED' 00:47:37 + omero certificates 00:47:39 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024) 00:47:39 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12 00:47:39 + '[' false = true ']' 00:47:39 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade' 00:47:39 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade 00:47:39 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG dbcommand => upgrade 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG dbhost => localhost 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG dbname => OMERO-server 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG dbpass => omero 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG dbuser => omero 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG rootpass => omero 00:47:39 2025-07-23 00:47:39,511 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server 00:47:39 2025-07-23 00:47:39,511 [omego.extern] INFO Executing : omero version 00:47:40 OMERO.py version: 00:47:40 OMERO.server version: 00:47:40 5.6.3-572-e40f7383aa-ice36-b476 00:47:40 5.21.1.dev0 00:47:40 2025-07-23 00:47:40,802 [omego.extern] INFO Completed [1.291 s] 00:47:40 2025-07-23 00:47:40,802 [omego.extern] DEBUG Using omero CLI from omero 00:47:40 2025-07-23 00:47:40,802 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ... 00:47:40 2025-07-23 00:47:40,803 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:47:40 2025-07-23 00:47:40,803 [omego.extern] INFO Executing : omero config get --show-password 00:47:42 2025-07-23 00:47:42,082 [omego.extern] INFO Completed [1.279 s] 00:47:42 2025-07-23 00:47:42,082 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:47:42 2025-07-23 00:47:42,082 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version 00:47:42 2025-07-23 00:47:42,489 [omego.extern] INFO Completed [0.407 s] 00:47:42 2025-07-23 00:47:42,489 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.9\n' 00:47:42 2025-07-23 00:47:42,489 [ omego.db] INFO psql version: psql (PostgreSQL) 16.9 00:47:42 00:47:42 2025-07-23 00:47:42,489 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:47:42 2025-07-23 00:47:42,489 [omego.extern] INFO Executing : omero config get --show-password 00:47:43 2025-07-23 00:47:43,723 [omego.extern] INFO Completed [1.234 s] 00:47:43 2025-07-23 00:47:43,723 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:47:43 2025-07-23 00:47:43,724 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo 00:47:43 2025-07-23 00:47:43,947 [omego.extern] INFO Completed [0.223 s] 00:47:43 2025-07-23 00:47:43,947 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.7") at port "5432".\n' 00:47:43 2025-07-23 00:47:43,947 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1 00:47:43 2025-07-23 00:47:43,947 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:47:43 2025-07-23 00:47:43,947 [omego.extern] INFO Executing : omero config get --show-password 00:47:45 2025-07-23 00:47:45,244 [omego.extern] INFO Completed [1.297 s] 00:47:45 2025-07-23 00:47:45,244 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:47:45 2025-07-23 00:47:45,244 [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 00:47:46 2025-07-23 00:47:46,016 [omego.extern] INFO Completed [0.772 s] 00:47:46 2025-07-23 00:47:46,016 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n' 00:47:46 2025-07-23 00:47:46,017 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0') 00:47:46 2025-07-23 00:47:46,018 [ omego.db] INFO Database is already at OMERO5.4__0 00:47:46 + export LANG=en_US.UTF-8 00:47:46 + LANG=en_US.UTF-8 00:47:46 + export LANGUAGE=en_US:en 00:47:46 + LANGUAGE=en_US:en 00:47:46 + export LC_ALL=en_US.UTF-8 00:47:46 + LC_ALL=en_US.UTF-8 00:47:46 + BUILD_ID=DONT_KILL_ME 00:47:46 + omero admin start 00:47:51 No descriptor given. Using etc/grid/default.xml 00:48:05 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master 00:48:05 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log 00:48:05 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry 00:48:05 Waiting on startup. Use CTRL-C to exit 00:48:06 + omero admin waitup 00:48:07 Waiting on startup. Use CTRL-C to exit 00:48:07 + omero admin diagnostics 00:48:08 00:48:08 ================================================================================ 00:48:08 OMERO Diagnostics (admin) 00:48:08 ================================================================================ 00:48:08 00:48:08 Commands: java -version 11.0.25 (/usr/bin/java) 00:48:08 Commands: python -V 3.11.11 (/home/omero/workspace/OMERO-server/.venv3/bin/python) 00:48:08 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode) 00:48:08 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin) 00:48:08 Commands: psql --version 16.9 (/usr/bin/psql) 00:48:08 Commands: openssl version 3.2.24 (/usr/bin/openssl) 00:48:08 00:48:08 Component: OMERO.py 5.21.1.dev0 00:48:08 Component: OMERO.server 5.6.3-572-e40f7383aa-ice36-b476 00:48:08 00:48:08 Server: icegridnode running 00:48:08 Server: Blitz-0 active (pid = 2361, enabled) 00:48:08 Server: Indexer-0 active (pid = 2385, enabled) 00:48:08 Server: OMERO.Glacier2 active (pid = 2388, enabled) 00:48:08 Server: OMERO.IceStorm active (pid = 2414, enabled) 00:48:08 Server: Processor-0 activating (enabled) 00:48:08 Server: Tables-0 activating (enabled) 00:48:08 00:48:08 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists 00:48:08 Log files: Blitz-0.log 14.0 KB errors=0 warnings=1 00:48:08 Log files: DropBox.log n/a 00:48:08 Log files: FileServer.log n/a 00:48:08 Log files: Indexer-0.log 2.6 KB 00:48:08 Log files: MonitorServer.log n/a 00:48:08 Log files: Processor-0.log 592 B 00:48:08 Log files: Tables-0.log 841 B 00:48:08 Log files: TestDropBox.log n/a 00:48:08 Log files: master.err empty 00:48:08 Log files: master.out 30.5 KB 00:48:08 Log files: Total size 0.05 MB 00:48:08 00:48:08 00:48:08 Environment:OMERO_HOME=(unset) 00:48:08 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:48:08 Environment:OMERO_NODE=(unset) 00:48:08 Environment:OMERO_MASTER=(unset) 00:48:08 Environment:OMERO_USERDIR=(unset) 00:48:08 Environment:OMERO_TMPDIR=(unset) 00:48:08 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 00:48:08 Environment:PYTHONPATH=(unset) 00:48:08 Environment:ICE_HOME=/opt/ice-3.6.5 00:48:08 Environment:LD_LIBRARY_PATH=(unset) 00:48:08 Environment:DYLD_LIBRARY_PATH=(unset) 00:48:08 00:48:08 OMERO SSL port:4064 00:48:08 OMERO TCP port:4063 00:48:08 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True 00:48:08 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0) 00:48:08 00:48:08 JVM settings: Blitz-${index} -Xmx7200m 00:48:08 JVM settings: Indexer-${index} -Xmx4800m 00:48:08 JVM settings: PixelData-${index} -Xmx7200m 00:48:08 JVM settings: Repository-${index} -Xmx4800m 00:48:08 00:48:08 Jar: lib/server/formats-api.jar Bio-Formats API 8.3.0-SNAPSHOT 23 July 2025 237e43ebc4b5c4eae6df495744e25bb90ea9cac3 00:48:08 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.3.0-SNAPSHOT 23 July 2025 237e43ebc4b5c4eae6df495744e25bb90ea9cac3 00:48:08 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.3.0-SNAPSHOT 23 July 2025 237e43ebc4b5c4eae6df495744e25bb90ea9cac3 00:48:08 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.2-SNAPSHOT 23 July 2025 5d65142a7d7df2f8a8e4aca27ed2f9c83b6b79db 00:48:08 Jar: lib/server/ome-common.jar OME Common Java 6.0.27-SNAPSHOT 23 July 2025 5d65142a7d7df2f8a8e4aca27ed2f9c83b6b79db 00:48:08 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 23 July 2025 5d65142a7d7df2f8a8e4aca27ed2f9c83b6b79db 00:48:08 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 23 July 2025 5d65142a7d7df2f8a8e4aca27ed2f9c83b6b79db 00:48:08 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 23 July 2025 5d65142a7d7df2f8a8e4aca27ed2f9c83b6b79db 00:48:08 Jar: lib/server/ome-xml.jar OME XML library 6.5.1-SNAPSHOT 23 July 2025 5d65142a7d7df2f8a8e4aca27ed2f9c83b6b79db 00:48:08 Jar: lib/server/omero-blitz.jar jar 5.8.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-common.jar jar 5.7.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-gateway.jar jar 5.10.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-model.jar jar 5.7.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-renderer.jar jar 5.6.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-romio.jar jar 5.8.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-server.jar jar 5.7.4-SNAPSHOT 00:48:09 Jar: lib/server/omero-zarr-pixel-buffer-0.5.1-SNAPSHOT.jar OMERO Zarr Pixel Buffer 0.5.1-SNAPSHOT 8ae8a9c70e8183cc278be8275732bcebc89829d7 00:48:09 + deactivate 00:48:09 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' 00:48:09 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:48:09 + export PATH 00:48:09 + unset _OLD_VIRTUAL_PATH 00:48:09 + '[' -n '' ']' 00:48:09 + hash -r 00:48:09 + '[' -n '' ']' 00:48:09 + unset VIRTUAL_ENV 00:48:09 + unset VIRTUAL_ENV_PROMPT 00:48:09 + '[' '!' '' = nondestructive ']' 00:48:09 + unset -f deactivate 00:48:09 Finished: SUCCESS