07:48:32 Started by upstream project "Trigger" build number 190
07:48:32 originally caused by:
07:48:32 Started by user devspace
07:48:32 Running as SYSTEM
07:48:33 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
07:48:33 [OMERO-server] $ /bin/bash -xe /tmp/jenkins4739316988611402277.sh
07:48:33 + source /home/settings.env
07:48:33 ++ OMERO_DB_HOST=pg
07:48:33 ++ OMERO_DB_USER=postgres
07:48:33 ++ OMERO_DB_PASS=
07:48:33 ++ OMERO_ROOT_PASS=omero
07:48:33 ++ OMERO_DATA_DIR=/OMERO
07:48:33 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
07:48:33 + OMERO_DB_NAME=OMERO-server
07:48:33 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
07:48:33 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:48:33 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:48:33 + OMERO_DATA_DIR=/home/omero/omero-server-data
07:48:33 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
07:48:33 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
07:48:33 ++ deactivate nondestructive
07:48:33 ++ '[' -n '' ']'
07:48:33 ++ '[' -n '' ']'
07:48:33 ++ hash -r
07:48:33 ++ '[' -n '' ']'
07:48:33 ++ unset VIRTUAL_ENV
07:48:33 ++ unset VIRTUAL_ENV_PROMPT
07:48:33 ++ '[' '!' nondestructive = nondestructive ']'
07:48:33 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
07:48:33 ++ export VIRTUAL_ENV
07:48:33 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:48:33 ++ 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
07:48:33 ++ export PATH
07:48:33 ++ '[' -n '' ']'
07:48:33 ++ '[' -z '' ']'
07:48:33 ++ _OLD_VIRTUAL_PS1=
07:48:33 ++ PS1='(.venv3) '
07:48:33 ++ export PS1
07:48:33 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
07:48:33 ++ export VIRTUAL_ENV_PROMPT
07:48:33 ++ hash -r
07:48:33 + omero admin stop
07:49:10 Server not running
07:49:10 + echo not running
07:49:10 not running
07:49:10 + sleep 5
07:49:15 + deactivate
07:49:15 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
07:49:15 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:49:15 + export PATH
07:49:15 + unset _OLD_VIRTUAL_PATH
07:49:15 + '[' -n '' ']'
07:49:15 + hash -r
07:49:15 + '[' -n '' ']'
07:49:15 + unset VIRTUAL_ENV
07:49:15 + unset VIRTUAL_ENV_PROMPT
07:49:15 + '[' '!' '' = nondestructive ']'
07:49:15 + unset -f deactivate
07:49:15 + rm -rf /home/omero/workspace/OMERO-server/.venv3
07:49:16 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
07:49:20 + '[' false = true ']'
07:49:20 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
07:49:20 Skipping PURGE_DATA:CleanDbAndRepo
07:49:20 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.5-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.22.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.10.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.31.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
07:49:23 Copied 1 artifact from "OMERO-build" build number 143
07:49:23 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 134
07:49:23 Copied 2 artifacts from "OMERO-build-build" build number 152
07:49:23 [OMERO-server] $ /bin/bash -xe /tmp/jenkins5109144493789564302.sh
07:49:23 + source /home/settings.env
07:49:23 ++ OMERO_DB_HOST=pg
07:49:23 ++ OMERO_DB_USER=postgres
07:49:23 ++ OMERO_DB_PASS=
07:49:23 ++ OMERO_ROOT_PASS=omero
07:49:23 ++ OMERO_DATA_DIR=/OMERO
07:49:23 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
07:49:23 + OMERO_DB_NAME=OMERO-server
07:49:23 + OMERO_DATA_DIR=/home/omero/omero-server-data
07:49:23 + mkdir -p /home/omero/omero-server-data
07:49:23 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
07:49:23 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:49:23 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:49:23 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
07:49:23 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
07:49:23 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
07:49:23 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
07:49:23 ++ ls OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143.zip
07:49:23 + ZIP=OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143.zip
07:49:23 + '[' '!' -z '' ']'
07:49:23 + DIST=OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143
07:49:23 + unzip OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143.zip
07:49:23 Archive: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143.zip
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/blitz/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/grid/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/profiles/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/error/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/grid/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/luts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/luts/janelia/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/luts/matplotlib/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/luts/ncsa_paledit/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/luts/seaborn/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/luts/wcif/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/analysis_scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/annotation_scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/export_scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/figure_scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/import_scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/scripts/omero/util_scripts/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/server/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/share/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/share/licenses/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/misc/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__1/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__10/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__11/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__2/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__3/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__4/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__5/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__6/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__7/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__8/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3A__9/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3__4/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3__5/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3__6/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO3__7/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO4.1__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO4.2__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO4.2__0/t/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO4.3__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO4.4__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO4__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.0__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.1__1/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.2__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4DEV__1/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4DEV__2/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4DEV__3/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/var/
07:49:23 creating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/var/tmp/
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/LICENSE.txt
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/backup.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/blitz/mail-senders.example
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/blitz/mail-server.example
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/build.properties
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/env.bat
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/env.sh
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/hibernate.properties
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/ice.config
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/logback-cli.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/logback-indexing-cli.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/logback-indexing.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/logback.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/mime.types
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/node1.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/node2.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/omero.properties
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/profiles/psql
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/rollover.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/Windows.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/error/maintainance.html
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/grid/README
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/grid/default.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/grid/templates.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/grid/windefault.xml
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/ice.config
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/internal.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/master.cfg
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/templates/robot.template
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/etc/testdropbox.config
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/history.rst
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/OMEZarrReader.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/accessors-smart.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/activation.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/aggdesigner-algorithm.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/aircompressor.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/antlr.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/aopalliance.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/apiguardian-api.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/asm.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/avatica-core.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/avatica-metrics.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/aws-java-sdk-core.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/aws-java-sdk-kms.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/aws-java-sdk-s3.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/base.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-anim.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-awt-util.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-bridge.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-codec.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-constants.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-css.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-dom.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-ext.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-gvt.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-i18n.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-parser.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-script.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-shared-resources.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-svg-dom.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-svggen.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-transcoder.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-util.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/batik-xml.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/btm.jar
07:49:23 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/lib/client/calcite-core.jar
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07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/psql-footer.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/psql-header.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/schema.sql
07:49:25 inflating: OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143/sql/psql/OMERO5.4__0/views.sql
07:49:25 + rm -f OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143.zip
07:49:25 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-594-18e7ec8f23-ice36-b143 /home/omero/workspace/OMERO-server/OMERO.server
07:49:25 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
07:49:25 ++ deactivate nondestructive
07:49:25 ++ '[' -n '' ']'
07:49:25 ++ '[' -n '' ']'
07:49:25 ++ hash -r
07:49:25 ++ '[' -n '' ']'
07:49:25 ++ unset VIRTUAL_ENV
07:49:25 ++ unset VIRTUAL_ENV_PROMPT
07:49:25 ++ '[' '!' nondestructive = nondestructive ']'
07:49:25 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
07:49:25 ++ export VIRTUAL_ENV
07:49:25 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:49:25 ++ 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
07:49:25 ++ export PATH
07:49:25 ++ '[' -n '' ']'
07:49:25 ++ '[' -z '' ']'
07:49:25 ++ _OLD_VIRTUAL_PS1=
07:49:25 ++ PS1='(.venv3) '
07:49:25 ++ export PS1
07:49:25 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
07:49:25 ++ export VIRTUAL_ENV_PROMPT
07:49:25 ++ hash -r
07:49:25 + pip install -U pip
07:49:25 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
07:49:26 Collecting pip
07:49:26 Downloading pip-26.1.1-py3-none-any.whl (1.8 MB)
07:49:26 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.8/1.8 MB 11.7 MB/s eta 0:00:00
07:49:26 Installing collected packages: pip
07:49:26 Attempting uninstall: pip
07:49:26 Found existing installation: pip 22.3.1
07:49:26 Uninstalling pip-22.3.1:
07:49:26 Successfully uninstalled pip-22.3.1
07:49:27 Successfully installed pip-26.1.1
07:49:27 WARNING: There was an error checking the latest version of pip.
07:49:28 + 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
07:49:28 Collecting zeroc-ice==3.6.5
07:49:28 Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
07:49:31 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 13.9 MB/s 0:00:02
07:49:31 Installing collected packages: zeroc-ice
07:49:32 Successfully installed zeroc-ice-3.6.5
07:49:32 + pip install markdown
07:49:32 Collecting markdown
07:49:32 Using cached markdown-3.10.2-py3-none-any.whl.metadata (5.1 kB)
07:49:32 Using cached markdown-3.10.2-py3-none-any.whl (108 kB)
07:49:32 Installing collected packages: markdown
07:49:32 Successfully installed markdown-3.10.2
07:49:32 + pip install reportlab
07:49:33 Collecting reportlab
07:49:33 Using cached reportlab-4.5.0-py3-none-any.whl.metadata (1.7 kB)
07:49:33 Collecting pillow>=9.0.0 (from reportlab)
07:49:33 Using cached pillow-12.2.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (8.8 kB)
07:49:34 Collecting charset-normalizer (from reportlab)
07:49:34 Using cached charset_normalizer-3.4.7-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (40 kB)
07:49:34 Using cached reportlab-4.5.0-py3-none-any.whl (2.0 MB)
07:49:34 Using cached pillow-12.2.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (7.1 MB)
07:49:34 Using cached charset_normalizer-3.4.7-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (214 kB)
07:49:34 Installing collected packages: pillow, charset-normalizer, reportlab
07:49:35
07:49:35 Successfully installed charset-normalizer-3.4.7 pillow-12.2.0 reportlab-4.5.0
07:49:35 + pip install omego
07:49:35 Collecting omego
07:49:35 Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
07:49:36 Collecting future (from omego)
07:49:36 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
07:49:36 Collecting yaclifw>=0.1.1 (from omego)
07:49:36 Using cached yaclifw-0.2.0-py3-none-any.whl
07:49:36 Collecting six (from yaclifw>=0.1.1->omego)
07:49:36 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
07:49:36 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
07:49:36 Using cached future-1.0.0-py3-none-any.whl (491 kB)
07:49:36 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
07:49:36 Installing collected packages: six, future, yaclifw, omego
07:49:37
07:49:37 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
07:49:37 + pip install tables
07:49:37 Collecting tables
07:49:37 Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.1 kB)
07:49:37 Collecting numpy>=1.20.0 (from tables)
07:49:37 Using cached numpy-2.4.4-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
07:49:37 Collecting numexpr>=2.6.2 (from tables)
07:49:37 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
07:49:37 Collecting packaging (from tables)
07:49:37 Using cached packaging-26.2-py3-none-any.whl.metadata (3.5 kB)
07:49:37 Collecting py-cpuinfo (from tables)
07:49:37 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
07:49:38 Collecting blosc2>=2.3.0 (from tables)
07:49:38 Using cached blosc2-4.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (6.2 kB)
07:49:38 Collecting ndindex (from blosc2>=2.3.0->tables)
07:49:38 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
07:49:38 Collecting msgpack (from blosc2>=2.3.0->tables)
07:49:38 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
07:49:38 Collecting requests (from blosc2>=2.3.0->tables)
07:49:38 Using cached requests-2.33.1-py3-none-any.whl.metadata (4.8 kB)
07:49:38 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->blosc2>=2.3.0->tables) (3.4.7)
07:49:38 Collecting idna<4,>=2.5 (from requests->blosc2>=2.3.0->tables)
07:49:38 Using cached idna-3.13-py3-none-any.whl.metadata (8.0 kB)
07:49:38 Collecting urllib3<3,>=1.26 (from requests->blosc2>=2.3.0->tables)
07:49:38 Using cached urllib3-2.6.3-py3-none-any.whl.metadata (6.9 kB)
07:49:38 Collecting certifi>=2023.5.7 (from requests->blosc2>=2.3.0->tables)
07:49:38 Using cached certifi-2026.4.22-py3-none-any.whl.metadata (2.5 kB)
07:49:38 Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (7.2 MB)
07:49:38 Using cached blosc2-4.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (5.2 MB)
07:49:38 Using cached numexpr-2.14.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (442 kB)
07:49:38 Using cached numpy-2.4.4-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
07:49:38 Using cached msgpack-1.1.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (426 kB)
07:49:38 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
07:49:38 Using cached packaging-26.2-py3-none-any.whl (100 kB)
07:49:38 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
07:49:38 Using cached requests-2.33.1-py3-none-any.whl (64 kB)
07:49:38 Using cached idna-3.13-py3-none-any.whl (68 kB)
07:49:38 Using cached urllib3-2.6.3-py3-none-any.whl (131 kB)
07:49:38 Using cached certifi-2026.4.22-py3-none-any.whl (135 kB)
07:49:39 Installing collected packages: py-cpuinfo, urllib3, packaging, numpy, ndindex, msgpack, idna, certifi, requests, numexpr, blosc2, tables
07:49:42
07:49:42 Successfully installed blosc2-4.1.2 certifi-2026.4.22 idna-3.13 msgpack-1.1.2 ndindex-1.10.1 numexpr-2.14.1 numpy-2.4.4 packaging-26.2 py-cpuinfo-9.0.0 requests-2.33.1 tables-3.11.1 urllib3-2.6.3
07:49:42 + pip install jinja2
07:49:42 Collecting jinja2
07:49:42 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
07:49:43 Collecting MarkupSafe>=2.0 (from jinja2)
07:49:43 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
07:49:43 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
07:49:43 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
07:49:43 Installing collected packages: MarkupSafe, jinja2
07:49:43
07:49:43 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
07:49:43 + pip install omero-py
07:49:43 Collecting omero-py
07:49:43 Using cached omero_py-5.22.1-py3-none-any.whl.metadata (6.5 kB)
07:49:43 Collecting appdirs (from omero-py)
07:49:43 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
07:49:43 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
07:49:43 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.4)
07:49:43 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.2.0)
07:49:44 Collecting PyYAML (from omero-py)
07:49:44 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
07:49:44 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
07:49:44 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.33.1)
07:49:44 Collecting portalocker (from omero-py)
07:49:44 Using cached portalocker-3.2.0-py3-none-any.whl.metadata (8.7 kB)
07:49:44 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.4.7)
07:49:44 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.13)
07:49:44 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2.6.3)
07:49:44 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.4.22)
07:49:44 Using cached omero_py-5.22.1-py3-none-any.whl (2.8 MB)
07:49:44 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
07:49:44 Using cached portalocker-3.2.0-py3-none-any.whl (22 kB)
07:49:44 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
07:49:44 Installing collected packages: appdirs, PyYAML, portalocker, omero-py
07:49:50
07:49:50 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.22.1 portalocker-3.2.0
07:49:50 + pip install pyarrow
07:49:50 Collecting pyarrow
07:49:50 Using cached pyarrow-24.0.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.0 kB)
07:49:50 Using cached pyarrow-24.0.0-cp311-cp311-manylinux_2_28_x86_64.whl (48.8 MB)
07:49:51 Installing collected packages: pyarrow
07:49:52 Successfully installed pyarrow-24.0.0
07:49:52 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
07:49:53 Collecting omero-metadata
07:49:53 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-_8z6_zs7/omero-metadata_c2f8bcb30cde42f19f3cc82a9baef62a
07:49:53 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-_8z6_zs7/omero-metadata_c2f8bcb30cde42f19f3cc82a9baef62a
07:49:54 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 644f3a97cc0d3d7290811f6f2fe372771441805b
07:49:54 Installing build dependencies: started
07:49:55 Installing build dependencies: finished with status 'done'
07:49:55 Getting requirements to build wheel: started
07:49:55 Getting requirements to build wheel: finished with status 'done'
07:49:55 Preparing metadata (pyproject.toml): started
07:49:55 Preparing metadata (pyproject.toml): finished with status 'done'
07:49:55 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.22.1)
07:49:55 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (6.0.3)
07:49:55 Requirement already satisfied: jinja2 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (3.1.6)
07:49:55 Collecting pandas (from omero-metadata)
07:49:56 Using cached pandas-3.0.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
07:49:56 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
07:49:56 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
07:49:56 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.4.4)
07:49:56 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (12.2.0)
07:49:56 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)
07:49:56 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.33.1)
07:49:56 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.2.0)
07:49:56 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib64/python3.11/site-packages (from jinja2->omero-metadata) (3.0.3)
07:49:56 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
07:49:56 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
07:49:56 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)
07:49:56 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.7)
07:49:56 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.13)
07:49:56 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.6.3)
07:49:56 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.4.22)
07:49:56 Using cached pandas-3.0.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (11.3 MB)
07:49:56 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
07:49:56 Building wheels for collected packages: omero-metadata
07:49:56 Building wheel for omero-metadata (pyproject.toml): started
07:49:56 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
07:49:56 Created wheel for omero-metadata: filename=omero_metadata-0.13.1.dev0-py3-none-any.whl size=39373 sha256=5a3546ba49c136707cd5466218909541c727be1f9d02cd6e1e5a1b9accba51f3
07:49:56 Stored in directory: /tmp/pip-ephem-wheel-cache-bsjhnmab/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
07:49:56 Successfully built omero-metadata
07:49:56 Installing collected packages: python-dateutil, pandas, omero-metadata
07:50:01
07:50:01 Successfully installed omero-metadata-0.13.1.dev0 pandas-3.0.2 python-dateutil-2.9.0.post0
07:50:01 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
07:50:01 Collecting omero-cli-render
07:50:01 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-4pcubgqs/omero-cli-render_ca73066cb3444fc590db26870a17acfc
07:50:01 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-4pcubgqs/omero-cli-render_ca73066cb3444fc590db26870a17acfc
07:50:02 Running command git checkout -b merge_ci --track origin/merge_ci
07:50:03 Switched to a new branch 'merge_ci'
07:50:03 branch 'merge_ci' set up to track 'origin/merge_ci'.
07:50:03 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 59fea6a195c5f58f6c4222f3df9f64df91f6c2b5
07:50:03 Installing build dependencies: started
07:50:03 Installing build dependencies: finished with status 'done'
07:50:03 Getting requirements to build wheel: started
07:50:04 Getting requirements to build wheel: finished with status 'done'
07:50:04 Preparing metadata (pyproject.toml): started
07:50:04 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:04 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
07:50:04 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.22.1)
07:50:04 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
07:50:04 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
07:50:04 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.4)
07:50:04 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (12.2.0)
07:50:04 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)
07:50:04 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.33.1)
07:50:04 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.2.0)
07:50:04 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.7)
07:50:04 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.13)
07:50:04 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.6.3)
07:50:04 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.4.22)
07:50:04 Building wheels for collected packages: omero-cli-render
07:50:04 Building wheel for omero-cli-render (pyproject.toml): started
07:50:04 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
07:50:04 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19839 sha256=40c8d4cc315ee9a63503f2b103fa736f98b97950a80f79839c0290659feb9edb
07:50:04 Stored in directory: /tmp/pip-ephem-wheel-cache-fjttlh0z/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
07:50:04 Successfully built omero-cli-render
07:50:04 Installing collected packages: omero-cli-render
07:50:04 Successfully installed omero-cli-render-0.8.2.dev0
07:50:04 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
07:50:04 Collecting omero-cli-duplicate
07:50:04 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-eaq86rip/omero-cli-duplicate_ec82b681d4534ee9ac74e70a7d7c3e71
07:50:04 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-eaq86rip/omero-cli-duplicate_ec82b681d4534ee9ac74e70a7d7c3e71
07:50:05 Running command git checkout -b merge_ci --track origin/merge_ci
07:50:06 Switched to a new branch 'merge_ci'
07:50:06 branch 'merge_ci' set up to track 'origin/merge_ci'.
07:50:06 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 27aeb065a6c47e664fccdad9ea810d1f7e09b4e8
07:50:06 Installing build dependencies: started
07:50:07 Installing build dependencies: finished with status 'done'
07:50:07 Getting requirements to build wheel: started
07:50:07 Getting requirements to build wheel: finished with status 'done'
07:50:07 Preparing metadata (pyproject.toml): started
07:50:07 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:07 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.22.1)
07:50:07 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
07:50:07 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
07:50:07 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.4)
07:50:07 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.2.0)
07:50:07 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
07:50:07 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)
07:50:07 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.33.1)
07:50:07 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.2.0)
07:50:07 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.7)
07:50:07 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.13)
07:50:07 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.6.3)
07:50:07 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.4.22)
07:50:07 Building wheels for collected packages: omero-cli-duplicate
07:50:07 Building wheel for omero-cli-duplicate (pyproject.toml): started
07:50:07 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
07:50:07 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11539 sha256=daa02a5050cc691070a57f06c0baea4b37eb5a1b1655abc3b3bb9d6f0cdbfb9e
07:50:07 Stored in directory: /tmp/pip-ephem-wheel-cache-x9mov7pf/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
07:50:07 Successfully built omero-cli-duplicate
07:50:07 Installing collected packages: omero-cli-duplicate
07:50:07 Successfully installed omero-cli-duplicate-0.4.1.dev0
07:50:07 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
07:50:08 Collecting omero-cli-zarr
07:50:08 Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-ohgi90sr/omero-cli-zarr_81236c7b0b5043a49066167225767e07
07:50:08 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-ohgi90sr/omero-cli-zarr_81236c7b0b5043a49066167225767e07
07:50:09 Running command git checkout -b merge_ci --track origin/merge_ci
07:50:09 Switched to a new branch 'merge_ci'
07:50:09 branch 'merge_ci' set up to track 'origin/merge_ci'.
07:50:09 Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit e72f366dbdd1274067aa1ff84fca584c03f91037
07:50:09 Installing build dependencies: started
07:50:10 Installing build dependencies: finished with status 'done'
07:50:10 Getting requirements to build wheel: started
07:50:10 Getting requirements to build wheel: finished with status 'done'
07:50:10 Installing backend dependencies: started
07:50:11 Installing backend dependencies: finished with status 'done'
07:50:11 Preparing metadata (pyproject.toml): started
07:50:12 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:12 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.22.1)
07:50:12 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
07:50:12 Using cached ome_zarr-0.16.0-py3-none-any.whl.metadata (2.9 kB)
07:50:12 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.4)
07:50:12 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:12 Using cached dask-2026.3.0-py3-none-any.whl.metadata (3.9 kB)
07:50:12 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:12 Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
07:50:12 Collecting fsspec!=2021.07.0,!=2023.9.0,>=0.8 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:12 Using cached fsspec-2026.4.0-py3-none-any.whl.metadata (10 kB)
07:50:13 Collecting aiohttp (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:13 Using cached aiohttp-3.13.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.1 kB)
07:50:13 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.33.1)
07:50:13 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:14 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
07:50:14 Collecting toolz (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:14 Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB)
07:50:14 Collecting rangehttpserver (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:14 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl.metadata (769 bytes)
07:50:16 Collecting Deprecated (from ome-zarr>=0.13.0->omero-cli-zarr)
07:50:16 Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB)
07:50:16 Collecting click>=8.1 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:16 Using cached click-8.3.3-py3-none-any.whl.metadata (2.6 kB)
07:50:17 Collecting cloudpickle>=3.0.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB)
07:50:17 Requirement already satisfied: packaging>=20.0 in ./.venv3/lib64/python3.11/site-packages (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr) (26.2)
07:50:17 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
07:50:17 Requirement already satisfied: pyyaml>=5.3.1 in ./.venv3/lib64/python3.11/site-packages (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr) (6.0.3)
07:50:17 Collecting importlib_metadata>=4.13.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached importlib_metadata-9.0.0-py3-none-any.whl.metadata (4.5 kB)
07:50:17 Collecting s3fs>2024.2.0 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached s3fs-2026.4.0-py3-none-any.whl.metadata (1.2 kB)
07:50:17 Collecting zipp>=3.20 (from importlib_metadata>=4.13.0->dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached zipp-3.23.1-py3-none-any.whl.metadata (3.6 kB)
07:50:17 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
07:50:17 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.0.0)
07:50:17 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (12.2.0)
07:50:17 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-zarr) (3.6.5)
07:50:17 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (3.2.0)
07:50:17 Collecting locket (from partd>=1.4.0->dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
07:50:17 Collecting aiobotocore<4.0.0,>=2.19.0 (from s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Downloading aiobotocore-3.6.0-py3-none-any.whl.metadata (27 kB)
07:50:17 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:17 Using cached aioitertools-0.13.0-py3-none-any.whl.metadata (3.3 kB)
07:50:18 Collecting botocore<1.43.1,>=1.42.90 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:18 Downloading botocore-1.43.0-py3-none-any.whl.metadata (5.5 kB)
07:50:18 Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in ./.venv3/lib64/python3.11/site-packages (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr) (2.9.0.post0)
07:50:18 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:18 Using cached jmespath-1.1.0-py3-none-any.whl.metadata (7.6 kB)
07:50:18 Collecting multidict<7.0.0,>=6.0.0 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:18 Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (5.3 kB)
07:50:19 Collecting wrapt<3.0.0,>=1.10.10 (from aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:19 Using cached wrapt-2.1.2-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (7.4 kB)
07:50:19 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:19 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl.metadata (5.9 kB)
07:50:19 Collecting aiosignal>=1.4.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:19 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
07:50:19 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:19 Using cached attrs-26.1.0-py3-none-any.whl.metadata (8.8 kB)
07:50:19 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:19 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (20 kB)
07:50:20 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:20 Using cached propcache-0.4.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (13 kB)
07:50:20 Collecting yarl<2.0,>=1.17.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:20 Using cached yarl-1.23.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (79 kB)
07:50:20 Requirement already satisfied: urllib3!=2.2.0,<3,>=1.25.4 in ./.venv3/lib64/python3.11/site-packages (from botocore<1.43.1,>=1.42.90->aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr) (2.6.3)
07:50:20 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil<3.0.0,>=2.1->aiobotocore<4.0.0,>=2.19.0->s3fs>2024.2.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr) (1.17.0)
07:50:20 Requirement already satisfied: idna>=2.0 in ./.venv3/lib64/python3.11/site-packages (from yarl<2.0,>=1.17.0->aiohttp->ome-zarr>=0.13.0->omero-cli-zarr) (3.13)
07:50:20 Collecting typing-extensions>=4.2 (from aiosignal>=1.4.0->aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:20 Using cached typing_extensions-4.15.0-py3-none-any.whl.metadata (3.3 kB)
07:50:20 Collecting scipy>=1.11.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:20 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
07:50:20 Collecting networkx>=3.0 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:20 Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
07:50:21 Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:21 Using cached imageio-2.37.3-py3-none-any.whl.metadata (9.7 kB)
07:50:21 Collecting tifffile>=2022.8.12 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:21 Using cached tifffile-2026.3.3-py3-none-any.whl.metadata (31 kB)
07:50:21 Collecting lazy-loader>=0.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:21 Using cached lazy_loader-0.5-py3-none-any.whl.metadata (5.9 kB)
07:50:21 Collecting donfig>=0.8 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:21 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
07:50:21 Collecting google-crc32c>=1.5 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:21 Using cached google_crc32c-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl.metadata (1.7 kB)
07:50:21 Collecting numcodecs>=0.14 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
07:50:21 Using cached numcodecs-0.16.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (3.4 kB)
07:50:21 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (3.4.7)
07:50:21 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (2026.4.22)
07:50:21 Using cached ome_zarr-0.16.0-py3-none-any.whl (46 kB)
07:50:21 Using cached dask-2026.3.0-py3-none-any.whl (1.5 MB)
07:50:22 Using cached click-8.3.3-py3-none-any.whl (110 kB)
07:50:22 Using cached cloudpickle-3.1.2-py3-none-any.whl (22 kB)
07:50:22 Using cached fsspec-2026.4.0-py3-none-any.whl (203 kB)
07:50:22 Using cached importlib_metadata-9.0.0-py3-none-any.whl (27 kB)
07:50:22 Using cached partd-1.4.2-py3-none-any.whl (18 kB)
07:50:22 Using cached s3fs-2026.4.0-py3-none-any.whl (32 kB)
07:50:22 Downloading aiobotocore-3.6.0-py3-none-any.whl (88 kB)
07:50:22 Using cached aiohttp-3.13.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.8 MB)
07:50:22 Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB)
07:50:22 Downloading botocore-1.43.0-py3-none-any.whl (15.0 MB)
07:50:23 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.0/15.0 MB 13.7 MB/s 0:00:01
07:50:23 Using cached jmespath-1.1.0-py3-none-any.whl (20 kB)
07:50:23 Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
07:50:23 Using cached wrapt-2.1.2-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (114 kB)
07:50:23 Using cached yarl-1.23.0-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (102 kB)
07:50:23 Using cached aiohappyeyeballs-2.6.1-py3-none-any.whl (15 kB)
07:50:23 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
07:50:23 Using cached attrs-26.1.0-py3-none-any.whl (67 kB)
07:50:24 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (231 kB)
07:50:24 Using cached propcache-0.4.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (210 kB)
07:50:24 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (13.7 MB)
07:50:24 Using cached imageio-2.37.3-py3-none-any.whl (317 kB)
07:50:24 Using cached lazy_loader-0.5-py3-none-any.whl (8.0 kB)
07:50:24 Using cached networkx-3.6.1-py3-none-any.whl (2.1 MB)
07:50:24 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.3 MB)
07:50:24 Using cached tifffile-2026.3.3-py3-none-any.whl (243 kB)
07:50:24 Using cached toolz-1.1.0-py3-none-any.whl (58 kB)
07:50:24 Using cached typing_extensions-4.15.0-py3-none-any.whl (44 kB)
07:50:24 Using cached zarr-3.1.6-py3-none-any.whl (295 kB)
07:50:24 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
07:50:24 Using cached google_crc32c-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (33 kB)
07:50:24 Using cached numcodecs-0.16.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (9.1 MB)
07:50:24 Using cached zipp-3.23.1-py3-none-any.whl (10 kB)
07:50:24 Using cached deprecated-1.3.1-py2.py3-none-any.whl (11 kB)
07:50:24 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
07:50:24 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
07:50:24 Building wheels for collected packages: omero-cli-zarr
07:50:24 Building wheel for omero-cli-zarr (pyproject.toml): started
07:50:25 Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
07:50:25 Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev162+ge72f366-py3-none-any.whl size=38287 sha256=5706d88e91f724caf86759d39bc677cf9ae4b3f87fade6b06bc2a13014995717
07:50:25 Stored in directory: /tmp/pip-ephem-wheel-cache-l5umhur5/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
07:50:25 Successfully built omero-cli-zarr
07:50:25 Installing collected packages: rangehttpserver, zipp, wrapt, typing-extensions, toolz, tifffile, scipy, propcache, networkx, multidict, locket, lazy-loader, jmespath, imageio, google-crc32c, fsspec, frozenlist, donfig, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, yarl, scikit-image, partd, numcodecs, importlib_metadata, Deprecated, botocore, aiosignal, zarr, dask, aiohttp, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
07:50:36
07:50:36 Successfully installed Deprecated-1.3.1 aiobotocore-3.6.0 aiohappyeyeballs-2.6.1 aiohttp-3.13.5 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.0 click-8.3.3 cloudpickle-3.1.2 dask-2026.3.0 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.4.0 google-crc32c-1.8.0 imageio-2.37.3 importlib_metadata-9.0.0 jmespath-1.1.0 lazy-loader-0.5 locket-1.0.0 multidict-6.7.1 networkx-3.6.1 numcodecs-0.16.5 ome-zarr-0.16.0 omero-cli-zarr-0.5.5.dev162+ge72f366 partd-1.4.2 propcache-0.4.1 rangehttpserver-1.4.0 s3fs-2026.4.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 typing-extensions-4.15.0 wrapt-2.1.2 yarl-1.23.0 zarr-3.1.6 zipp-3.23.1
07:50:36 + pip install omero-certificates
07:50:36 Collecting omero-certificates
07:50:36 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
07:50:37 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.22.1)
07:50:37 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
07:50:37 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
07:50:37 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.4)
07:50:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.2.0)
07:50:37 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
07:50:37 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)
07:50:37 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.33.1)
07:50:37 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.2.0)
07:50:37 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.7)
07:50:37 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.13)
07:50:37 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.6.3)
07:50:37 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.4.22)
07:50:37 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
07:50:37 Installing collected packages: omero-certificates
07:50:37 Successfully installed omero-certificates-0.4.0
07:50:37 + for x in *.tar.gz
07:50:37 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
07:50:37 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
07:50:37 Installing build dependencies: started
07:50:38 Installing build dependencies: finished with status 'done'
07:50:38 Getting requirements to build wheel: started
07:50:38 Getting requirements to build wheel: finished with status 'done'
07:50:38 Preparing metadata (pyproject.toml): started
07:50:38 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:38 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.22.1)
07:50:38 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
07:50:38 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
07:50:38 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.4)
07:50:38 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.2.0)
07:50:38 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
07:50:38 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)
07:50:38 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.33.1)
07:50:38 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.2.0)
07:50:38 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.7)
07:50:38 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.13)
07:50:38 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.6.3)
07:50:38 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.4.22)
07:50:38 Building wheels for collected packages: omero-dropbox
07:50:38 Building wheel for omero-dropbox (pyproject.toml): started
07:50:39 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
07:50:39 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49154 sha256=53b91269eb3780c8a866cf5c2a7f0b79278b6bbb0d400caf0d632afb6c7120e5
07:50:39 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
07:50:39 Successfully built omero-dropbox
07:50:39 Installing collected packages: omero-dropbox
07:50:39 Successfully installed omero-dropbox-5.7.1.dev0
07:50:39 + for x in *.tar.gz
07:50:39 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
07:50:39 Processing ./omero_marshal-0.9.2.dev0.tar.gz
07:50:39 Installing build dependencies: started
07:50:40 Installing build dependencies: finished with status 'done'
07:50:40 Getting requirements to build wheel: started
07:50:40 Getting requirements to build wheel: finished with status 'done'
07:50:40 Preparing metadata (pyproject.toml): started
07:50:40 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:40 Building wheels for collected packages: omero_marshal
07:50:40 Building wheel for omero_marshal (pyproject.toml): started
07:50:41 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
07:50:41 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88131 sha256=05412695e727d23291244db73c779852a8f911023240bf8059f69560275250c8
07:50:41 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
07:50:41 Successfully built omero_marshal
07:50:41 Installing collected packages: omero_marshal
07:50:41 Successfully installed omero_marshal-0.9.2.dev0
07:50:41 + for x in *.tar.gz
07:50:41 + pip install -U omero_py-5.22.2.dev0.tar.gz
07:50:41 Processing ./omero_py-5.22.2.dev0.tar.gz
07:50:42 Installing build dependencies: started
07:50:43 Installing build dependencies: finished with status 'done'
07:50:43 Getting requirements to build wheel: started
07:50:43 Getting requirements to build wheel: finished with status 'done'
07:50:43 Preparing metadata (pyproject.toml): started
07:50:43 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:43 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.4.4)
07:50:43 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (1.0.0)
07:50:43 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.4.4)
07:50:43 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (12.2.0)
07:50:43 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (6.0.3)
07:50:43 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.6.5)
07:50:43 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (2.33.1)
07:50:43 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.22.2.dev0) (3.2.0)
07:50:43 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.4.7)
07:50:43 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (3.13)
07:50:43 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2.6.3)
07:50:43 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.22.2.dev0) (2026.4.22)
07:50:43 Building wheels for collected packages: omero-py
07:50:43 Building wheel for omero-py (pyproject.toml): started
07:50:44 Building wheel for omero-py (pyproject.toml): finished with status 'done'
07:50:44 Created wheel for omero-py: filename=omero_py-5.22.2.dev0-py3-none-any.whl size=2786692 sha256=000514c935e4bf72dc716e2d8c726b75e5569047789132717f8557ea8cf8f1a1
07:50:44 Stored in directory: /home/omero/.cache/pip/wheels/ec/3f/72/4027ca0a7faf1f66d4577cc07619b0497ac8e99396d43dd8fa
07:50:44 Successfully built omero-py
07:50:44 Installing collected packages: omero-py
07:50:44 Attempting uninstall: omero-py
07:50:44 Found existing installation: omero-py 5.22.1
07:50:44 Uninstalling omero-py-5.22.1:
07:50:45 Successfully uninstalled omero-py-5.22.1
07:50:47 Successfully installed omero-py-5.22.2.dev0
07:50:47 + for x in *.tar.gz
07:50:47 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
07:50:47 Processing ./omero_scripts-5.10.1.dev0.tar.gz
07:50:47 Installing build dependencies: started
07:50:48 Installing build dependencies: finished with status 'done'
07:50:48 Getting requirements to build wheel: started
07:50:48 Getting requirements to build wheel: finished with status 'done'
07:50:48 Preparing metadata (pyproject.toml): started
07:50:48 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:48 Building wheels for collected packages: omero-scripts
07:50:48 Building wheel for omero-scripts (pyproject.toml): started
07:50:49 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
07:50:49 Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137001 sha256=995f7ee3c82838d3b1dfb39dd0ee786aba0a74ce580798283f0288a670b4b019
07:50:49 Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
07:50:49 Successfully built omero-scripts
07:50:49 Installing collected packages: omero-scripts
07:50:49 Successfully installed omero-scripts-5.10.1.dev0
07:50:49 + for x in *.tar.gz
07:50:49 + pip install -U omero_web-5.31.1.dev0.tar.gz
07:50:49 Processing ./omero_web-5.31.1.dev0.tar.gz
07:50:49 Installing build dependencies: started
07:50:50 Installing build dependencies: finished with status 'done'
07:50:50 Getting requirements to build wheel: started
07:50:51 Getting requirements to build wheel: finished with status 'done'
07:50:51 Preparing metadata (pyproject.toml): started
07:50:51 Preparing metadata (pyproject.toml): finished with status 'done'
07:50:51 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.31.1.dev0) (5.22.2.dev0)
07:50:51 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.31.1.dev0)
07:50:51 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
07:50:51 Collecting Django<5.3,>=5.2.9 (from omero-web==5.31.1.dev0)
07:50:51 Using cached django-5.2.13-py3-none-any.whl.metadata (4.1 kB)
07:50:51 Collecting django-pipeline>=4.1.0 (from omero-web==5.31.1.dev0)
07:50:51 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
07:50:51 Collecting django-cors-headers==3.7.0 (from omero-web==5.31.1.dev0)
07:50:51 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
07:50:51 Collecting whitenoise>=5.3.0 (from omero-web==5.31.1.dev0)
07:50:51 Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
07:50:52 Collecting gunicorn>=19.3 (from omero-web==5.31.1.dev0)
07:50:52 Downloading gunicorn-26.0.0-py3-none-any.whl.metadata (5.4 kB)
07:50:52 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.31.1.dev0) (0.9.2.dev0)
07:50:52 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.31.1.dev0) (12.2.0)
07:50:52 Collecting pytz (from omero-web==5.31.1.dev0)
07:50:52 Downloading pytz-2026.2-py2.py3-none-any.whl.metadata (22 kB)
07:50:52 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.31.1.dev0) (3.2.0)
07:50:52 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.31.1.dev0) (26.2)
07:50:52 Collecting importlib-resources (from omero-web==5.31.1.dev0)
07:50:52 Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
07:50:52 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.31.1.dev0)
07:50:52 Using cached asgiref-3.11.1-py3-none-any.whl.metadata (9.3 kB)
07:50:52 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.31.1.dev0)
07:50:52 Using cached sqlparse-0.5.5-py3-none-any.whl.metadata (4.7 kB)
07:50:52 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline>=4.1.0->omero-web==5.31.1.dev0) (65.5.1)
07:50:52 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.31.1.dev0)
07:50:52 Using cached wheel-0.47.0-py3-none-any.whl.metadata (2.3 kB)
07:50:52 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.31.1.dev0) (1.4.4)
07:50:52 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.31.1.dev0) (1.0.0)
07:50:52 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.31.1.dev0) (2.4.4)
07:50:52 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.31.1.dev0) (6.0.3)
07:50:52 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==5.31.1.dev0) (3.6.5)
07:50:52 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.31.1.dev0) (2.33.1)
07:50:52 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.31.1.dev0) (3.4.7)
07:50:52 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.31.1.dev0) (3.13)
07:50:52 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.31.1.dev0) (2.6.3)
07:50:52 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.31.1.dev0) (2026.4.22)
07:50:52 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
07:50:52 Using cached django-5.2.13-py3-none-any.whl (8.3 MB)
07:50:52 Using cached asgiref-3.11.1-py3-none-any.whl (24 kB)
07:50:52 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
07:50:52 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
07:50:53 Downloading gunicorn-26.0.0-py3-none-any.whl (212 kB)
07:50:53 Using cached sqlparse-0.5.5-py3-none-any.whl (46 kB)
07:50:53 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
07:50:53 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
07:50:53 Downloading pytz-2026.2-py2.py3-none-any.whl (510 kB)
07:50:53 Using cached wheel-0.47.0-py3-none-any.whl (32 kB)
07:50:53 Building wheels for collected packages: omero-web
07:50:53 Building wheel for omero-web (pyproject.toml): started
07:50:54 Building wheel for omero-web (pyproject.toml): finished with status 'done'
07:50:54 Created wheel for omero-web: filename=omero_web-5.31.1.dev0-py3-none-any.whl size=2819315 sha256=b88411250107b6db1cf4aaacc039d52fa0d7f6465b3edb364420856422673812
07:50:54 Stored in directory: /home/omero/.cache/pip/wheels/48/a3/5b/968853abf49b64e1726fdb37874d77f08ddad2d06b53de06b3
07:50:54 Successfully built omero-web
07:50:54 Installing collected packages: pytz, whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
07:50:57
07:50:57 Successfully installed Django-5.2.13 asgiref-3.11.1 concurrent-log-handler-0.9.29 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-26.0.0 importlib-resources-7.1.0 omero-web-5.31.1.dev0 pytz-2026.2 sqlparse-0.5.5 wheel-0.47.0 whitenoise-6.12.0
07:50:57 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
07:50:58 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
07:50:58 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
07:50:58 --2026-05-05 07:50:58-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
07:50:58 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
07:50:58 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
07:50:58 HTTP request sent, awaiting response... 200 OK
07:50:58 Length: 139337 (136K) [text/plain]
07:50:58 Saving to: ‘Figure_To_Pdf.py’
07:50:58
07:50:58 0K .......... .......... .......... .......... .......... 36% 2.81M 0s
07:50:58 50K .......... .......... .......... .......... .......... 73% 6.10M 0s
07:50:58 100K .......... .......... .......... ...... 100% 4.36M=0.03s
07:50:58
07:50:58 2026-05-05 07:50:58 (3.97 MB/s) - ‘Figure_To_Pdf.py’ saved [139337/139337]
07:50:58
07:50:58 + chmod 755 Figure_To_Pdf.py
07:50:58 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
07:50:58 + omero config set omero.db.name OMERO-server
07:51:00 + omero config set omero.db.host pg
07:51:02 + omero config set omero.db.user postgres
07:51:04 + omero config set omero.data.dir /home/omero/omero-server-data
07:51:06 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
07:51:08 + omero config set omero.db.poolsize 25
07:51:10 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
07:51:12 + omero config set omero.security.trustStorePassword changeit
07:51:14 + omero config set omero.mail.config true
07:51:16 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
07:51:18 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED'
07:51:20 + omero certificates
07:51:22 OpenSSL 3.5.1 1 Jul 2025 (Library: OpenSSL 3.5.1 1 Jul 2025)
07:51:22 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
07:51:22 + '[' false = true ']'
07:51:22 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
07:51:22 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
07:51:22 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG dbcommand => upgrade
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG dbhost => localhost
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG dbname => OMERO-server
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG dbpass => omero
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG dbuser => omero
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG rootpass => omero
07:51:22 2026-05-05 07:51:22,683 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
07:51:22 2026-05-05 07:51:22,683 [omego.extern] INFO Executing : omero version
07:51:24 OMERO.py version:
07:51:24 OMERO.server version:
07:51:24 5.6.3-594-18e7ec8f23-ice36-b143
07:51:24 5.22.2.dev0
07:51:24 2026-05-05 07:51:24,684 [omego.extern] INFO Completed [2.000 s]
07:51:24 2026-05-05 07:51:24,684 [omego.extern] DEBUG Using omero CLI from omero
07:51:24 2026-05-05 07:51:24,684 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
07:51:24 2026-05-05 07:51:24,684 [omego.extern] INFO Running [current environment]: omero config get --show-password
07:51:24 2026-05-05 07:51:24,684 [omego.extern] INFO Executing : omero config get --show-password
07:51:26 2026-05-05 07:51:26,706 [omego.extern] INFO Completed [2.022 s]
07:51:26 2026-05-05 07:51:26,707 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
07:51:26 2026-05-05 07:51:26,707 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
07:51:27 2026-05-05 07:51:27,062 [omego.extern] INFO Completed [0.355 s]
07:51:27 2026-05-05 07:51:27,062 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.11\n'
07:51:27 2026-05-05 07:51:27,062 [ omego.db] INFO psql version: psql (PostgreSQL) 16.11
07:51:27
07:51:27 2026-05-05 07:51:27,062 [omego.extern] INFO Running [current environment]: omero config get --show-password
07:51:27 2026-05-05 07:51:27,062 [omego.extern] INFO Executing : omero config get --show-password
07:51:29 2026-05-05 07:51:29,036 [omego.extern] INFO Completed [1.973 s]
07:51:29 2026-05-05 07:51:29,036 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
07:51:29 2026-05-05 07:51:29,036 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
07:51:29 2026-05-05 07:51:29,397 [omego.extern] INFO Completed [0.361 s]
07:51:29 2026-05-05 07:51:29,397 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.4") at port "5432".\n'
07:51:29 2026-05-05 07:51:29,397 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
07:51:29 2026-05-05 07:51:29,398 [omego.extern] INFO Running [current environment]: omero config get --show-password
07:51:29 2026-05-05 07:51:29,398 [omego.extern] INFO Executing : omero config get --show-password
07:51:31 2026-05-05 07:51:31,385 [omego.extern] INFO Completed [1.987 s]
07:51:31 2026-05-05 07:51:31,385 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
07:51:31 2026-05-05 07:51:31,385 [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
07:51:32 2026-05-05 07:51:32,061 [omego.extern] INFO Completed [0.676 s]
07:51:32 2026-05-05 07:51:32,062 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
07:51:32 2026-05-05 07:51:32,062 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
07:51:32 2026-05-05 07:51:32,063 [ omego.db] INFO Database is already at OMERO5.4__0
07:51:32 + export LANG=en_US.UTF-8
07:51:32 + LANG=en_US.UTF-8
07:51:32 + export LANGUAGE=en_US:en
07:51:32 + LANGUAGE=en_US:en
07:51:32 + export LC_ALL=en_US.UTF-8
07:51:32 + LC_ALL=en_US.UTF-8
07:51:32 + BUILD_ID=DONT_KILL_ME
07:51:32 + omero admin start
07:51:37 No descriptor given. Using etc/grid/default.xml
07:51:47 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
07:51:47 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
07:51:47 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
07:51:47 Waiting on startup. Use CTRL-C to exit
07:51:48 + omero admin waitup
07:51:50 Waiting on startup. Use CTRL-C to exit
07:51:50 + omero admin diagnostics
07:51:52
07:51:52 ================================================================================
07:51:52 OMERO Diagnostics (admin)
07:51:52 ================================================================================
07:51:52
07:51:52 Commands: java -version 17.0.17 (/usr/bin/java)
07:51:52 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
07:51:52 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
07:51:52 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
07:51:52 Commands: psql --version 16.11 (/usr/bin/psql)
07:51:52 Commands: openssl version 3.5.11 (/usr/bin/openssl)
07:51:52
07:51:52 Component: OMERO.py 5.22.2.dev0
07:51:52 Component: OMERO.server 5.6.3-594-18e7ec8f23-ice36-b143
07:51:52
07:51:52 Server: icegridnode running
07:51:52 Server: Blitz-0 active (pid = 3302, enabled)
07:51:52 Server: Indexer-0 activating (enabled)
07:51:52 Server: OMERO.Glacier2 active (pid = 3334, enabled)
07:51:52 Server: OMERO.IceStorm active (pid = 3360, enabled)
07:51:52 Server: Processor-0 activating (enabled)
07:51:52 Server: Tables-0 activating (enabled)
07:51:52
07:51:52 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
07:51:52 Log files: Blitz-0.log 23.7 KB errors=0 warnings=1
07:51:52 Log files: DropBox.log n/a
07:51:52 Log files: FileServer.log n/a
07:51:52 Log files: Indexer-0.log 2.1 KB
07:51:52 Log files: MonitorServer.log n/a
07:51:52 Log files: Processor-0.log 592 B
07:51:52 Log files: Tables-0.log 841 B
07:51:52 Log files: TestDropBox.log n/a
07:51:52 Log files: master.err empty
07:51:52 Log files: master.out 30.5 KB
07:51:52 Log files: Total size 0.06 MB
07:51:52
07:51:52
07:51:52 Environment:OMERO_HOME=(unset)
07:51:52 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:51:52 Environment:OMERO_NODE=(unset)
07:51:52 Environment:OMERO_MASTER=(unset)
07:51:52 Environment:OMERO_USERDIR=(unset)
07:51:52 Environment:OMERO_TMPDIR=(unset)
07:51:52 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
07:51:52 Environment:PYTHONPATH=(unset)
07:51:52 Environment:ICE_HOME=/opt/ice-3.6.5
07:51:52 Environment:LD_LIBRARY_PATH=(unset)
07:51:52 Environment:DYLD_LIBRARY_PATH=(unset)
07:51:52
07:51:52 OMERO SSL port:4064
07:51:52 OMERO TCP port:4063
07:51:52 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
07:51:52 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
07:51:52
07:51:52 JVM settings: Blitz-${index} -Xmx7200m
07:51:52 JVM settings: Indexer-${index} -Xmx4800m
07:51:52 JVM settings: PixelData-${index} -Xmx7200m
07:51:52 JVM settings: Repository-${index} -Xmx4800m
07:51:52
07:51:52 Jar: lib/server/formats-api.jar Bio-Formats API 8.6.0-SNAPSHOT 5 May 2026 f44393cb07d096649659b51be39548947fa56135
07:51:52 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.6.0-SNAPSHOT 5 May 2026 f44393cb07d096649659b51be39548947fa56135
07:51:52 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.6.0-SNAPSHOT 5 May 2026 f44393cb07d096649659b51be39548947fa56135
07:51:52 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.4-SNAPSHOT 5 May 2026 2109216039980beb312e2a5ee915100e26bd66cf
07:51:52 Jar: lib/server/ome-common.jar OME Common Java 6.2.2-SNAPSHOT 5 May 2026 2109216039980beb312e2a5ee915100e26bd66cf
07:51:52 Jar: lib/server/ome-jai.jar OME JAI 0.1.6-SNAPSHOT 5 May 2026 2109216039980beb312e2a5ee915100e26bd66cf
07:51:52 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.5-SNAPSHOT 5 May 2026 2109216039980beb312e2a5ee915100e26bd66cf
07:51:52 Jar: lib/server/ome-poi.jar OME POI 5.3.11-SNAPSHOT 5 May 2026 2109216039980beb312e2a5ee915100e26bd66cf
07:51:52 Jar: lib/server/ome-xml.jar OME XML library 6.5.4-SNAPSHOT 5 May 2026 2109216039980beb312e2a5ee915100e26bd66cf
07:51:53 Jar: lib/server/omero-blitz.jar jar 5.8.5-SNAPSHOT
07:51:53 Jar: lib/server/omero-common.jar jar 5.7.6-SNAPSHOT
07:51:53 Jar: lib/server/omero-gateway.jar jar 5.10.6-SNAPSHOT
07:51:53 Jar: lib/server/omero-model.jar jar 5.7.6-SNAPSHOT
07:51:53 Jar: lib/server/omero-renderer.jar jar 5.6.6-SNAPSHOT
07:51:53 Jar: lib/server/omero-romio.jar jar 5.8.6-SNAPSHOT
07:51:53 Jar: lib/server/omero-server.jar jar 5.7.5-SNAPSHOT
07:51:53 + deactivate
07:51:53 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
07:51:53 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:51:53 + export PATH
07:51:53 + unset _OLD_VIRTUAL_PATH
07:51:53 + '[' -n '' ']'
07:51:53 + hash -r
07:51:53 + '[' -n '' ']'
07:51:53 + unset VIRTUAL_ENV
07:51:53 + unset VIRTUAL_ENV_PROMPT
07:51:53 + '[' '!' '' = nondestructive ']'
07:51:53 + unset -f deactivate
07:51:53 Finished: SUCCESS
