00:55:48 Started by upstream project "Trigger" build number 477
00:55:48 originally caused by:
00:55:48 Started by timer
00:55:48 Running as SYSTEM
00:55:49 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:55:49 [OMERO-server] $ /bin/bash -xe /tmp/jenkins8555988061040042555.sh
00:55:49 + source /home/settings.env
00:55:49 ++ OMERO_DB_HOST=pg
00:55:49 ++ OMERO_DB_USER=postgres
00:55:49 ++ OMERO_DB_PASS=
00:55:49 ++ OMERO_ROOT_PASS=omero
00:55:49 ++ OMERO_DATA_DIR=/OMERO
00:55:49 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:55:49 + OMERO_DB_NAME=OMERO-server
00:55:49 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:55:49 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:55:49 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:55:49 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:55:49 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:55:49 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:55:49 ++ deactivate nondestructive
00:55:49 ++ '[' -n '' ']'
00:55:49 ++ '[' -n '' ']'
00:55:49 ++ hash -r
00:55:49 ++ '[' -n '' ']'
00:55:49 ++ unset VIRTUAL_ENV
00:55:49 ++ unset VIRTUAL_ENV_PROMPT
00:55:49 ++ '[' '!' nondestructive = nondestructive ']'
00:55:49 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:55:49 ++ export VIRTUAL_ENV
00:55:49 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:55:49 ++ 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
00:55:49 ++ export PATH
00:55:49 ++ '[' -n '' ']'
00:55:49 ++ '[' -z '' ']'
00:55:49 ++ _OLD_VIRTUAL_PS1=
00:55:49 ++ PS1='(.venv3) '
00:55:49 ++ export PS1
00:55:49 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:55:49 ++ export VIRTUAL_ENV_PROMPT
00:55:49 ++ hash -r
00:55:49 + omero admin stop
00:56:28 Server not running
00:56:28 + echo not running
00:56:28 not running
00:56:28 + sleep 5
00:56:33 + deactivate
00:56:33 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:56:33 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:56:33 + export PATH
00:56:33 + unset _OLD_VIRTUAL_PATH
00:56:33 + '[' -n '' ']'
00:56:33 + hash -r
00:56:33 + '[' -n '' ']'
00:56:33 + unset VIRTUAL_ENV
00:56:33 + unset VIRTUAL_ENV_PROMPT
00:56:33 + '[' '!' '' = nondestructive ']'
00:56:33 + unset -f deactivate
00:56:33 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:56:34 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:56:41 + '[' false = true ']'
00:56:41 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:56:41 Skipping PURGE_DATA:CleanDbAndRepo
00:56:41 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.3-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.20.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.29.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:56:43 Copied 1 artifact from "OMERO-build" build number 411
00:56:43 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 403
00:56:43 Copied 2 artifacts from "OMERO-build-build" build number 429
00:56:43 [OMERO-server] $ /bin/bash -xe /tmp/jenkins17984672543672172046.sh
00:56:43 + source /home/settings.env
00:56:43 ++ OMERO_DB_HOST=pg
00:56:43 ++ OMERO_DB_USER=postgres
00:56:43 ++ OMERO_DB_PASS=
00:56:43 ++ OMERO_ROOT_PASS=omero
00:56:43 ++ OMERO_DATA_DIR=/OMERO
00:56:43 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:56:43 + OMERO_DB_NAME=OMERO-server
00:56:43 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:56:43 + mkdir -p /home/omero/omero-server-data
00:56:43 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:56:43 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:56:43 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:56:43 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:56:43 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:56:43 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:56:43 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:56:43 ++ ls OMERO.server-5.6.3-552-3c3352813e-ice36-b411.zip
00:56:43 + ZIP=OMERO.server-5.6.3-552-3c3352813e-ice36-b411.zip
00:56:43 + '[' '!' -z '' ']'
00:56:43 + DIST=OMERO.server-5.6.3-552-3c3352813e-ice36-b411
00:56:43 + unzip OMERO.server-5.6.3-552-3c3352813e-ice36-b411.zip
00:56:43 Archive: OMERO.server-5.6.3-552-3c3352813e-ice36-b411.zip
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/blitz/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/grid/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/profiles/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/error/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/grid/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/luts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/luts/janelia/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/luts/matplotlib/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/luts/ncsa_paledit/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/luts/seaborn/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/luts/wcif/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/analysis_scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/annotation_scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/export_scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/figure_scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/import_scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/scripts/omero/util_scripts/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/server/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/share/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/share/licenses/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/misc/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__1/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__10/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__11/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__2/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__3/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__4/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__5/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__6/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__7/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__8/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3A__9/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3__4/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3__5/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3__6/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO3__7/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO4.1__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO4.2__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO4.2__0/t/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO4.3__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO4.4__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO4__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.0__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.1__1/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.2__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4DEV__1/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4DEV__2/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4DEV__3/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/
00:56:43 creating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/var/
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/LICENSE.txt
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/backup.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/blitz/mail-senders.example
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/blitz/mail-server.example
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/build.properties
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/env.bat
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/env.sh
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/hibernate.properties
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/ice.config
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/logback-cli.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/logback-indexing-cli.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/logback-indexing.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/logback.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/mime.types
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/node1.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/node2.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/omero.properties
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/profiles/psql
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/rollover.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/Windows.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/error/maintainance.html
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/grid/README
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/grid/default.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/grid/templates.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/grid/windefault.xml
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/ice.config
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/internal.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/master.cfg
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/templates/robot.template
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/etc/testdropbox.config
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/history.rst
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/OMEZarrReader.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/activation.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/aggdesigner-algorithm.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/aircompressor.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/antlr.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/aopalliance.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/avatica-core.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/avatica-metrics.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/aws-java-sdk-core.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/aws-java-sdk-kms.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/aws-java-sdk-s3.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/base.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-all.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-anim.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-awt-util.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-bridge.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-codec.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-constants.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-css.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-dom.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-ext.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-extension.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-gui-util.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-gvt.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-i18n.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-parser.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-rasterizer-ext.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-rasterizer.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-script.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-slideshow.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-squiggle-ext.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-squiggle.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-svg-dom.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-svgbrowser.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-svggen.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-svgpp.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-svgrasterizer.jar
00:56:43 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/lib/client/batik-swing.jar
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00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/psql-footer.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/psql-header.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/schema.sql
00:56:46 inflating: OMERO.server-5.6.3-552-3c3352813e-ice36-b411/sql/psql/OMERO5.4__0/views.sql
00:56:46 + rm -f OMERO.server-5.6.3-552-3c3352813e-ice36-b411.zip
00:56:46 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-552-3c3352813e-ice36-b411 /home/omero/workspace/OMERO-server/OMERO.server
00:56:46 + wget --no-hsts -P /home/omero/workspace/OMERO-server/OMERO.server/lib/server/ https://artifacts.glencoesoftware.com:443/artifactory/omero-plus/com/glencoesoftware/omero/omero-zarr-pixel-buffer/0.4.1/omero-zarr-pixel-buffer-0.4.1.jar
00:56:47 --2025-05-14 00:56:47-- https://artifacts.glencoesoftware.com/artifactory/omero-plus/com/glencoesoftware/omero/omero-zarr-pixel-buffer/0.4.1/omero-zarr-pixel-buffer-0.4.1.jar
00:56:47 Resolving artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)... 67.205.169.144, 2604:a880:400:d0::19b7:6001
00:56:47 Connecting to artifacts.glencoesoftware.com (artifacts.glencoesoftware.com)|67.205.169.144|:443... connected.
00:56:47 HTTP request sent, awaiting response... 200 OK
00:56:48 Length: 26159 (26K) [application/java-archive]
00:56:48 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’
00:56:48
00:56:48 0K .......... .......... ..... 100% 156M=0s
00:56:48
00:56:48 2025-05-14 00:56:48 (156 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/omero-zarr-pixel-buffer-0.4.1.jar’ saved [26159/26159]
00:56:48
00:56:48 + 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
00:56:48 --2025-05-14 00:56:48-- https://repo1.maven.org/maven2/com/github/ben-manes/caffeine/caffeine/3.1.8/caffeine-3.1.8.jar
00:56:48 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:56:48 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:56:48 HTTP request sent, awaiting response... 200 OK
00:56:48 Length: 889211 (868K) [application/java-archive]
00:56:48 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’
00:56:48
00:56:48 0K .......... .......... .......... .......... .......... 5% 3.30M 0s
00:56:48 50K .......... .......... .......... .......... .......... 11% 5.19M 0s
00:56:48 100K .......... .......... .......... .......... .......... 17% 20.5M 0s
00:56:48 150K .......... .......... .......... .......... .......... 23% 7.07M 0s
00:56:48 200K .......... .......... .......... .......... .......... 28% 34.4M 0s
00:56:48 250K .......... .......... .......... .......... .......... 34% 26.9M 0s
00:56:48 300K .......... .......... .......... .......... .......... 40% 37.6M 0s
00:56:48 350K .......... .......... .......... .......... .......... 46% 9.54M 0s
00:56:48 400K .......... .......... .......... .......... .......... 51% 23.1M 0s
00:56:48 450K .......... .......... .......... .......... .......... 57% 124M 0s
00:56:48 500K .......... .......... .......... .......... .......... 63% 27.2M 0s
00:56:48 550K .......... .......... .......... .......... .......... 69% 8.89M 0s
00:56:48 600K .......... .......... .......... .......... .......... 74% 28.8M 0s
00:56:48 650K .......... .......... .......... .......... .......... 80% 28.5M 0s
00:56:48 700K .......... .......... .......... .......... .......... 86% 112M 0s
00:56:48 750K .......... .......... .......... .......... .......... 92% 33.4M 0s
00:56:48 800K .......... .......... .......... .......... .......... 97% 7.89M 0s
00:56:48 850K .......... ........ 100% 191M=0.06s
00:56:48
00:56:48 2025-05-14 00:56:48 (13.1 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/caffeine-3.1.8.jar’ saved [889211/889211]
00:56:48
00:56:48 + 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
00:56:48 --2025-05-14 00:56:48-- https://repo1.maven.org/maven2/dev/zarr/jzarr/0.4.2/jzarr-0.4.2.jar
00:56:48 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:56:48 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:56:48 HTTP request sent, awaiting response... 200 OK
00:56:48 Length: 73309 (72K) [application/java-archive]
00:56:48 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’
00:56:48
00:56:48 0K .......... .......... .......... .......... .......... 69% 3.22M 0s
00:56:48 50K .......... .......... . 100% 3.15M=0.02s
00:56:48
00:56:48 2025-05-14 00:56:48 (3.20 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/jzarr-0.4.2.jar’ saved [73309/73309]
00:56:48
00:56:48 + 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
00:56:48 --2025-05-14 00:56:48-- https://repo1.maven.org/maven2/org/lasersonlab/s3fs/2.2.3/s3fs-2.2.3.jar
00:56:48 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:56:48 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:56:48 HTTP request sent, awaiting response... 200 OK
00:56:48 Length: 63303 (62K) [application/java-archive]
00:56:48 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’
00:56:48
00:56:48 0K .......... .......... .......... .......... .......... 80% 3.40M 0s
00:56:48 50K .......... . 100% 27.9M=0.01s
00:56:48
00:56:48 2025-05-14 00:56:48 (4.09 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/s3fs-2.2.3.jar’ saved [63303/63303]
00:56:48
00:56:48 + 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
00:56:48 --2025-05-14 00:56:48-- https://repo1.maven.org/maven2/com/amazonaws/aws-java-sdk-s3/1.12.659/aws-java-sdk-s3-1.12.659.jar
00:56:49 Resolving repo1.maven.org (repo1.maven.org)... 146.75.72.209, 2a04:4e42:82::209
00:56:49 Connecting to repo1.maven.org (repo1.maven.org)|146.75.72.209|:443... connected.
00:56:49 HTTP request sent, awaiting response... 200 OK
00:56:49 Length: 1271272 (1.2M) [application/java-archive]
00:56:49 Saving to: ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’
00:56:49
00:56:49 0K .......... .......... .......... .......... .......... 4% 3.27M 0s
00:56:49 50K .......... .......... .......... .......... .......... 8% 5.27M 0s
00:56:49 100K .......... .......... .......... .......... .......... 12% 17.9M 0s
00:56:49 150K .......... .......... .......... .......... .......... 16% 7.20M 0s
00:56:49 200K .......... .......... .......... .......... .......... 20% 28.7M 0s
00:56:49 250K .......... .......... .......... .......... .......... 24% 43.8M 0s
00:56:49 300K .......... .......... .......... .......... .......... 28% 8.51M 0s
00:56:49 350K .......... .......... .......... .......... .......... 32% 34.2M 0s
00:56:49 400K .......... .......... .......... .......... .......... 36% 39.0M 0s
00:56:49 450K .......... .......... .......... .......... .......... 40% 35.9M 0s
00:56:49 500K .......... .......... .......... .......... .......... 44% 28.0M 0s
00:56:49 550K .......... .......... .......... .......... .......... 48% 8.25M 0s
00:56:49 600K .......... .......... .......... .......... .......... 52% 128M 0s
00:56:49 650K .......... .......... .......... .......... .......... 56% 36.7M 0s
00:56:49 700K .......... .......... .......... .......... .......... 60% 31.5M 0s
00:56:49 750K .......... .......... .......... .......... .......... 64% 34.6M 0s
00:56:49 800K .......... .......... .......... .......... .......... 68% 7.91M 0s
00:56:49 850K .......... .......... .......... .......... .......... 72% 105M 0s
00:56:49 900K .......... .......... .......... .......... .......... 76% 48.1M 0s
00:56:49 950K .......... .......... .......... .......... .......... 80% 31.3M 0s
00:56:49 1000K .......... .......... .......... .......... .......... 84% 37.8M 0s
00:56:49 1050K .......... .......... .......... .......... .......... 88% 151M 0s
00:56:49 1100K .......... .......... .......... .......... .......... 92% 7.79M 0s
00:56:49 1150K .......... .......... .......... .......... .......... 96% 44.0M 0s
00:56:49 1200K .......... .......... .......... .......... . 100% 30.4M=0.08s
00:56:49
00:56:49 2025-05-14 00:56:49 (15.5 MB/s) - ‘/home/omero/workspace/OMERO-server/OMERO.server/lib/server/aws-java-sdk-s3-1.12.659.jar’ saved [1271272/1271272]
00:56:49
00:56:49 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:56:49 ++ deactivate nondestructive
00:56:49 ++ '[' -n '' ']'
00:56:49 ++ '[' -n '' ']'
00:56:49 ++ hash -r
00:56:49 ++ '[' -n '' ']'
00:56:49 ++ unset VIRTUAL_ENV
00:56:49 ++ unset VIRTUAL_ENV_PROMPT
00:56:49 ++ '[' '!' nondestructive = nondestructive ']'
00:56:49 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:56:49 ++ export VIRTUAL_ENV
00:56:49 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:56:49 ++ 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
00:56:49 ++ export PATH
00:56:49 ++ '[' -n '' ']'
00:56:49 ++ '[' -z '' ']'
00:56:49 ++ _OLD_VIRTUAL_PS1=
00:56:49 ++ PS1='(.venv3) '
00:56:49 ++ export PS1
00:56:49 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:56:49 ++ export VIRTUAL_ENV_PROMPT
00:56:49 ++ hash -r
00:56:49 + pip install -U pip
00:56:49 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:56:50 Collecting pip
00:56:50 Using cached pip-25.1.1-py3-none-any.whl (1.8 MB)
00:56:50 Installing collected packages: pip
00:56:50 Attempting uninstall: pip
00:56:50 Found existing installation: pip 22.3.1
00:56:51 Uninstalling pip-22.3.1:
00:56:51 Successfully uninstalled pip-22.3.1
00:56:52 Successfully installed pip-25.1.1
00:56:52 WARNING: There was an error checking the latest version of pip.
00:56:52 + 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
00:56:52 Collecting zeroc-ice==3.6.5
00:56:53 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)
00:56:55 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 23.4 MB/s eta 0:00:00
00:56:55 Installing collected packages: zeroc-ice
00:56:56 Successfully installed zeroc-ice-3.6.5
00:56:56 + pip install markdown
00:56:56 Collecting markdown
00:56:56 Using cached markdown-3.8-py3-none-any.whl.metadata (5.1 kB)
00:56:56 Using cached markdown-3.8-py3-none-any.whl (106 kB)
00:56:56 Installing collected packages: markdown
00:56:56 Successfully installed markdown-3.8
00:56:56 + pip install reportlab
00:56:57 Collecting reportlab
00:56:57 Using cached reportlab-4.4.0-py3-none-any.whl.metadata (1.8 kB)
00:56:57 Collecting pillow>=9.0.0 (from reportlab)
00:56:57 Using cached pillow-11.2.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (8.9 kB)
00:56:57 Collecting chardet (from reportlab)
00:56:57 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
00:56:57 Using cached reportlab-4.4.0-py3-none-any.whl (2.0 MB)
00:56:57 Using cached pillow-11.2.1-cp311-cp311-manylinux_2_28_x86_64.whl (4.6 MB)
00:56:58 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
00:56:58 Installing collected packages: pillow, chardet, reportlab
00:56:59
00:56:59 Successfully installed chardet-5.2.0 pillow-11.2.1 reportlab-4.4.0
00:56:59 + pip install omego
00:57:00 Collecting omego
00:57:00 Using cached omego-0.7.0-py3-none-any.whl
00:57:00 Collecting future (from omego)
00:57:00 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:57:00 Collecting yaclifw>=0.1.1 (from omego)
00:57:00 Using cached yaclifw-0.2.0-py3-none-any.whl
00:57:00 Collecting six (from yaclifw>=0.1.1->omego)
00:57:00 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:57:00 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:57:01 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:57:01 Installing collected packages: six, future, yaclifw, omego
00:57:01
00:57:01 Successfully installed future-1.0.0 omego-0.7.0 six-1.17.0 yaclifw-0.2.0
00:57:01 + pip install tables
00:57:02 Collecting tables
00:57:02 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.0 kB)
00:57:02 Collecting numpy>=1.20.0 (from tables)
00:57:02 Using cached numpy-2.2.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
00:57:02 Collecting numexpr>=2.6.2 (from tables)
00:57:02 Using cached numexpr-2.10.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
00:57:02 Collecting packaging (from tables)
00:57:02 Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
00:57:02 Collecting py-cpuinfo (from tables)
00:57:02 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:57:03 Collecting blosc2>=2.3.0 (from tables)
00:57:03 Using cached blosc2-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.9 kB)
00:57:03 Collecting typing-extensions>=4.4.0 (from tables)
00:57:03 Using cached typing_extensions-4.13.2-py3-none-any.whl.metadata (3.0 kB)
00:57:03 Collecting ndindex (from blosc2>=2.3.0->tables)
00:57:03 Using cached ndindex-1.9.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB)
00:57:03 Collecting msgpack (from blosc2>=2.3.0->tables)
00:57:03 Using cached msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:57:03 Collecting platformdirs (from blosc2>=2.3.0->tables)
00:57:04 Using cached platformdirs-4.3.8-py3-none-any.whl.metadata (12 kB)
00:57:04 Collecting requests (from blosc2>=2.3.0->tables)
00:57:04 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
00:57:04 Collecting charset-normalizer<4,>=2 (from requests->blosc2>=2.3.0->tables)
00:57:04 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
00:57:04 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
00:57:04 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:57:04 Collecting urllib3<3,>=1.21.1 (from requests->blosc2>=2.3.0->tables)
00:57:04 Using cached urllib3-2.4.0-py3-none-any.whl.metadata (6.5 kB)
00:57:05 Collecting certifi>=2017.4.17 (from requests->blosc2>=2.3.0->tables)
00:57:05 Using cached certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB)
00:57:05 Using cached tables-3.10.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:57:05 Using cached blosc2-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
00:57:05 Using cached numexpr-2.10.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (398 kB)
00:57:05 Using cached numpy-2.2.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.4 MB)
00:57:05 Using cached typing_extensions-4.13.2-py3-none-any.whl (45 kB)
00:57:05 Using cached msgpack-1.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (403 kB)
00:57:05 Using cached ndindex-1.9.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (506 kB)
00:57:06 Using cached packaging-25.0-py3-none-any.whl (66 kB)
00:57:06 Using cached platformdirs-4.3.8-py3-none-any.whl (18 kB)
00:57:06 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:57:06 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
00:57:06 Using cached charset_normalizer-3.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (147 kB)
00:57:06 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:57:06 Using cached urllib3-2.4.0-py3-none-any.whl (128 kB)
00:57:06 Using cached certifi-2025.4.26-py3-none-any.whl (159 kB)
00:57:07 Installing collected packages: py-cpuinfo, urllib3, typing-extensions, platformdirs, packaging, numpy, ndindex, msgpack, idna, charset-normalizer, certifi, requests, numexpr, blosc2, tables
00:57:10
00:57:10 Successfully installed blosc2-3.3.2 certifi-2025.4.26 charset-normalizer-3.4.2 idna-3.10 msgpack-1.1.0 ndindex-1.9.2 numexpr-2.10.2 numpy-2.2.5 packaging-25.0 platformdirs-4.3.8 py-cpuinfo-9.0.0 requests-2.32.3 tables-3.10.2 typing-extensions-4.13.2 urllib3-2.4.0
00:57:10 + pip install jinja2
00:57:11 Collecting jinja2
00:57:11 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:57:11 Collecting MarkupSafe>=2.0 (from jinja2)
00:57:11 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:57:11 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:57:11 Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
00:57:11 Installing collected packages: MarkupSafe, jinja2
00:57:11
00:57:11 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.6
00:57:11 + pip install omero-py
00:57:12 Collecting omero-py
00:57:12 Using cached omero_py-5.20.0-py3-none-any.whl.metadata (6.5 kB)
00:57:12 Collecting urllib3<2 (from omero-py)
00:57:12 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:57:12 Collecting appdirs (from omero-py)
00:57:12 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:57:12 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:57:12 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.2.5)
00:57:12 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (11.2.1)
00:57:12 Collecting PyYAML (from omero-py)
00:57:12 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:57:12 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:57:12 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.32.3)
00:57:12 Collecting portalocker (from omero-py)
00:57:12 Using cached portalocker-3.1.1-py3-none-any.whl.metadata (8.6 kB)
00:57:12 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.2)
00:57:12 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.10)
00:57:12 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2025.4.26)
00:57:12 Using cached omero_py-5.20.0-py3-none-any.whl (2.8 MB)
00:57:13 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:57:13 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:57:13 Using cached portalocker-3.1.1-py3-none-any.whl (19 kB)
00:57:13 Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
00:57:13 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, omero-py
00:57:13 Attempting uninstall: urllib3
00:57:13 Found existing installation: urllib3 2.4.0
00:57:13 Uninstalling urllib3-2.4.0:
00:57:13 Successfully uninstalled urllib3-2.4.0
00:57:15
00:57:15 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 omero-py-5.20.0 portalocker-3.1.1 urllib3-1.26.20
00:57:15 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:57:15 Collecting omero-metadata
00:57:15 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-tynt1bec/omero-metadata_6cc7cad4dcb34cf686fdc574e67a7636
00:57:15 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-tynt1bec/omero-metadata_6cc7cad4dcb34cf686fdc574e67a7636
00:57:17 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 36a84f212209decfc1025b4758b1971dd3a379d3
00:57:17 Installing build dependencies: started
00:57:18 Installing build dependencies: finished with status 'done'
00:57:18 Getting requirements to build wheel: started
00:57:18 Getting requirements to build wheel: finished with status 'done'
00:57:18 Preparing metadata (pyproject.toml): started
00:57:18 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:18 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.20.0)
00:57:18 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.2)
00:57:18 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
00:57:19 Collecting pandas (from omero-metadata)
00:57:19 Using cached pandas-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
00:57:19 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:57:19 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:57:19 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:57:19 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.2.5)
00:57:19 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (11.2.1)
00:57:19 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)
00:57:19 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
00:57:19 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.1.1)
00:57:19 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.2)
00:57:19 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
00:57:19 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:57:19 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:57:19 Using cached pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB)
00:57:19 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:57:19 Using cached tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:57:19 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)
00:57:19 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)
00:57:19 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)
00:57:19 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2025.4.26)
00:57:19 Using cached pandas-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
00:57:19 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:57:20 Using cached pytz-2025.2-py2.py3-none-any.whl (509 kB)
00:57:20 Using cached tzdata-2025.2-py2.py3-none-any.whl (347 kB)
00:57:20 Building wheels for collected packages: omero-metadata
00:57:20 Building wheel for omero-metadata (pyproject.toml): started
00:57:22 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:57:22 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39280 sha256=7b0db01a44219e8266f7d4691597540ffd64158c60209a1a659dbd602a410eac
00:57:22 Stored in directory: /tmp/pip-ephem-wheel-cache-esjvh9f2/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:57:22 Successfully built omero-metadata
00:57:22 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
00:57:27
00:57:27 Successfully installed omero-metadata-0.13.1.dev0 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 tzdata-2025.2
00:57:27 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:57:27 Collecting omero-cli-render
00:57:27 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-0hixlrd5/omero-cli-render_a4aa54bcd69b490ead8ec9fd4a4d0fa9
00:57:27 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-0hixlrd5/omero-cli-render_a4aa54bcd69b490ead8ec9fd4a4d0fa9
00:57:28 Running command git checkout -b merge_ci --track origin/merge_ci
00:57:28 Switched to a new branch 'merge_ci'
00:57:28 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:57:28 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 0c1ea55380714e757841a9807d8aa6f0ed894844
00:57:28 Installing build dependencies: started
00:57:29 Installing build dependencies: finished with status 'done'
00:57:29 Getting requirements to build wheel: started
00:57:29 Getting requirements to build wheel: finished with status 'done'
00:57:29 Preparing metadata (pyproject.toml): started
00:57:30 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:30 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.2)
00:57:30 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.20.0)
00:57:30 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:57:30 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:57:30 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:57:30 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.2.5)
00:57:30 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.2.1)
00:57:30 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)
00:57:30 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
00:57:30 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.1.1)
00:57:30 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)
00:57:30 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)
00:57:30 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2025.4.26)
00:57:30 Building wheels for collected packages: omero-cli-render
00:57:30 Building wheel for omero-cli-render (pyproject.toml): started
00:57:30 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:57:30 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19694 sha256=2719eb659e313f4bfba932ec47eeb7fd42bc716d7a822311b7aff47683f80ed0
00:57:30 Stored in directory: /tmp/pip-ephem-wheel-cache-g7fi8top/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:57:30 Successfully built omero-cli-render
00:57:30 Installing collected packages: omero-cli-render
00:57:30 Successfully installed omero-cli-render-0.8.2.dev0
00:57:30 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:57:30 Collecting omero-cli-duplicate
00:57:30 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-en69rji5/omero-cli-duplicate_9f2521d1cf114d3bbae3778e0479299b
00:57:30 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-en69rji5/omero-cli-duplicate_9f2521d1cf114d3bbae3778e0479299b
00:57:31 Running command git checkout -b merge_ci --track origin/merge_ci
00:57:31 Switched to a new branch 'merge_ci'
00:57:31 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:57:31 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 4ddf4a0043ced93f753960795c68d3f930dde987
00:57:31 Installing build dependencies: started
00:57:32 Installing build dependencies: finished with status 'done'
00:57:32 Getting requirements to build wheel: started
00:57:33 Getting requirements to build wheel: finished with status 'done'
00:57:33 Preparing metadata (pyproject.toml): started
00:57:33 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:33 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.20.0)
00:57:33 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:57:33 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:57:33 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:57:33 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.2.5)
00:57:33 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.2.1)
00:57:33 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:57:33 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)
00:57:33 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
00:57:33 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.1.1)
00:57:33 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)
00:57:33 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)
00:57:33 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2025.4.26)
00:57:33 Building wheels for collected packages: omero-cli-duplicate
00:57:33 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:57:33 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:57:33 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11538 sha256=d5d802f8ac289ea6cf34a5882dc7892fab975ff5505052140ffe806fbdda977a
00:57:33 Stored in directory: /tmp/pip-ephem-wheel-cache-jsvt61gt/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:57:33 Successfully built omero-cli-duplicate
00:57:33 Installing collected packages: omero-cli-duplicate
00:57:34 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:57:34 + pip install omero-certificates
00:57:35 Collecting omero-certificates
00:57:35 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:57:35 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.20.0)
00:57:35 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:57:35 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:57:35 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:57:35 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.2.5)
00:57:35 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (11.2.1)
00:57:35 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:57:35 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)
00:57:35 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
00:57:35 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.1.1)
00:57:35 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)
00:57:35 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)
00:57:35 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2025.4.26)
00:57:35 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:57:35 Installing collected packages: omero-certificates
00:57:35 Successfully installed omero-certificates-0.4.0
00:57:35 + for x in *.tar.gz
00:57:35 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:57:35 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:57:35 Installing build dependencies: started
00:57:36 Installing build dependencies: finished with status 'done'
00:57:36 Getting requirements to build wheel: started
00:57:36 Getting requirements to build wheel: finished with status 'done'
00:57:36 Preparing metadata (pyproject.toml): started
00:57:37 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:37 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.20.0)
00:57:37 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
00:57:37 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:57:37 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:57:37 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.2.5)
00:57:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.2.1)
00:57:37 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:57:37 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)
00:57:37 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3)
00:57:37 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.1.1)
00:57:37 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)
00:57:37 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)
00:57:37 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2025.4.26)
00:57:37 Building wheels for collected packages: omero-dropbox
00:57:37 Building wheel for omero-dropbox (pyproject.toml): started
00:57:37 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:57:37 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49140 sha256=07bc358af03a96db7a16b3c2940b02d222b3d599c6bbfeb1f672e47dbf405910
00:57:37 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:57:37 Successfully built omero-dropbox
00:57:37 Installing collected packages: omero-dropbox
00:57:37 Successfully installed omero-dropbox-5.7.1.dev0
00:57:37 + for x in *.tar.gz
00:57:37 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:57:37 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:57:38 Installing build dependencies: started
00:57:38 Installing build dependencies: finished with status 'done'
00:57:38 Getting requirements to build wheel: started
00:57:39 Getting requirements to build wheel: finished with status 'done'
00:57:39 Preparing metadata (pyproject.toml): started
00:57:39 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:39 Building wheels for collected packages: omero_marshal
00:57:39 Building wheel for omero_marshal (pyproject.toml): started
00:57:39 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:57:39 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88124 sha256=a7d8919e4f25876604f542c4b7d4dc782b5c15e3f2b2cb410cc02b11518b3359
00:57:39 Stored in directory: /home/omero/.cache/pip/wheels/c6/fe/20/4909beb8cad01183b3ea19e12252f8ddec6c22448a9830df18
00:57:39 Successfully built omero_marshal
00:57:40 Installing collected packages: omero_marshal
00:57:40 Successfully installed omero_marshal-0.9.1.dev0
00:57:40 + for x in *.tar.gz
00:57:40 + pip install -U omero_py-5.20.1.dev0.tar.gz
00:57:40 Processing ./omero_py-5.20.1.dev0.tar.gz
00:57:40 Installing build dependencies: started
00:57:41 Installing build dependencies: finished with status 'done'
00:57:41 Getting requirements to build wheel: started
00:57:42 Getting requirements to build wheel: finished with status 'done'
00:57:42 Preparing metadata (pyproject.toml): started
00:57:42 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:42 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (1.26.20)
00:57:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (1.4.4)
00:57:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (1.0.0)
00:57:42 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (2.2.5)
00:57:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (11.2.1)
00:57:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (6.0.2)
00:57:42 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (3.6.5)
00:57:42 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (2.32.3)
00:57:42 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.20.1.dev0) (3.1.1)
00:57:42 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.20.1.dev0) (3.4.2)
00:57:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.20.1.dev0) (3.10)
00:57:42 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.20.1.dev0) (2025.4.26)
00:57:42 Building wheels for collected packages: omero-py
00:57:42 Building wheel for omero-py (pyproject.toml): started
00:57:43 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:57:43 Created wheel for omero-py: filename=omero_py-5.20.1.dev0-py3-none-any.whl size=2783232 sha256=9af495df0f25480ae04b2a7e602ecf4152fed866b201c7ca65e8ab7b64645c21
00:57:43 Stored in directory: /home/omero/.cache/pip/wheels/32/f0/8b/0c9b8cf4f8a22d20fdbdb6d870eee959c7bb16ef86f85fd19c
00:57:43 Successfully built omero-py
00:57:43 Installing collected packages: omero-py
00:57:43 Attempting uninstall: omero-py
00:57:43 Found existing installation: omero-py 5.20.0
00:57:43 Uninstalling omero-py-5.20.0:
00:57:44 Successfully uninstalled omero-py-5.20.0
00:57:45 Successfully installed omero-py-5.20.1.dev0
00:57:46 + for x in *.tar.gz
00:57:46 + pip install -U omero_scripts-5.9.1.dev0.tar.gz
00:57:46 Processing ./omero_scripts-5.9.1.dev0.tar.gz
00:57:46 Installing build dependencies: started
00:57:47 Installing build dependencies: finished with status 'done'
00:57:47 Getting requirements to build wheel: started
00:57:47 Getting requirements to build wheel: finished with status 'done'
00:57:47 Preparing metadata (pyproject.toml): started
00:57:47 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:47 Building wheels for collected packages: omero-scripts
00:57:47 Building wheel for omero-scripts (pyproject.toml): started
00:57:48 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:57:48 Created wheel for omero-scripts: filename=omero_scripts-5.9.1.dev0-py3-none-any.whl size=136849 sha256=c9766c5a016bbd65f5bd681be9a6e563d0344b726090088997acc1391ac5242e
00:57:48 Stored in directory: /home/omero/.cache/pip/wheels/5d/64/64/66c19773daf66dee2b16f9ebd49fde08680f277d4fff67beed
00:57:48 Successfully built omero-scripts
00:57:48 Installing collected packages: omero-scripts
00:57:48 Successfully installed omero-scripts-5.9.1.dev0
00:57:48 + for x in *.tar.gz
00:57:48 + pip install -U omero_web-5.29.1.dev0.tar.gz
00:57:48 Processing ./omero_web-5.29.1.dev0.tar.gz
00:57:49 Installing build dependencies: started
00:57:49 Installing build dependencies: finished with status 'done'
00:57:49 Getting requirements to build wheel: started
00:57:50 Getting requirements to build wheel: finished with status 'done'
00:57:50 Preparing metadata (pyproject.toml): started
00:57:50 Preparing metadata (pyproject.toml): finished with status 'done'
00:57:50 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (5.20.1.dev0)
00:57:50 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.29.1.dev0)
00:57:50 Using cached concurrent_log_handler-0.9.26-py3-none-any.whl.metadata (19 kB)
00:57:51 Collecting Django<4.3,>=4.2.3 (from omero-web==5.29.1.dev0)
00:57:51 Using cached django-4.2.21-py3-none-any.whl.metadata (4.2 kB)
00:57:51 Collecting django-pipeline (from omero-web==5.29.1.dev0)
00:57:51 Using cached django_pipeline-4.0.0-py3-none-any.whl.metadata (5.8 kB)
00:57:51 Collecting django-cors-headers==3.7.0 (from omero-web==5.29.1.dev0)
00:57:51 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:57:51 Collecting django-csp (from omero-web==5.29.1.dev0)
00:57:51 Using cached django_csp-4.0-py3-none-any.whl.metadata (3.6 kB)
00:57:51 Collecting whitenoise>=5.3.0 (from omero-web==5.29.1.dev0)
00:57:51 Using cached whitenoise-6.9.0-py3-none-any.whl.metadata (3.6 kB)
00:57:51 Collecting gunicorn>=19.3 (from omero-web==5.29.1.dev0)
00:57:51 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:57:51 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (0.9.1.dev0)
00:57:51 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (11.2.1)
00:57:51 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (2025.2)
00:57:51 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (3.1.1)
00:57:51 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.29.1.dev0) (25.0)
00:57:51 Collecting importlib-resources (from omero-web==5.29.1.dev0)
00:57:51 Using cached importlib_resources-6.5.2-py3-none-any.whl.metadata (3.9 kB)
00:57:51 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.29.1.dev0)
00:57:51 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
00:57:51 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.29.1.dev0)
00:57:51 Using cached sqlparse-0.5.3-py3-none-any.whl.metadata (3.9 kB)
00:57:51 Requirement already satisfied: urllib3<2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (1.26.20)
00:57:51 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (1.4.4)
00:57:51 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (1.0.0)
00:57:51 Requirement already satisfied: numpy<3 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (2.2.5)
00:57:51 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (6.0.2)
00:57:51 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (3.6.5)
00:57:51 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.29.1.dev0) (2.32.3)
00:57:52 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline->omero-web==5.29.1.dev0) (65.5.1)
00:57:52 Collecting wheel (from django-pipeline->omero-web==5.29.1.dev0)
00:57:52 Using cached wheel-0.45.1-py3-none-any.whl.metadata (2.3 kB)
00:57:52 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.1.dev0) (3.4.2)
00:57:52 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.1.dev0) (3.10)
00:57:52 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.29.1.dev0) (2025.4.26)
00:57:52 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:57:52 Using cached django-4.2.21-py3-none-any.whl (8.0 MB)
00:57:52 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
00:57:52 Using cached concurrent_log_handler-0.9.26-py3-none-any.whl (28 kB)
00:57:52 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:57:52 Using cached sqlparse-0.5.3-py3-none-any.whl (44 kB)
00:57:52 Using cached whitenoise-6.9.0-py3-none-any.whl (20 kB)
00:57:52 Using cached django_csp-4.0-py3-none-any.whl (25 kB)
00:57:52 Using cached django_pipeline-4.0.0-py3-none-any.whl (75 kB)
00:57:53 Using cached importlib_resources-6.5.2-py3-none-any.whl (37 kB)
00:57:53 Using cached wheel-0.45.1-py3-none-any.whl (72 kB)
00:57:53 Building wheels for collected packages: omero-web
00:57:53 Building wheel for omero-web (pyproject.toml): started
00:57:54 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:57:54 Created wheel for omero-web: filename=omero_web-5.29.1.dev0-py3-none-any.whl size=2817974 sha256=8429f59f3928d6dae1cd7a367ccfc97506b90e8985860988ce13ccdbb20b7a58
00:57:54 Stored in directory: /home/omero/.cache/pip/wheels/b6/72/73/a29488e9ae7a2242fcfdc532a2c6f9884a34cc378eb261962a
00:57:54 Successfully built omero-web
00:57:54 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-csp, django-cors-headers, omero-web
00:57:57
00:57:57 Successfully installed Django-4.2.21 asgiref-3.8.1 concurrent-log-handler-0.9.26 django-cors-headers-3.7.0 django-csp-4.0 django-pipeline-4.0.0 gunicorn-23.0.0 importlib-resources-6.5.2 omero-web-5.29.1.dev0 sqlparse-0.5.3 wheel-0.45.1 whitenoise-6.9.0
00:57:57 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:57:57 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:57:57 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:57:57 --2025-05-14 00:57:57-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:57:57 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.108.133, 185.199.110.133, 185.199.109.133, ...
00:57:57 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.108.133|:443... connected.
00:57:57 HTTP request sent, awaiting response... 200 OK
00:57:57 Length: 122144 (119K) [text/plain]
00:57:57 Saving to: ‘Figure_To_Pdf.py’
00:57:57
00:57:57 0K .......... .......... .......... .......... .......... 41% 3.43M 0s
00:57:57 50K .......... .......... .......... .......... .......... 83% 5.04M 0s
00:57:58 100K .......... ......... 100% 253M=0.02s
00:57:58
00:57:58 2025-05-14 00:57:58 (4.85 MB/s) - ‘Figure_To_Pdf.py’ saved [122144/122144]
00:57:58
00:57:58 + chmod 755 Figure_To_Pdf.py
00:57:58 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:57:58 + omero config set omero.db.name OMERO-server
00:57:59 + omero config set omero.db.host pg
00:58:00 + omero config set omero.db.user postgres
00:58:01 + omero config set omero.data.dir /home/omero/omero-server-data
00:58:02 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:58:03 + omero config set omero.db.poolsize 25
00:58:05 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:58:06 + omero config set omero.security.trustStorePassword changeit
00:58:07 + omero config set omero.mail.config true
00:58:08 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:58:09 + omero config set omero.mail.host smtp.dundee.ac.uk
00:58:11 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:58:12 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:58:13 + omero certificates
00:58:14 OpenSSL 3.2.2 4 Jun 2024 (Library: OpenSSL 3.2.2 4 Jun 2024)
00:58:14 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:58:14 + '[' false = true ']'
00:58:14 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:58:14 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:58:14 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG dbcommand => upgrade
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG dbhost => localhost
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG dbname => OMERO-server
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG dbpass => omero
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG dbuser => omero
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG rootpass => omero
00:58:15 2025-05-14 00:58:15,074 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:58:15 2025-05-14 00:58:15,074 [omego.extern] INFO Executing : omero version
00:58:16 OMERO.py version:
00:58:16 OMERO.server version:
00:58:16 5.6.3-552-3c3352813e-ice36-b411
00:58:16 5.20.1.dev0
00:58:16 2025-05-14 00:58:16,295 [omego.extern] INFO Completed [1.220 s]
00:58:16 2025-05-14 00:58:16,295 [omego.extern] DEBUG Using omero CLI from omero
00:58:16 2025-05-14 00:58:16,295 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:58:16 2025-05-14 00:58:16,295 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:58:16 2025-05-14 00:58:16,295 [omego.extern] INFO Executing : omero config get --show-password
00:58:17 2025-05-14 00:58:17,502 [omego.extern] INFO Completed [1.207 s]
00:58:17 2025-05-14 00:58:17,502 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:58:17 2025-05-14 00:58:17,502 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:58:18 2025-05-14 00:58:18,098 [omego.extern] INFO Completed [0.595 s]
00:58:18 2025-05-14 00:58:18,098 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.8\n'
00:58:18 2025-05-14 00:58:18,098 [ omego.db] INFO psql version: psql (PostgreSQL) 16.8
00:58:18
00:58:18 2025-05-14 00:58:18,098 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:58:18 2025-05-14 00:58:18,098 [omego.extern] INFO Executing : omero config get --show-password
00:58:19 2025-05-14 00:58:19,278 [omego.extern] INFO Completed [1.180 s]
00:58:19 2025-05-14 00:58:19,278 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:58:19 2025-05-14 00:58:19,278 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:58:19 2025-05-14 00:58:19,406 [omego.extern] INFO Completed [0.128 s]
00:58:19 2025-05-14 00:58:19,406 [ 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'
00:58:19 2025-05-14 00:58:19,406 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:58:19 2025-05-14 00:58:19,406 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:58:19 2025-05-14 00:58:19,406 [omego.extern] INFO Executing : omero config get --show-password
00:58:20 2025-05-14 00:58:20,592 [omego.extern] INFO Completed [1.186 s]
00:58:20 2025-05-14 00:58:20,592 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:58:20 2025-05-14 00:58:20,592 [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
00:58:21 2025-05-14 00:58:21,158 [omego.extern] INFO Completed [0.565 s]
00:58:21 2025-05-14 00:58:21,158 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:58:21 2025-05-14 00:58:21,158 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:58:21 2025-05-14 00:58:21,160 [ omego.db] INFO Database is already at OMERO5.4__0
00:58:21 + export LANG=en_US.UTF-8
00:58:21 + LANG=en_US.UTF-8
00:58:21 + export LANGUAGE=en_US:en
00:58:21 + LANGUAGE=en_US:en
00:58:21 + export LC_ALL=en_US.UTF-8
00:58:21 + LC_ALL=en_US.UTF-8
00:58:21 + BUILD_ID=DONT_KILL_ME
00:58:21 + omero admin start
00:58:27 No descriptor given. Using etc/grid/default.xml
00:58:34 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:58:34 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:58:34 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:58:34 Waiting on startup. Use CTRL-C to exit
00:58:34 .............................
01:03:25 Failed to startup some components after 300 seconds
01:03:25 Calling "stop" on remaining components
01:03:25 Waiting on shutdown. Use CTRL-C to exit
01:03:25 ......Build step 'Execute shell' marked build as failure
01:04:26 Finished: FAILURE
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