09:48:39 Started by user devspace
09:48:39 Running as SYSTEM
09:48:39 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
09:48:39 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13479585265227500436.sh
09:48:39 + source /home/settings.env
09:48:39 ++ OMERO_DB_HOST=pg
09:48:39 ++ OMERO_DB_USER=postgres
09:48:39 ++ OMERO_DB_PASS=
09:48:39 ++ OMERO_ROOT_PASS=omero
09:48:39 ++ OMERO_DATA_DIR=/OMERO
09:48:39 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:48:39 + OMERO_DB_NAME=OMERO-server
09:48:39 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:48:39 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:48:39 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:48:39 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:48:39 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
09:48:39 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:48:39 ++ deactivate nondestructive
09:48:39 ++ '[' -n '' ']'
09:48:39 ++ '[' -n '' ']'
09:48:39 ++ hash -r
09:48:39 ++ '[' -n '' ']'
09:48:39 ++ unset VIRTUAL_ENV
09:48:39 ++ unset VIRTUAL_ENV_PROMPT
09:48:39 ++ '[' '!' nondestructive = nondestructive ']'
09:48:39 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:48:39 ++ export VIRTUAL_ENV
09:48:39 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:48:39 ++ 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
09:48:39 ++ export PATH
09:48:39 ++ '[' -n '' ']'
09:48:39 ++ '[' -z '' ']'
09:48:39 ++ _OLD_VIRTUAL_PS1=
09:48:39 ++ PS1='(.venv3) '
09:48:39 ++ export PS1
09:48:39 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
09:48:39 ++ export VIRTUAL_ENV_PROMPT
09:48:39 ++ hash -r
09:48:39 + omero admin stop
09:49:30 Server not running
09:49:32 + echo not running
09:49:32 not running
09:49:32 + sleep 5
09:49:37 + deactivate
09:49:37 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:49:37 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:49:37 + export PATH
09:49:37 + unset _OLD_VIRTUAL_PATH
09:49:37 + '[' -n '' ']'
09:49:37 + hash -r
09:49:37 + '[' -n '' ']'
09:49:37 + unset VIRTUAL_ENV
09:49:37 + unset VIRTUAL_ENV_PROMPT
09:49:37 + '[' '!' '' = nondestructive ']'
09:49:37 + unset -f deactivate
09:49:37 + rm -rf /home/omero/workspace/OMERO-server/.venv3
09:52:17 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
09:52:41 + '[' false = true ']'
09:52:41 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
09:52:41 Skipping PURGE_DATA:CleanDbAndRepo
09:52:41 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.6-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-5.23.1.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-5.33.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
09:52:55 Copied 1 artifact from "OMERO-build" build number 62
09:52:56 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 53
09:52:56 Copied 2 artifacts from "OMERO-build-build" build number 64
09:52:56 [OMERO-server] $ /bin/bash -xe /tmp/jenkins438554362697765678.sh
09:52:56 + source /home/settings.env
09:52:56 ++ OMERO_DB_HOST=pg
09:52:56 ++ OMERO_DB_USER=postgres
09:52:56 ++ OMERO_DB_PASS=
09:52:56 ++ OMERO_ROOT_PASS=omero
09:52:56 ++ OMERO_DATA_DIR=/OMERO
09:52:56 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:52:56 + OMERO_DB_NAME=OMERO-server
09:52:56 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:52:56 + mkdir -p /home/omero/omero-server-data
09:52:56 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:52:56 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:52:56 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:52:56 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:52:56 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:52:56 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:52:56 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:52:56 ++ ls OMERO.server-5.6.3-676-ca157c25f4-ice36-b62.zip
09:52:56 + ZIP=OMERO.server-5.6.3-676-ca157c25f4-ice36-b62.zip
09:52:56 + '[' '!' -z '' ']'
09:52:56 + DIST=OMERO.server-5.6.3-676-ca157c25f4-ice36-b62
09:52:56 + unzip OMERO.server-5.6.3-676-ca157c25f4-ice36-b62.zip
09:52:56 Archive: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62.zip
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/blitz/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/grid/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/profiles/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/error/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/grid/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/luts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/luts/janelia/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/luts/matplotlib/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/luts/ncsa_paledit/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/luts/seaborn/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/luts/wcif/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/analysis_scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/annotation_scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/export_scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/figure_scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/import_scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/scripts/omero/util_scripts/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/misc/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__1/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__10/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__11/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__2/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__3/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__4/
09:52:56 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__5/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__6/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__7/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__8/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__9/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__4/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__5/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__6/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__7/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.1__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.2__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.2__0/t/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.3__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.4__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.0__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.1__1/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.2__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4DEV__1/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4DEV__2/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4DEV__3/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/var/
09:52:57 creating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/var/tmp/
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/LICENSE.txt
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/backup.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/blitz/mail-senders.example
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/blitz/mail-server.example
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/build.properties
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/env.bat
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/env.sh
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/hibernate.properties
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/ice.config
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/logback-cli.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/logback-indexing-cli.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/logback-indexing.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/logback.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/mime.types
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/node1.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/node2.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/omero.properties
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/profiles/psql
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/rollover.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/Windows.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/error/maintainance.html
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/grid/README
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/grid/default.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/grid/templates.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/grid/windefault.xml
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/ice.config
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/internal.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/master.cfg
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/templates/robot.template
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/etc/testdropbox.config
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/history.rst
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/OMEZarrReader.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/accessors-smart.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/activation.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aggdesigner-algorithm.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aircompressor.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/annotations.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/antlr.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aopalliance.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/apache-client.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/apiguardian-api.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/arns.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/asm.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/auth.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/avatica-core.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/avatica-metrics.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aws-core.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aws-java-sdk-core.jar
09:52:57 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aws-java-sdk-kms.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aws-java-sdk-s3.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aws-query-protocol.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/aws-xml-protocol.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/base.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-anim.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-awt-util.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-bridge.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-codec.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-constants.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-css.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-dom.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-ext.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-gvt.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-i18n.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-parser.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-script.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-shared-resources.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-svg-dom.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-svggen.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-transcoder.jar
09:52:58 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/client/batik-util.jar
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09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/spring-security-ldap.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/spring-tx.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/sqlite-jdbc.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/subethasmtp.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/third-party-jackson-core.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/turbojpeg.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/udunits.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/url-connection-client.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/utils-lite.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/utils.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/uzaygezen-core.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xalan.jar
09:53:16 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xercesImpl.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xml-apis-ext.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xml-apis.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xmlgraphics-commons.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xmpcore.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/xpp3.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/zarr-java.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/lib/server/zstd-jni.jar
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/README
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/agpl.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/antlr.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/apache-v1.1.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/apache-v2.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/asm.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/bouncy_castle_license.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/bsd.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/cddl-v1.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/cpl-v10.html
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/crystalclear.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/django.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/dom4j.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/epl-v1.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/fbsd.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/freemarker.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/gpl-v2.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/gpl.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/gtest.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/iconsweets_license.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/jamon.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/jmock.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/jquery.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/jtidy.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/lgpl-3.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/lgpl-v2.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/lgpl-v2.1.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/lgpl-v3.0.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/lgpl.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/matplotlib.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/mit.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/mpl-v1_0.htm
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/npl-1_1.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/path.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/pil.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/postgresql.txt
09:53:17 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/psf-v2.0.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/psf-v2.5.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/scons.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/slf4j.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/tablelayout.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/which.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/zlib-libpng.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/share/licenses/zpl-v2.1.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/README.txt
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/misc/Makefile
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/misc/current.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/misc/enums.py
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__1/OMERO3__7.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__10/OMERO3A__9.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__11/OMERO3A__10.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__11/OMERO3A__5.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__2/OMERO3A__1.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__3/OMERO3A__2.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__3/OMERO3__5.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__4/OMERO3A__3.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__4/OMERO3__5.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__5/OMERO3A__4.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__6/OMERO3A__5.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__7/OMERO3A__6.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__8/OMERO3A__6.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3A__9/OMERO3A__8.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__4/OMERO3__1.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__5/OMERO3__4.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__6/OMERO3__5.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO3__7/OMERO3__6.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.1__0/OMERO4__0.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.2__0/OMERO4.1__0.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO4__0/OMERO3A__11.sql
09:53:18 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/psql-footer.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/psql-header.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/schema.sql
09:53:19 inflating: OMERO.server-5.6.3-676-ca157c25f4-ice36-b62/sql/psql/OMERO5.4__0/views.sql
09:53:19 + rm -f OMERO.server-5.6.3-676-ca157c25f4-ice36-b62.zip
09:53:19 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-676-ca157c25f4-ice36-b62 /home/omero/workspace/OMERO-server/OMERO.server
09:53:19 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:53:19 ++ deactivate nondestructive
09:53:19 ++ '[' -n '' ']'
09:53:19 ++ '[' -n '' ']'
09:53:19 ++ hash -r
09:53:19 ++ '[' -n '' ']'
09:53:19 ++ unset VIRTUAL_ENV
09:53:19 ++ unset VIRTUAL_ENV_PROMPT
09:53:19 ++ '[' '!' nondestructive = nondestructive ']'
09:53:19 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:53:19 ++ export VIRTUAL_ENV
09:53:19 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:53:19 ++ 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
09:53:19 ++ export PATH
09:53:19 ++ '[' -n '' ']'
09:53:19 ++ '[' -z '' ']'
09:53:19 ++ _OLD_VIRTUAL_PS1=
09:53:19 ++ PS1='(.venv3) '
09:53:19 ++ export PS1
09:53:19 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
09:53:19 ++ export VIRTUAL_ENV_PROMPT
09:53:19 ++ hash -r
09:53:19 + pip install -U pip
09:53:20 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
09:53:21 Collecting pip
09:53:21 Using cached pip-26.2.1-py3-none-any.whl (1.8 MB)
09:53:21 Installing collected packages: pip
09:53:21 Attempting uninstall: pip
09:53:21 Found existing installation: pip 22.3.1
09:53:22 Uninstalling pip-22.3.1:
09:53:22 Successfully uninstalled pip-22.3.1
09:53:39 Successfully installed pip-26.2.1
09:53:39 + 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
09:53:41 Collecting zeroc-ice==3.6.5
09:53:42 Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
09:53:44 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 15.3 MB/s 0:00:02
09:53:44 Installing collected packages: zeroc-ice
09:53:48 Successfully installed zeroc-ice-3.6.5
09:53:48 + pip install markdown
09:53:49 Collecting markdown
09:53:49 Using cached markdown-3.10.3-py3-none-any.whl.metadata (5.1 kB)
09:53:49 Using cached markdown-3.10.3-py3-none-any.whl (110 kB)
09:53:49 Installing collected packages: markdown
09:53:51 Successfully installed markdown-3.10.3
09:53:51 + pip install reportlab
09:53:52 Collecting reportlab
09:53:52 Using cached reportlab-5.0.1-py3-none-any.whl.metadata (1.6 kB)
09:53:52 Collecting pillow>=9.0.0 (from reportlab)
09:53:52 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
09:53:53 Collecting charset-normalizer (from reportlab)
09:53:53 Using cached charset_normalizer-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (45 kB)
09:53:53 Using cached reportlab-5.0.1-py3-none-any.whl (2.0 MB)
09:53:53 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
09:53:53 Using cached charset_normalizer-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (262 kB)
09:53:53 Installing collected packages: pillow, charset-normalizer, reportlab
09:54:03
09:54:03 Successfully installed charset-normalizer-3.5.1 pillow-12.3.0 reportlab-5.0.1
09:54:03 + pip install omego
09:54:04 Collecting omego
09:54:04 Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
09:54:04 Collecting future (from omego)
09:54:04 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
09:54:05 Collecting yaclifw>=0.1.1 (from omego)
09:54:05 Using cached yaclifw-0.2.0-py3-none-any.whl
09:54:05 Collecting six (from yaclifw>=0.1.1->omego)
09:54:05 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
09:54:05 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
09:54:05 Using cached future-1.0.0-py3-none-any.whl (491 kB)
09:54:05 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
09:54:05 Installing collected packages: six, future, yaclifw, omego
09:54:12
09:54:12 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
09:54:12 + pip install tables
09:54:13 Collecting tables
09:54:13 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)
09:54:14 Collecting numpy>=1.20.0 (from tables)
09:54:14 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
09:54:14 Collecting numexpr>=2.6.2 (from tables)
09:54:14 Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
09:54:14 Collecting packaging (from tables)
09:54:14 Using cached packaging-26.3-py3-none-any.whl.metadata (3.5 kB)
09:54:14 Collecting py-cpuinfo (from tables)
09:54:14 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
09:54:14 Collecting blosc2>=2.3.0 (from tables)
09:54:14 Using cached blosc2-4.11.0-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (7.8 kB)
09:54:15 Collecting ndindex (from blosc2>=2.3.0->tables)
09:54:15 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
09:54:15 Collecting msgpack (from blosc2>=2.3.0->tables)
09:54:15 Downloading msgpack-1.2.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
09:54:15 Collecting pydantic (from blosc2>=2.3.0->tables)
09:54:15 Using cached pydantic-2.13.4-py3-none-any.whl.metadata (109 kB)
09:54:15 Collecting httpx[http2] (from blosc2>=2.3.0->tables)
09:54:15 Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
09:54:16 Collecting rich (from blosc2>=2.3.0->tables)
09:54:16 Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
09:54:16 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
09:54:16 Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
09:54:16 Collecting anyio (from httpx[http2]->blosc2>=2.3.0->tables)
09:54:16 Using cached anyio-4.14.2-py3-none-any.whl.metadata (4.6 kB)
09:54:16 Collecting certifi (from httpx[http2]->blosc2>=2.3.0->tables)
09:54:16 Using cached certifi-2026.7.22-py3-none-any.whl.metadata (2.5 kB)
09:54:16 Collecting httpcore==1.* (from httpx[http2]->blosc2>=2.3.0->tables)
09:54:16 Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB)
09:54:16 Collecting idna (from httpx[http2]->blosc2>=2.3.0->tables)
09:54:16 Using cached idna-3.19-py3-none-any.whl.metadata (9.2 kB)
09:54:16 Collecting h2<5,>=3 (from httpx[http2]->blosc2>=2.3.0->tables)
09:54:17 Using cached h2-4.4.1-py3-none-any.whl.metadata (3.8 kB)
09:54:17 Collecting hyperframe<7,>=6.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
09:54:17 Using cached hyperframe-6.1.0-py3-none-any.whl.metadata (4.3 kB)
09:54:17 Collecting hpack<5,>=4.2 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
09:54:17 Using cached hpack-4.2.0-py3-none-any.whl.metadata (3.3 kB)
09:54:17 Collecting h11>=0.16 (from httpcore==1.*->httpx[http2]->blosc2>=2.3.0->tables)
09:54:17 Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB)
09:54:17 Collecting typing_extensions>=4.5 (from anyio->httpx[http2]->blosc2>=2.3.0->tables)
09:54:17 Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
09:54:17 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
09:54:17 Using cached annotated_types-0.8.0-py3-none-any.whl.metadata (15 kB)
09:54:18 Collecting pydantic-core==2.46.4 (from pydantic->blosc2>=2.3.0->tables)
09:54:18 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
09:54:18 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
09:54:18 Using cached typing_inspection-0.4.4-py3-none-any.whl.metadata (2.6 kB)
09:54:18 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
09:54:18 Using cached markdown_it_py-4.2.0-py3-none-any.whl.metadata (7.4 kB)
09:54:18 Collecting pygments<3.0.0,>=2.13.0 (from rich->blosc2>=2.3.0->tables)
09:54:18 Using cached pygments-2.21.0-py3-none-any.whl.metadata (2.5 kB)
09:54:18 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
09:54:18 Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
09:54:18 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)
09:54:19 Using cached blosc2-4.11.0-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.5 MB)
09:54:19 Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (443 kB)
09:54:19 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (16.9 MB)
09:54:19 Using cached httpx-0.28.1-py3-none-any.whl (73 kB)
09:54:19 Using cached h2-4.4.1-py3-none-any.whl (62 kB)
09:54:19 Using cached hpack-4.2.0-py3-none-any.whl (34 kB)
09:54:19 Using cached httpcore-1.0.9-py3-none-any.whl (78 kB)
09:54:19 Using cached hyperframe-6.1.0-py3-none-any.whl (13 kB)
09:54:19 Using cached h11-0.16.0-py3-none-any.whl (37 kB)
09:54:19 Using cached anyio-4.14.2-py3-none-any.whl (125 kB)
09:54:19 Using cached idna-3.19-py3-none-any.whl (68 kB)
09:54:19 Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB)
09:54:19 Using cached certifi-2026.7.22-py3-none-any.whl (136 kB)
09:54:19 Downloading msgpack-1.2.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (422 kB)
09:54:19 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
09:54:20 Using cached packaging-26.3-py3-none-any.whl (129 kB)
09:54:20 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
09:54:20 Using cached pydantic-2.13.4-py3-none-any.whl (472 kB)
09:54:20 Using cached pydantic_core-2.46.4-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
09:54:20 Using cached annotated_types-0.8.0-py3-none-any.whl (13 kB)
09:54:20 Using cached typing_inspection-0.4.4-py3-none-any.whl (14 kB)
09:54:20 Using cached rich-15.0.0-py3-none-any.whl (310 kB)
09:54:20 Using cached pygments-2.21.0-py3-none-any.whl (1.3 MB)
09:54:20 Using cached markdown_it_py-4.2.0-py3-none-any.whl (91 kB)
09:54:20 Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
09:54:20 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
09:54:21 Installing collected packages: py-cpuinfo, typing_extensions, threadpoolctl, pygments, packaging, numpy, ndindex, msgpack, mdurl, idna, hyperframe, hpack, h11, certifi, annotated-types, typing-inspection, pydantic-core, numexpr, markdown-it-py, httpcore, h2, anyio, rich, pydantic, httpx, blosc2, tables
09:55:18
09:55:18 Successfully installed annotated-types-0.8.0 anyio-4.14.2 blosc2-4.11.0 certifi-2026.7.22 h11-0.16.0 h2-4.4.1 hpack-4.2.0 httpcore-1.0.9 httpx-0.28.1 hyperframe-6.1.0 idna-3.19 markdown-it-py-4.2.0 mdurl-0.1.2 msgpack-1.2.2 ndindex-1.10.1 numexpr-2.14.2 numpy-2.4.6 packaging-26.3 py-cpuinfo-9.0.0 pydantic-2.13.4 pydantic-core-2.46.4 pygments-2.21.0 rich-15.0.0 tables-3.11.1 threadpoolctl-3.6.0 typing-inspection-0.4.4 typing_extensions-4.16.0
09:55:18 + pip install jinja2
09:55:20 Collecting jinja2
09:55:20 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
09:55:20 Collecting MarkupSafe>=2.0 (from jinja2)
09:55:20 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)
09:55:20 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
09:55:20 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
09:55:21 Installing collected packages: MarkupSafe, jinja2
09:55:22
09:55:22 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
09:55:22 + pip install omero-py
09:55:23 Collecting omero-py
09:55:23 Using cached omero_py-5.23.0-py3-none-any.whl.metadata (6.5 kB)
09:55:23 Collecting appdirs (from omero-py)
09:55:23 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
09:55:23 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
09:55:23 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
09:55:23 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
09:55:23 Collecting PyYAML (from omero-py)
09:55:23 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)
09:55:23 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
09:55:23 Collecting requests (from omero-py)
09:55:24 Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
09:55:24 Collecting portalocker (from omero-py)
09:55:24 Using cached portalocker-4.3.0-py3-none-any.whl.metadata (11 kB)
09:55:24 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.5.1)
09:55:24 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.19)
09:55:24 Collecting urllib3<3,>=1.26 (from requests->omero-py)
09:55:24 Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
09:55:24 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.7.22)
09:55:24 Using cached omero_py-5.23.0-py3-none-any.whl (2.8 MB)
09:55:24 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
09:55:24 Using cached portalocker-4.3.0-py3-none-any.whl (129 kB)
09:55:24 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
09:55:24 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
09:55:24 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
09:55:24 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, requests, omero-py
09:55:45
09:55:45 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.23.0 portalocker-4.3.0 requests-2.34.2 urllib3-2.7.0
09:55:45 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
09:55:45 Collecting omero-metadata
09:55:45 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-6r7wnspy/omero-metadata_300b63cfc0064e74873a8eb2141a3f70
09:55:46 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-6r7wnspy/omero-metadata_300b63cfc0064e74873a8eb2141a3f70
09:55:47 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 74e7e8ea7b58024ecc271c8b2b7c65a670a540a2
09:55:47 Installing build dependencies: started
09:55:49 Installing build dependencies: finished with status 'done'
09:55:49 Getting requirements to build wheel: started
09:55:49 Getting requirements to build wheel: finished with status 'done'
09:55:49 Preparing metadata (pyproject.toml): started
09:55:49 Preparing metadata (pyproject.toml): finished with status 'done'
09:55:49 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.23.0)
09:55:50 Collecting pandas<3,>=2 (from omero-metadata)
09:55:50 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
09:55:50 Requirement already satisfied: numpy>=1.23.2 in ./.venv3/lib64/python3.11/site-packages (from pandas<3,>=2->omero-metadata) (2.4.6)
09:55:50 Collecting python-dateutil>=2.8.2 (from pandas<3,>=2->omero-metadata)
09:55:50 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
09:55:50 Collecting pytz>=2020.1 (from pandas<3,>=2->omero-metadata)
09:55:50 Using cached pytz-2026.3.post1-py2.py3-none-any.whl.metadata (22 kB)
09:55:50 Collecting tzdata>=2022.7 (from pandas<3,>=2->omero-metadata)
09:55:50 Using cached tzdata-2026.3-py2.py3-none-any.whl.metadata (1.4 kB)
09:55:50 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
09:55:50 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
09:55:50 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (12.3.0)
09:55:50 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (6.0.3)
09:55:50 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
09:55:50 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
09:55:50 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (4.3.0)
09:55:50 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil>=2.8.2->pandas<3,>=2->omero-metadata) (1.17.0)
09:55:50 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.5.1)
09:55:50 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.19)
09:55:50 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.7.0)
09:55:50 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.7.22)
09:55:50 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB)
09:55:51 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
09:55:51 Using cached pytz-2026.3.post1-py2.py3-none-any.whl (508 kB)
09:55:51 Using cached tzdata-2026.3-py2.py3-none-any.whl (348 kB)
09:55:51 Building wheels for collected packages: omero-metadata
09:55:51 Building wheel for omero-metadata (pyproject.toml): started
09:55:51 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
09:55:51 Created wheel for omero-metadata: filename=omero_metadata-0.14.1.dev0-py3-none-any.whl size=39360 sha256=37838e878af8454d9934d1d582c2b20d706f52404527f568a190e46bf3166f74
09:55:51 Stored in directory: /tmp/pip-ephem-wheel-cache-t11g2eg9/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
09:55:51 Successfully built omero-metadata
09:55:51 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
09:56:51
09:56:51 Successfully installed omero-metadata-0.14.1.dev0 pandas-2.3.3 python-dateutil-2.9.0.post0 pytz-2026.3.post1 tzdata-2026.3
09:56:51 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
09:56:53 Collecting omero-cli-render
09:56:53 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-yi7xh025/omero-cli-render_bfba6f2fc6b846e19d5dbd6e814be506
09:56:53 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-yi7xh025/omero-cli-render_bfba6f2fc6b846e19d5dbd6e814be506
09:56:54 Running command git checkout -b merge_ci --track origin/merge_ci
09:56:55 Switched to a new branch 'merge_ci'
09:56:55 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:56:55 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit adeef23a87e87aeed8442106b9738117c186fe85
09:56:55 Installing build dependencies: started
09:56:56 Installing build dependencies: finished with status 'done'
09:56:56 Getting requirements to build wheel: started
09:56:56 Getting requirements to build wheel: finished with status 'done'
09:56:56 Preparing metadata (pyproject.toml): started
09:56:56 Preparing metadata (pyproject.toml): finished with status 'done'
09:56:56 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
09:56:56 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.23.0)
09:56:56 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
09:56:56 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
09:56:56 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.6)
09:56:56 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (12.3.0)
09:56:56 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
09:56:56 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
09:56:56 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (4.3.0)
09:56:56 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.5.1)
09:56:56 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.19)
09:56:56 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.7.0)
09:56:56 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.7.22)
09:56:56 Building wheels for collected packages: omero-cli-render
09:56:56 Building wheel for omero-cli-render (pyproject.toml): started
09:56:57 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
09:56:57 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19841 sha256=50472a0bdb2709bb8c9db39fc180443e2467545c07f8be48e25ebb5d4b9d296d
09:56:57 Stored in directory: /tmp/pip-ephem-wheel-cache-5bwbznqy/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
09:56:57 Successfully built omero-cli-render
09:56:57 Installing collected packages: omero-cli-render
09:56:57 Successfully installed omero-cli-render-0.8.2.dev0
09:56:57 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
09:56:59 Collecting omero-cli-duplicate
09:56:59 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-ejiixzta/omero-cli-duplicate_eda6cab3b736413aac6f8b63481ce54d
09:56:59 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-ejiixzta/omero-cli-duplicate_eda6cab3b736413aac6f8b63481ce54d
09:57:00 Running command git checkout -b merge_ci --track origin/merge_ci
09:57:00 Switched to a new branch 'merge_ci'
09:57:00 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:57:00 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 36ff46c599ab8da5748c1cba9866a719a3d05179
09:57:00 Installing build dependencies: started
09:57:02 Installing build dependencies: finished with status 'done'
09:57:02 Getting requirements to build wheel: started
09:57:02 Getting requirements to build wheel: finished with status 'done'
09:57:02 Preparing metadata (pyproject.toml): started
09:57:02 Preparing metadata (pyproject.toml): finished with status 'done'
09:57:02 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.23.0)
09:57:02 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
09:57:02 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
09:57:02 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
09:57:02 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.3.0)
09:57:02 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
09:57:02 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)
09:57:02 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.34.2)
09:57:02 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (4.3.0)
09:57:02 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.5.1)
09:57:02 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.19)
09:57:02 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2.7.0)
09:57:02 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2026.7.22)
09:57:02 Building wheels for collected packages: omero-cli-duplicate
09:57:02 Building wheel for omero-cli-duplicate (pyproject.toml): started
09:57:03 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
09:57:03 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11540 sha256=ce2373b69dd0692dbee0b394503e74708cf7832f5f4df74dbc5d9d6fc48f1990
09:57:03 Stored in directory: /tmp/pip-ephem-wheel-cache-e2d3z99r/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
09:57:03 Successfully built omero-cli-duplicate
09:57:03 Installing collected packages: omero-cli-duplicate
09:57:03 Successfully installed omero-cli-duplicate-0.4.1.dev0
09:57:03 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
09:57:04 Collecting omero-cli-zarr
09:57:04 Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-maobryx1/omero-cli-zarr_a5a63635f8db4613b67ce8a2a54f77f1
09:57:04 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-maobryx1/omero-cli-zarr_a5a63635f8db4613b67ce8a2a54f77f1
09:57:05 Running command git checkout -b merge_ci --track origin/merge_ci
09:57:06 Switched to a new branch 'merge_ci'
09:57:06 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:57:06 Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit 84421e3e42c8b87180f84afca165a1f032bb8638
09:57:06 Installing build dependencies: started
09:57:07 Installing build dependencies: finished with status 'done'
09:57:07 Getting requirements to build wheel: started
09:57:08 Getting requirements to build wheel: finished with status 'done'
09:57:08 Installing backend dependencies: started
09:57:09 Installing backend dependencies: finished with status 'done'
09:57:09 Preparing metadata (pyproject.toml): started
09:57:10 Preparing metadata (pyproject.toml): finished with status 'done'
09:57:10 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.23.0)
09:57:10 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
09:57:10 Using cached ome_zarr-0.18.0-py3-none-any.whl.metadata (2.9 kB)
09:57:10 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.6)
09:57:10 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:10 Using cached dask-2026.8.0-py3-none-any.whl.metadata (3.8 kB)
09:57:10 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:10 Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
09:57:11 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)
09:57:11 Using cached fsspec-2026.7.0-py3-none-any.whl.metadata (10 kB)
09:57:11 Collecting aiohttp (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:11 Using cached aiohttp-3.14.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
09:57:11 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.34.2)
09:57:12 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:12 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
09:57:12 Collecting toolz (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:12 Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB)
09:57:12 Collecting rangehttpserver (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:12 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl.metadata (769 bytes)
09:57:12 Collecting ome-zarr-models>=1.6 (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:12 Using cached ome_zarr_models-1.7-py3-none-any.whl.metadata (3.0 kB)
09:57:12 Collecting Deprecated (from ome-zarr>=0.13.0->omero-cli-zarr)
09:57:12 Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB)
09:57:12 Collecting click>=8.1 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:13 Downloading click-8.5.0-py3-none-any.whl.metadata (2.6 kB)
09:57:13 Collecting cloudpickle>=3.0.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:13 Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB)
09:57:13 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) (26.3)
09:57:13 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:13 Using cached partd-1.4.2-py3-none-any.whl.metadata (4.6 kB)
09:57:13 Requirement already satisfied: pyyaml>=5.4.1 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)
09:57:13 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)
09:57:13 Using cached importlib_metadata-9.0.0-py3-none-any.whl.metadata (4.5 kB)
09:57:13 Collecting s3fs>=2026.6.0 (from fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:13 Using cached s3fs-2026.7.0-py3-none-any.whl.metadata (1.2 kB)
09:57:13 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)
09:57:13 Using cached zipp-4.1.0-py3-none-any.whl.metadata (3.6 kB)
09:57:14 Collecting pydantic-zarr>=0.8.2 (from ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:14 Using cached pydantic_zarr-0.9.2-py3-none-any.whl.metadata (4.0 kB)
09:57:14 Collecting pydantic<2.13,>=2.11.5 (from ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:14 Using cached pydantic-2.12.5-py3-none-any.whl.metadata (90 kB)
09:57:14 Requirement already satisfied: annotated-types>=0.6.0 in ./.venv3/lib64/python3.11/site-packages (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr) (0.8.0)
09:57:14 Collecting pydantic-core==2.41.5 (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:14 Using cached pydantic_core-2.41.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.3 kB)
09:57:15 Requirement already satisfied: typing-extensions>=4.14.1 in ./.venv3/lib64/python3.11/site-packages (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr) (4.16.0)
09:57:15 Requirement already satisfied: typing-inspection>=0.4.2 in ./.venv3/lib64/python3.11/site-packages (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr) (0.4.4)
09:57:15 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
09:57:15 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.0.0)
09:57:15 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (12.3.0)
09:57:15 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)
09:57:15 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (4.3.0)
09:57:15 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)
09:57:15 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
09:57:15 Collecting aiobotocore<4.0.0,>=2.19.0 (from s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:15 Using cached aiobotocore-3.9.0-py3-none-any.whl.metadata (30 kB)
09:57:15 Collecting aioitertools<1.0.0,>=0.5.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:15 Using cached aioitertools-0.13.0-py3-none-any.whl.metadata (3.3 kB)
09:57:15 Collecting botocore<1.43.57,>=1.43.3 (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:15 Using cached botocore-1.43.56-py3-none-any.whl.metadata (5.6 kB)
09:57:15 Collecting jmespath<2.0.0,>=0.7.1 (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:15 Using cached jmespath-1.1.0-py3-none-any.whl.metadata (7.6 kB)
09:57:16 Collecting multidict<7.0.0,>=6.0.0 (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:16 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)
09:57:16 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>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr) (2.9.0.post0)
09:57:16 Collecting wrapt<3.0.0,>=1.10.10 (from aiobotocore<4.0.0,>=2.19.0->s3fs>=2026.6.0->fsspec[s3]!=2021.07.0,!=2023.9.0,>=0.8->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:16 Using cached wrapt-2.3.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl.metadata (7.4 kB)
09:57:16 Collecting aiohappyeyeballs>=2.5.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:16 Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl.metadata (5.9 kB)
09:57:17 Collecting aiosignal>=1.4.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:17 Using cached aiosignal-1.4.0-py3-none-any.whl.metadata (3.7 kB)
09:57:17 Collecting attrs>=17.3.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:17 Using cached attrs-26.1.0-py3-none-any.whl.metadata (8.8 kB)
09:57:17 Collecting frozenlist>=1.1.1 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:17 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)
09:57:17 Collecting propcache>=0.2.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:17 Using cached propcache-0.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (16 kB)
09:57:17 Collecting yarl<2.0,>=1.17.0 (from aiohttp->ome-zarr>=0.13.0->omero-cli-zarr)
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09:57:18 Collecting scipy>=1.11.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:18 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (62 kB)
09:57:18 Collecting networkx>=3.0 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:18 Using cached networkx-3.6.1-py3-none-any.whl.metadata (6.8 kB)
09:57:18 Collecting imageio!=2.35.0,>=2.33 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:18 Using cached imageio-2.37.4-py3-none-any.whl.metadata (9.6 kB)
09:57:18 Collecting tifffile>=2022.8.12 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
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09:57:18 Collecting lazy-loader>=0.4 (from scikit-image>=0.19.0->ome-zarr>=0.13.0->omero-cli-zarr)
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09:57:18 Collecting donfig>=0.8 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:18 Using cached donfig-0.8.1.post1-py3-none-any.whl.metadata (5.0 kB)
09:57:19 Collecting google-crc32c>=1.5 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:19 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)
09:57:19 Collecting numcodecs>=0.14 (from zarr>=3.0.0->ome-zarr>=0.13.0->omero-cli-zarr)
09:57:19 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)
09:57:19 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (3.5.1)
09:57:19 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->ome-zarr>=0.13.0->omero-cli-zarr) (2026.7.22)
09:57:19 Using cached ome_zarr-0.18.0-py3-none-any.whl (57 kB)
09:57:19 Using cached dask-2026.8.0-py3-none-any.whl (1.5 MB)
09:57:19 Downloading click-8.5.0-py3-none-any.whl (125 kB)
09:57:19 Using cached cloudpickle-3.1.2-py3-none-any.whl (22 kB)
09:57:19 Using cached fsspec-2026.7.0-py3-none-any.whl (206 kB)
09:57:19 Using cached importlib_metadata-9.0.0-py3-none-any.whl (27 kB)
09:57:19 Using cached ome_zarr_models-1.7-py3-none-any.whl (64 kB)
09:57:19 Using cached pydantic-2.12.5-py3-none-any.whl (463 kB)
09:57:19 Using cached pydantic_core-2.41.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
09:57:19 Using cached partd-1.4.2-py3-none-any.whl (18 kB)
09:57:19 Using cached pydantic_zarr-0.9.2-py3-none-any.whl (52 kB)
09:57:19 Using cached s3fs-2026.7.0-py3-none-any.whl (32 kB)
09:57:19 Using cached aiobotocore-3.9.0-py3-none-any.whl (100 kB)
09:57:19 Using cached aiohttp-3.14.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (1.8 MB)
09:57:20 Using cached aioitertools-0.13.0-py3-none-any.whl (24 kB)
09:57:20 Using cached botocore-1.43.56-py3-none-any.whl (15.4 MB)
09:57:20 Using cached jmespath-1.1.0-py3-none-any.whl (20 kB)
09:57:20 Using cached multidict-6.7.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (246 kB)
09:57:20 Using cached wrapt-2.3.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (161 kB)
09:57:20 Using cached yarl-1.24.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (111 kB)
09:57:20 Using cached aiohappyeyeballs-2.7.1-py3-none-any.whl (15 kB)
09:57:20 Using cached aiosignal-1.4.0-py3-none-any.whl (7.5 kB)
09:57:20 Using cached attrs-26.1.0-py3-none-any.whl (67 kB)
09:57:20 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (231 kB)
09:57:20 Using cached propcache-0.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (58 kB)
09:57:20 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (13.7 MB)
09:57:20 Using cached imageio-2.37.4-py3-none-any.whl (318 kB)
09:57:20 Using cached lazy_loader-0.5-py3-none-any.whl (8.0 kB)
09:57:20 Using cached networkx-3.6.1-py3-none-any.whl (2.1 MB)
09:57:20 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.3 MB)
09:57:20 Using cached tifffile-2026.3.3-py3-none-any.whl (243 kB)
09:57:20 Using cached toolz-1.1.0-py3-none-any.whl (58 kB)
09:57:21 Using cached zarr-3.1.6-py3-none-any.whl (295 kB)
09:57:21 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
09:57:21 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 (33 kB)
09:57:21 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)
09:57:21 Using cached zipp-4.1.0-py3-none-any.whl (10 kB)
09:57:21 Using cached deprecated-1.3.1-py2.py3-none-any.whl (11 kB)
09:57:21 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
09:57:21 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
09:57:21 Building wheels for collected packages: omero-cli-zarr
09:57:21 Building wheel for omero-cli-zarr (pyproject.toml): started
09:57:22 Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
09:57:22 Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev179+g84421e3-py3-none-any.whl size=39368 sha256=da1077070d1b16c67f364340a8c52a14d959cbe265a8162bad0d8b926d327a0e
09:57:22 Stored in directory: /tmp/pip-ephem-wheel-cache-z_h6d2h8/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
09:57:22 Successfully built omero-cli-zarr
09:57:22 Installing collected packages: rangehttpserver, zipp, wrapt, toolz, tifffile, scipy, pydantic-core, propcache, numcodecs, networkx, multidict, locket, lazy-loader, jmespath, imageio, google-crc32c, fsspec, frozenlist, donfig, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, zarr, yarl, scikit-image, pydantic, partd, importlib_metadata, Deprecated, botocore, aiosignal, pydantic-zarr, dask, aiohttp, ome-zarr-models, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
09:58:05 Attempting uninstall: pydantic-core
09:58:05 Found existing installation: pydantic_core 2.46.4
09:58:05 Uninstalling pydantic_core-2.46.4:
09:58:05 Successfully uninstalled pydantic_core-2.46.4
09:58:44 Attempting uninstall: pydantic
09:58:44 Found existing installation: pydantic 2.13.4
09:58:45 Uninstalling pydantic-2.13.4:
09:58:45 Successfully uninstalled pydantic-2.13.4
09:59:31
09:59:31 Successfully installed Deprecated-1.3.1 aiobotocore-3.9.0 aiohappyeyeballs-2.7.1 aiohttp-3.14.3 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.56 click-8.5.0 cloudpickle-3.1.2 dask-2026.8.0 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.7.0 google-crc32c-1.8.0 imageio-2.37.4 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-0.18.0 ome-zarr-models-1.7 omero-cli-zarr-0.5.5.dev179+g84421e3 partd-1.4.2 propcache-0.5.2 pydantic-2.12.5 pydantic-core-2.41.5 pydantic-zarr-0.9.2 rangehttpserver-1.4.0 s3fs-2026.7.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 wrapt-2.3.0 yarl-1.24.5 zarr-3.1.6 zipp-4.1.0
09:59:31 + pip install omero-certificates
09:59:33 Collecting omero-certificates
09:59:33 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
09:59:33 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.23.0)
09:59:33 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
09:59:33 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
09:59:33 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.6)
09:59:33 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.3.0)
09:59:33 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
09:59:33 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)
09:59:33 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.34.2)
09:59:33 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (4.3.0)
09:59:33 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.5.1)
09:59:33 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.19)
09:59:33 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.7.0)
09:59:33 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.7.22)
09:59:33 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
09:59:33 Installing collected packages: omero-certificates
09:59:33 Successfully installed omero-certificates-0.4.0
09:59:33 + for x in *.tar.gz
09:59:33 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
09:59:34 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
09:59:34 Installing build dependencies: started
09:59:36 Installing build dependencies: finished with status 'done'
09:59:36 Getting requirements to build wheel: started
09:59:36 Getting requirements to build wheel: finished with status 'done'
09:59:36 Preparing metadata (pyproject.toml): started
09:59:36 Preparing metadata (pyproject.toml): finished with status 'done'
09:59:36 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.23.0)
09:59:36 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
09:59:36 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
09:59:36 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.6)
09:59:36 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.3.0)
09:59:36 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
09:59:36 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)
09:59:36 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
09:59:36 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (4.3.0)
09:59:36 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.5.1)
09:59:36 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.19)
09:59:36 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.7.0)
09:59:36 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.7.22)
09:59:36 Building wheels for collected packages: omero-dropbox
09:59:37 Building wheel for omero-dropbox (pyproject.toml): started
09:59:37 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
09:59:37 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49155 sha256=2824116b4cf02f04eac3e4f2b3258e244d8e3f0dc6a0e25f1697be2d30712af7
09:59:37 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
09:59:37 Successfully built omero-dropbox
09:59:37 Installing collected packages: omero-dropbox
09:59:38 Successfully installed omero-dropbox-5.7.1.dev0
09:59:38 + for x in *.tar.gz
09:59:38 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
09:59:39 Processing ./omero_marshal-0.9.2.dev0.tar.gz
09:59:39 Installing build dependencies: started
09:59:40 Installing build dependencies: finished with status 'done'
09:59:40 Getting requirements to build wheel: started
09:59:41 Getting requirements to build wheel: finished with status 'done'
09:59:41 Preparing metadata (pyproject.toml): started
09:59:41 Preparing metadata (pyproject.toml): finished with status 'done'
09:59:41 Building wheels for collected packages: omero_marshal
09:59:41 Building wheel for omero_marshal (pyproject.toml): started
09:59:41 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
09:59:41 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88121 sha256=69036e2c05d68871ec1a9e5730665c65f2a2cc946f08ef280a9c4e1abb33617b
09:59:41 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
09:59:41 Successfully built omero_marshal
09:59:42 Installing collected packages: omero_marshal
09:59:44 Successfully installed omero_marshal-0.9.2.dev0
09:59:45 + for x in *.tar.gz
09:59:45 + pip install -U omero_py-5.23.1.dev0.tar.gz
09:59:46 Processing ./omero_py-5.23.1.dev0.tar.gz
09:59:46 Installing build dependencies: started
09:59:48 Installing build dependencies: finished with status 'done'
09:59:48 Getting requirements to build wheel: started
09:59:49 Getting requirements to build wheel: finished with status 'done'
09:59:49 Preparing metadata (pyproject.toml): started
09:59:49 Preparing metadata (pyproject.toml): finished with status 'done'
09:59:49 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (1.4.4)
09:59:49 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (1.0.0)
09:59:49 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (2.4.6)
09:59:49 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (12.3.0)
09:59:49 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (6.0.3)
09:59:49 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (3.6.5)
09:59:49 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (2.34.2)
09:59:49 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (4.3.0)
09:59:49 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (3.5.1)
09:59:49 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (3.19)
09:59:49 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (2.7.0)
09:59:49 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (2026.7.22)
09:59:49 Building wheels for collected packages: omero-py
09:59:49 Building wheel for omero-py (pyproject.toml): started
09:59:50 Building wheel for omero-py (pyproject.toml): finished with status 'done'
09:59:50 Created wheel for omero-py: filename=omero_py-5.23.1.dev0-py3-none-any.whl size=2787095 sha256=1ba67c68f0dc19f00ab84783950d4c983ee3af0871b3feb00b56c4609099777e
09:59:50 Stored in directory: /home/omero/.cache/pip/wheels/99/0a/38/75d301c3c2feff37b61c572a590c9d07ab2e52df205857b74d
09:59:50 Successfully built omero-py
09:59:50 Installing collected packages: omero-py
09:59:50 Attempting uninstall: omero-py
09:59:50 Found existing installation: omero-py 5.23.0
09:59:51 Uninstalling omero-py-5.23.0:
10:00:06 Successfully uninstalled omero-py-5.23.0
10:00:27 Successfully installed omero-py-5.23.1.dev0
10:00:27 + for x in *.tar.gz
10:00:27 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
10:00:29 Processing ./omero_scripts-5.10.1.dev0.tar.gz
10:00:29 Installing build dependencies: started
10:00:30 Installing build dependencies: finished with status 'done'
10:00:30 Getting requirements to build wheel: started
10:00:31 Getting requirements to build wheel: finished with status 'done'
10:00:31 Preparing metadata (pyproject.toml): started
10:00:31 Preparing metadata (pyproject.toml): finished with status 'done'
10:00:31 Building wheels for collected packages: omero-scripts
10:00:31 Building wheel for omero-scripts (pyproject.toml): started
10:00:31 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
10:00:31 Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137217 sha256=78bd1e775c6aa9fd53a75514df1dfef09681f60c33f261d7cb24a8a405c1fd76
10:00:31 Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
10:00:31 Successfully built omero-scripts
10:00:32 Installing collected packages: omero-scripts
10:00:33 Successfully installed omero-scripts-5.10.1.dev0
10:00:33 + for x in *.tar.gz
10:00:33 + pip install -U omero_web-5.33.1.dev0.tar.gz
10:00:34 Processing ./omero_web-5.33.1.dev0.tar.gz
10:00:34 Installing build dependencies: started
10:00:36 Installing build dependencies: finished with status 'done'
10:00:36 Getting requirements to build wheel: started
10:00:37 Getting requirements to build wheel: finished with status 'done'
10:00:37 Preparing metadata (pyproject.toml): started
10:00:37 Preparing metadata (pyproject.toml): finished with status 'done'
10:00:37 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.1.dev0) (5.23.1.dev0)
10:00:37 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.33.1.dev0)
10:00:37 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
10:00:37 Collecting Django<5.3,>=5.2.9 (from omero-web==5.33.1.dev0)
10:00:37 Using cached django-5.2.17-py3-none-any.whl.metadata (4.1 kB)
10:00:37 Collecting django-pipeline>=4.1.0 (from omero-web==5.33.1.dev0)
10:00:37 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
10:00:38 Collecting django-cors-headers==3.7.0 (from omero-web==5.33.1.dev0)
10:00:38 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
10:00:38 Collecting whitenoise>=5.3.0 (from omero-web==5.33.1.dev0)
10:00:38 Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
10:00:38 Collecting gunicorn>=19.3 (from omero-web==5.33.1.dev0)
10:00:38 Using cached gunicorn-26.2.0-py3-none-any.whl.metadata (5.5 kB)
10:00:38 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.1.dev0) (0.9.2.dev0)
10:00:38 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.1.dev0) (12.3.0)
10:00:38 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.1.dev0) (2026.3.post1)
10:00:38 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.1.dev0) (4.3.0)
10:00:38 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.1.dev0) (26.3)
10:00:38 Collecting importlib-resources (from omero-web==5.33.1.dev0)
10:00:38 Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
10:00:38 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.33.1.dev0)
10:00:38 Using cached asgiref-3.12.1-py3-none-any.whl.metadata (9.4 kB)
10:00:38 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.33.1.dev0)
10:00:38 Using cached sqlparse-0.6.0-py3-none-any.whl.metadata (6.0 kB)
10:00:38 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline>=4.1.0->omero-web==5.33.1.dev0) (65.5.1)
10:00:38 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.33.1.dev0)
10:00:38 Using cached wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB)
10:00:38 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.1.dev0) (1.4.4)
10:00:38 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.1.dev0) (1.0.0)
10:00:38 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.1.dev0) (2.4.6)
10:00:38 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.1.dev0) (6.0.3)
10:00:38 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==5.33.1.dev0) (3.6.5)
10:00:38 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.1.dev0) (2.34.2)
10:00:38 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.1.dev0) (3.5.1)
10:00:39 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.1.dev0) (3.19)
10:00:39 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.1.dev0) (2.7.0)
10:00:39 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.1.dev0) (2026.7.22)
10:00:39 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
10:00:39 Using cached django-5.2.17-py3-none-any.whl (8.3 MB)
10:00:39 Using cached asgiref-3.12.1-py3-none-any.whl (25 kB)
10:00:39 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
10:00:39 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
10:00:39 Using cached gunicorn-26.2.0-py3-none-any.whl (228 kB)
10:00:39 Using cached sqlparse-0.6.0-py3-none-any.whl (50 kB)
10:00:39 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
10:00:39 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
10:00:39 Using cached wheel-0.48.0-py3-none-any.whl (33 kB)
10:00:39 Building wheels for collected packages: omero-web
10:00:39 Building wheel for omero-web (pyproject.toml): started
10:00:40 Building wheel for omero-web (pyproject.toml): finished with status 'done'
10:00:40 Created wheel for omero-web: filename=omero_web-5.33.1.dev0-py3-none-any.whl size=2821635 sha256=c6c0d621a629aa2059dbb22c0d142b2fda705bd98789b5b2b9bf4866d9187b0d
10:00:40 Stored in directory: /home/omero/.cache/pip/wheels/77/f6/23/fc9c2b5a287f0e430435deaa5ed7a3a49a9c9a8f56769f82c4
10:00:40 Successfully built omero-web
10:00:41 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
10:02:06
10:02:06 Successfully installed Django-5.2.17 asgiref-3.12.1 concurrent-log-handler-0.9.29 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-26.2.0 importlib-resources-7.1.0 omero-web-5.33.1.dev0 sqlparse-0.6.0 wheel-0.48.0 whitenoise-6.12.0
10:02:06 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
10:02:07 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
10:02:07 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
10:02:07 --2026-08-28 10:02:07-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
10:02:07 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.110.133, ...
10:02:07 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
10:02:07 HTTP request sent, awaiting response... 200 OK
10:02:07 Length: 133661 (131K) [text/plain]
10:02:07 Saving to: ‘Figure_To_Pdf.py’
10:02:07
10:02:07 0K .......... .......... .......... .......... .......... 38% 2.90M 0s
10:02:07 50K .......... .......... .......... .......... .......... 76% 6.85M 0s
10:02:07 100K .......... .......... .......... 100% 3.93M=0.03s
10:02:07
10:02:07 2026-08-28 10:02:07 (4.04 MB/s) - ‘Figure_To_Pdf.py’ saved [133661/133661]
10:02:07
10:02:07 + chmod 755 Figure_To_Pdf.py
10:02:07 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
10:02:08 + omero config set omero.db.name OMERO-server
10:02:30 + omero config set omero.db.host pg
10:02:34 + omero config set omero.db.user postgres
10:02:39 + omero config set omero.data.dir /home/omero/omero-server-data
10:02:43 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
10:02:48 + omero config set omero.db.poolsize 25
10:02:53 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
10:02:58 + omero config set omero.security.trustStorePassword changeit
10:03:02 + omero config set omero.mail.config true
10:03:07 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
10:03:12 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED'
10:03:16 + omero certificates
10:03:20 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
10:03:20 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
10:03:21 + '[' false = true ']'
10:03:21 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
10:03:21 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
10:03:21 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
10:03:21 2026-08-28 10:03:21,557 [ omego.db] DEBUG dbcommand => upgrade
10:03:21 2026-08-28 10:03:21,557 [ omego.db] DEBUG dbhost => localhost
10:03:21 2026-08-28 10:03:21,558 [ omego.db] DEBUG dbname => OMERO-server
10:03:21 2026-08-28 10:03:21,558 [ omego.db] DEBUG dbpass => omero
10:03:21 2026-08-28 10:03:21,558 [ omego.db] DEBUG dbuser => omero
10:03:21 2026-08-28 10:03:21,558 [ omego.db] DEBUG rootpass => omero
10:03:21 2026-08-28 10:03:21,558 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
10:03:21 2026-08-28 10:03:21,558 [omego.extern] INFO Executing : omero version
10:03:25 OMERO.py version:
10:03:25 OMERO.server version:
10:03:25 5.6.3-676-ca157c25f4-ice36-b62
10:03:25 5.23.1.dev0
10:03:26 2026-08-28 10:03:26,222 [omego.extern] INFO Completed [4.664 s]
10:03:26 2026-08-28 10:03:26,222 [omego.extern] DEBUG Using omero CLI from omero
10:03:26 2026-08-28 10:03:26,222 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
10:03:26 2026-08-28 10:03:26,223 [omego.extern] INFO Running [current environment]: omero config get --show-password
10:03:26 2026-08-28 10:03:26,223 [omego.extern] INFO Executing : omero config get --show-password
10:03:30 2026-08-28 10:03:30,930 [omego.extern] INFO Completed [4.708 s]
10:03:30 2026-08-28 10:03:30,931 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
10:03:30 2026-08-28 10:03:30,931 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
10:03:31 2026-08-28 10:03:31,110 [omego.extern] INFO Completed [0.180 s]
10:03:31 2026-08-28 10:03:31,110 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.14\n'
10:03:31 2026-08-28 10:03:31,110 [ omego.db] INFO psql version: psql (PostgreSQL) 16.14
10:03:31
10:03:31 2026-08-28 10:03:31,110 [omego.extern] INFO Running [current environment]: omero config get --show-password
10:03:31 2026-08-28 10:03:31,110 [omego.extern] INFO Executing : omero config get --show-password
10:03:35 2026-08-28 10:03:35,652 [omego.extern] INFO Completed [4.541 s]
10:03:35 2026-08-28 10:03:35,652 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
10:03:35 2026-08-28 10:03:35,652 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
10:03:35 2026-08-28 10:03:35,713 [omego.extern] INFO Completed [0.061 s]
10:03:35 2026-08-28 10:03:35,713 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.11") at port "5432".\n'
10:03:35 2026-08-28 10:03:35,713 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
10:03:35 2026-08-28 10:03:35,713 [omego.extern] INFO Running [current environment]: omero config get --show-password
10:03:35 2026-08-28 10:03:35,713 [omego.extern] INFO Executing : omero config get --show-password
10:03:40 2026-08-28 10:03:40,357 [omego.extern] INFO Completed [4.644 s]
10:03:40 2026-08-28 10:03:40,357 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
10:03:40 2026-08-28 10:03:40,357 [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
10:03:40 2026-08-28 10:03:40,973 [omego.extern] INFO Completed [0.616 s]
10:03:40 2026-08-28 10:03:40,973 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
10:03:40 2026-08-28 10:03:40,973 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
10:03:41 2026-08-28 10:03:41,026 [ omego.db] INFO Database is already at OMERO5.4__0
10:03:41 + export LANG=en_US.UTF-8
10:03:41 + LANG=en_US.UTF-8
10:03:41 + export LANGUAGE=en_US:en
10:03:41 + LANGUAGE=en_US:en
10:03:41 + export LC_ALL=en_US.UTF-8
10:03:41 + LC_ALL=en_US.UTF-8
10:03:41 + BUILD_ID=DONT_KILL_ME
10:03:41 + omero admin start
10:03:55 WARNING: lock files in /home/omero/omero-server-data
10:03:55 ----------------------------------------
10:03:55 /home/omero/omero-server-data/.omero/repository/a3d421b1-9991-42f6-9eb8-867f8e8779af/.lock
10:03:55 ----------------------------------------
10:03:55
10:03:55 You may want to stop all server processes and remove
10:03:55 these files manually. Lock files can remain after an
10:03:55 abrupt server outage and are especially frequent on
10:03:55 remotely mounted filesystems like NFS.
10:03:55
10:03:55 No descriptor given. Using etc/grid/default.xml
10:04:12 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
10:04:12 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
10:04:12 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
10:04:12 Waiting on startup. Use CTRL-C to exit
10:04:14 + omero admin waitup
10:04:20 Waiting on startup. Use CTRL-C to exit
10:04:21 + omero admin diagnostics
10:04:26
10:04:26 ================================================================================
10:04:26 OMERO Diagnostics (admin)
10:04:26 ================================================================================
10:04:26
10:04:26 Commands: java -version 21.0.12 (/usr/bin/java)
10:04:26 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
10:04:26 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
10:04:26 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
10:04:26 Commands: psql --version 16.14 (/usr/bin/psql)
10:04:26 Commands: openssl version 3.5.527 (/usr/bin/openssl)
10:04:26
10:04:26 Component: OMERO.py 5.23.1.dev0
10:04:26 Component: OMERO.server 5.6.3-676-ca157c25f4-ice36-b62
10:04:26
10:04:26 Server: icegridnode running
10:04:26 Server: Blitz-0 active (pid = 1348, enabled)
10:04:26 Server: Indexer-0 active (pid = 1366, enabled)
10:04:26 Server: OMERO.Glacier2 active (pid = 1371, enabled)
10:04:26 Server: OMERO.IceStorm active (pid = 1398, enabled)
10:04:26 Server: Processor-0 active (pid = 1387, enabled)
10:04:26 Server: Tables-0 active (pid = 1396, enabled)
10:04:26
10:04:26 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
10:04:26 Log files: Blitz-0.log 32.4 KB errors=0 warnings=1
10:04:26 Log files: DropBox.log n/a
10:04:26 Log files: FileServer.log n/a
10:04:26 Log files: Indexer-0.log 2.6 KB
10:04:26 Log files: MonitorServer.log n/a
10:04:26 Log files: Processor-0.log 856 B
10:04:26 Log files: Tables-0.log 1.1 KB
10:04:26 Log files: TestDropBox.log n/a
10:04:26 Log files: master.err empty
10:04:26 Log files: master.out 30.7 KB
10:04:26 Log files: Total size 0.07 MB
10:04:26
10:04:26
10:04:26 Environment:OMERO_HOME=(unset)
10:04:26 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
10:04:26 Environment:OMERO_NODE=(unset)
10:04:26 Environment:OMERO_MASTER=(unset)
10:04:26 Environment:OMERO_USERDIR=(unset)
10:04:26 Environment:OMERO_TMPDIR=(unset)
10:04:26 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
10:04:26 Environment:PYTHONPATH=(unset)
10:04:26 Environment:ICE_HOME=/opt/ice-3.6.5
10:04:26 Environment:LD_LIBRARY_PATH=(unset)
10:04:26 Environment:DYLD_LIBRARY_PATH=(unset)
10:04:26
10:04:26 OMERO SSL port:4064
10:04:26 OMERO TCP port:4063
10:04:26 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
10:04:26 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
10:04:26
10:04:26 JVM settings: Blitz-${index} -Xmx5007m
10:04:26 JVM settings: Indexer-${index} -Xmx3338m
10:04:26 JVM settings: PixelData-${index} -Xmx5007m
10:04:26 JVM settings: Repository-${index} -Xmx3338m
10:04:27
10:04:27 Jar: lib/server/formats-api.jar Bio-Formats API 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
10:04:27 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
10:04:27 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
10:04:27 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3 26 February 2026 70fd9b72a9834f1af4852c1e5b5676c57a2c360e
10:04:27 Jar: lib/server/ome-common.jar OME Common Java 6.2.1 27 February 2026 a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
10:04:27 Jar: lib/server/ome-jai.jar OME JAI 0.1.5 30 June 2025 257a1c1410c0103485248d05752a5174262a38b6
10:04:27 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4 25 June 2025 57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
10:04:27 Jar: lib/server/ome-poi.jar OME POI 5.3.11 11 November 2025 a2f3944ac71db9e7e51a6f64ec46beeb60613afb
10:04:27 Jar: lib/server/ome-xml.jar OME XML library 6.5.3 22 January 2026 21d1362abd9ce26e13888d2b2d028753d21ac96e
10:04:27 Jar: lib/server/omero-blitz.jar jar 5.8.6-SNAPSHOT
10:04:27 Jar: lib/server/omero-common.jar jar 5.7.6-SNAPSHOT
10:04:27 Jar: lib/server/omero-gateway.jar jar 5.11.1-SNAPSHOT
10:04:27 Jar: lib/server/omero-model.jar jar 5.7.6-SNAPSHOT
10:04:27 Jar: lib/server/omero-renderer.jar jar 5.6.6-SNAPSHOT
10:04:27 Jar: lib/server/omero-romio.jar jar 5.8.6-SNAPSHOT
10:04:27 Jar: lib/server/omero-server.jar jar 5.7.6-SNAPSHOT
10:04:27 Jar: lib/server/omero-zarr-pixel-buffer.jar OMERO Zarr Pixel Buffer 0.7.0-rc3 4c6a6c7d8fb12449c8080808fd12bf95e996e398
10:04:27 + deactivate
10:04:27 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
10:04:27 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
10:04:27 + export PATH
10:04:27 + unset _OLD_VIRTUAL_PATH
10:04:27 + '[' -n '' ']'
10:04:27 + hash -r
10:04:27 + '[' -n '' ']'
10:04:27 + unset VIRTUAL_ENV
10:04:27 + unset VIRTUAL_ENV_PROMPT
10:04:27 + '[' '!' '' = nondestructive ']'
10:04:27 + unset -f deactivate
10:04:28 Finished: SUCCESS
