00:49:19 Started by upstream project "Trigger" build number 261
00:49:19 originally caused by:
00:49:19 Started by timer
00:49:19 Running as SYSTEM
00:49:19 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:49:19 [OMERO-server] $ /bin/bash -xe /tmp/jenkins14201104971773207185.sh
00:49:20 + source /home/settings.env
00:49:20 ++ OMERO_DB_HOST=pg
00:49:20 ++ OMERO_DB_USER=postgres
00:49:20 ++ OMERO_DB_PASS=
00:49:20 ++ OMERO_ROOT_PASS=omero
00:49:20 ++ OMERO_DATA_DIR=/OMERO
00:49:20 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:49:20 + OMERO_DB_NAME=OMERO-server
00:49:20 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:49:20 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:49:20 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:49:20 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:49:20 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:49:20 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:49:20 ++ deactivate nondestructive
00:49:20 ++ '[' -n '' ']'
00:49:20 ++ '[' -n '' ']'
00:49:20 ++ '[' -n /bin/bash -o -n '' ']'
00:49:20 ++ hash -r
00:49:20 ++ '[' -n '' ']'
00:49:20 ++ unset VIRTUAL_ENV
00:49:20 ++ '[' '!' nondestructive = nondestructive ']'
00:49:20 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:49:20 ++ export VIRTUAL_ENV
00:49:20 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:49:20 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:49:20 ++ export PATH
00:49:20 ++ '[' -n '' ']'
00:49:20 ++ '[' -z '' ']'
00:49:20 ++ _OLD_VIRTUAL_PS1=
00:49:20 ++ PS1='(.venv3) '
00:49:20 ++ export PS1
00:49:20 ++ '[' -n /bin/bash -o -n '' ']'
00:49:20 ++ hash -r
00:49:20 + omero admin stop
00:49:39 Waiting on shutdown. Use CTRL-C to exit
00:49:39 .+ sleep 5
00:49:55 + deactivate
00:49:55 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:49:55 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:49:55 + export PATH
00:49:55 + unset _OLD_VIRTUAL_PATH
00:49:55 + '[' -n '' ']'
00:49:55 + '[' -n /bin/bash -o -n '' ']'
00:49:55 + hash -r
00:49:55 + '[' -n '' ']'
00:49:55 + unset VIRTUAL_ENV
00:49:55 + '[' '!' '' = nondestructive ']'
00:49:55 + unset -f deactivate
00:49:55 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:50:00 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
00:50:06 + '[' false = true ']'
00:50:06 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:50:06 Skipping PURGE_DATA:CleanDbAndRepo
00:50:06 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.7.5-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.19.6.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.8.4.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.27.3.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:50:09 Copied 1 artifact from "OMERO-build" build number 217
00:50:09 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 214
00:50:09 Copied 2 artifacts from "OMERO-build-build" build number 225
00:50:09 [OMERO-server] $ /bin/bash -xe /tmp/jenkins10199768895435279584.sh
00:50:09 + source /home/settings.env
00:50:09 ++ OMERO_DB_HOST=pg
00:50:09 ++ OMERO_DB_USER=postgres
00:50:09 ++ OMERO_DB_PASS=
00:50:09 ++ OMERO_ROOT_PASS=omero
00:50:09 ++ OMERO_DATA_DIR=/OMERO
00:50:09 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:50:09 + OMERO_DB_NAME=OMERO-server
00:50:09 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:50:09 + mkdir -p /home/omero/omero-server-data
00:50:09 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:50:09 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:50:09 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:50:09 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:50:09 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:50:09 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:50:09 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:50:09 ++ ls OMERO.server-5.6.3-513-85571adcc5-ice36.zip
00:50:09 + ZIP=OMERO.server-5.6.3-513-85571adcc5-ice36.zip
00:50:09 + '[' '!' -z '' ']'
00:50:09 + DIST=OMERO.server-5.6.3-513-85571adcc5-ice36
00:50:09 + unzip OMERO.server-5.6.3-513-85571adcc5-ice36.zip
00:50:09 Archive: OMERO.server-5.6.3-513-85571adcc5-ice36.zip
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/blitz/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/grid/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/profiles/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/error/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/grid/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/luts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/luts/janelia/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/luts/ncsa_paledit/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/luts/wcif/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/analysis_scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/annotation_scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/export_scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/figure_scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/import_scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/scripts/omero/util_scripts/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/misc/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__1/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__10/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__11/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__2/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__3/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__4/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__5/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__6/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__7/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__8/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__9/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__4/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__5/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__6/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__7/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.1__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.2__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.2__0/t/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.3__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.4__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.0__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.1__1/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.2__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4DEV__1/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4DEV__2/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4DEV__3/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/
00:50:09 creating: OMERO.server-5.6.3-513-85571adcc5-ice36/var/
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/LICENSE.txt
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/backup.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/blitz/mail-senders.example
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/blitz/mail-server.example
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/build.properties
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/env.bat
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/env.sh
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/hibernate.properties
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/ice.config
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/logback-cli.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/logback-indexing-cli.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/logback-indexing.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/logback.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/mime.types
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/node1.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/node2.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/omero.properties
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/profiles/psql
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/rollover.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/Windows.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/error/maintainance.html
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/grid/README
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/grid/default.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/grid/templates.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/grid/windefault.xml
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/ice.config
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/internal.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/master.cfg
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/templates/robot.template
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/etc/testdropbox.config
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/history.rst
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/OMEZarrReader.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/activation.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/aggdesigner-algorithm.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/aircompressor.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/annotations.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/antlr.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/aopalliance.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/avatica-core.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/avatica-metrics.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/aws-java-sdk-core.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/aws-java-sdk-kms.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/aws-java-sdk-s3.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/base.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-all.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-anim.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-awt-util.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-bridge.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-codec.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-constants.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-css.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-dom.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-ext.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-extension.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-gui-util.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-gvt.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-i18n.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-parser.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-rasterizer-ext.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-rasterizer.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-script.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-slideshow.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-squiggle-ext.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-squiggle.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-svg-dom.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-svgbrowser.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-svggen.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-svgpp.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-svgrasterizer.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-swing.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-transcoder.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-ttf2svg.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-util.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/batik-xml.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/btm.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/bufr.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/c3p0.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/calcite-core.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/calcite-linq4j.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/cdm-core.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/checker-qual.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/commons-beanutils.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/commons-codec.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/commons-collections.jar
00:50:09 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/client/commons-collections4.jar
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00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/perf4j.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/postgresql.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/protobuf-java.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/quartz.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/re2j.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/reflectasm.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/rhino.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/serializer.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/sketches-core.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/slf4j-api.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/snakeyaml.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/solr-analysis-extras.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/solr-commons-csv.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/solr-core.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/solr-solrj.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/specification.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-aop.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-beans.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-context-support.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-context.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-core.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-expression.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-jdbc.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-jms.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-ldap-core.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-messaging.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-orm.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-security-core.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-security-ldap.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/spring-tx.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/sqlite-jdbc.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/subethasmtp.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/turbojpeg.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/udunits.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xalan.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xercesImpl.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xml-apis-ext.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xml-apis.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xmlgraphics-commons.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xmpcore.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/lib/server/xpp3.jar
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/README
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/agpl.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/antlr.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/apache-v1.1.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/apache-v2.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/asm.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/bouncy_castle_license.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/bsd.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/cddl-v1.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/cpl-v10.html
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/crystalclear.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/django.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/dom4j.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/epl-v1.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/fbsd.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/freemarker.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/gpl-v2.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/gpl.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/gtest.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/iconsweets_license.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/jamon.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/jmock.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/jquery.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/jtidy.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/lgpl-3.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/lgpl-v2.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/lgpl-v2.1.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/lgpl-v3.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/lgpl.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/matplotlib.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/mit.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/mpl-v1_0.htm
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/npl-1_1.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/path.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/pil.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/postgresql.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/psf-v2.0.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/psf-v2.5.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/scons.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/slf4j.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/tablelayout.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/which.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/zlib-libpng.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/share/licenses/zpl-v2.1.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/README.txt
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/misc/Makefile
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/misc/current.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/misc/enums.py
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__1/OMERO3__7.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__10/OMERO3A__9.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__11/OMERO3A__10.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__11/OMERO3A__5.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__2/OMERO3A__1.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__3/OMERO3A__2.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__3/OMERO3__5.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__4/OMERO3A__3.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__4/OMERO3__5.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__5/OMERO3A__4.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__6/OMERO3A__5.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__7/OMERO3A__6.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__8/OMERO3A__6.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3A__9/OMERO3A__8.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__4/OMERO3__1.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__5/OMERO3__4.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__6/OMERO3__5.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO3__7/OMERO3__6.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.1__0/OMERO4__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.2__0/OMERO4.1__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO4__0/OMERO3A__11.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/psql-footer.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/psql-header.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/schema.sql
00:50:12 inflating: OMERO.server-5.6.3-513-85571adcc5-ice36/sql/psql/OMERO5.4__0/views.sql
00:50:12 + rm -f OMERO.server-5.6.3-513-85571adcc5-ice36.zip
00:50:12 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-513-85571adcc5-ice36 /home/omero/workspace/OMERO-server/OMERO.server
00:50:12 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:50:12 ++ deactivate nondestructive
00:50:12 ++ '[' -n '' ']'
00:50:12 ++ '[' -n '' ']'
00:50:12 ++ '[' -n /bin/bash -o -n '' ']'
00:50:12 ++ hash -r
00:50:12 ++ '[' -n '' ']'
00:50:12 ++ unset VIRTUAL_ENV
00:50:12 ++ '[' '!' nondestructive = nondestructive ']'
00:50:12 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:50:12 ++ export VIRTUAL_ENV
00:50:12 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:12 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:12 ++ export PATH
00:50:12 ++ '[' -n '' ']'
00:50:12 ++ '[' -z '' ']'
00:50:12 ++ _OLD_VIRTUAL_PS1=
00:50:12 ++ PS1='(.venv3) '
00:50:12 ++ export PS1
00:50:12 ++ '[' -n /bin/bash -o -n '' ']'
00:50:12 ++ hash -r
00:50:12 + pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl
00:50:12 Collecting zeroc-ice==3.6.5
00:50:13 Downloading https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl (31.3 MB)
00:50:14 Installing collected packages: zeroc-ice
00:50:15 Successfully installed zeroc-ice-3.6.5
00:50:15 + pip install -U pip future
00:50:16 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
00:50:16 Collecting pip
00:50:16 Using cached pip-24.2-py3-none-any.whl (1.8 MB)
00:50:16 Collecting future
00:50:16 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:50:16 Installing collected packages: pip, future
00:50:16 Attempting uninstall: pip
00:50:16 Found existing installation: pip 21.2.3
00:50:17 Uninstalling pip-21.2.3:
00:50:17 Successfully uninstalled pip-21.2.3
00:50:18 Successfully installed future-1.0.0 pip-24.2
00:50:18 + pip install markdown
00:50:19 Collecting markdown
00:50:19 Using cached Markdown-3.7-py3-none-any.whl.metadata (7.0 kB)
00:50:19 Collecting importlib-metadata>=4.4 (from markdown)
00:50:19 Using cached importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
00:50:19 Collecting zipp>=3.20 (from importlib-metadata>=4.4->markdown)
00:50:19 Using cached zipp-3.20.2-py3-none-any.whl.metadata (3.7 kB)
00:50:20 Using cached Markdown-3.7-py3-none-any.whl (106 kB)
00:50:20 Using cached importlib_metadata-8.5.0-py3-none-any.whl (26 kB)
00:50:20 Using cached zipp-3.20.2-py3-none-any.whl (9.2 kB)
00:50:20 Installing collected packages: zipp, importlib-metadata, markdown
00:50:20 Successfully installed importlib-metadata-8.5.0 markdown-3.7 zipp-3.20.2
00:50:20 + pip install reportlab
00:50:21 Collecting reportlab
00:50:21 Using cached reportlab-4.2.5-py3-none-any.whl.metadata (1.5 kB)
00:50:21 Collecting pillow>=9.0.0 (from reportlab)
00:50:21 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
00:50:21 Collecting chardet (from reportlab)
00:50:21 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
00:50:21 Using cached reportlab-4.2.5-py3-none-any.whl (1.9 MB)
00:50:21 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.4 MB)
00:50:22 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
00:50:22 Installing collected packages: pillow, chardet, reportlab
00:50:23 Successfully installed chardet-5.2.0 pillow-11.0.0 reportlab-4.2.5
00:50:23 + pip install omego
00:50:24 Collecting omego
00:50:24 Using cached omego-0.7.0-py3-none-any.whl
00:50:24 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
00:50:24 Collecting yaclifw>=0.1.1 (from omego)
00:50:24 Using cached yaclifw-0.2.0-py3-none-any.whl
00:50:24 Collecting six (from yaclifw>=0.1.1->omego)
00:50:24 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
00:50:24 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
00:50:24 Installing collected packages: six, yaclifw, omego
00:50:24 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
00:50:24 + pip install tables
00:50:25 Collecting tables
00:50:25 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
00:50:25 Collecting numpy>=1.19.0 (from tables)
00:50:25 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
00:50:26 Collecting numexpr>=2.6.2 (from tables)
00:50:26 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.2 kB)
00:50:26 Collecting packaging (from tables)
00:50:26 Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
00:50:26 Collecting py-cpuinfo (from tables)
00:50:26 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:50:26 Collecting blosc2>=2.3.0 (from tables)
00:50:26 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
00:50:26 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
00:50:26 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB)
00:50:26 Collecting msgpack (from blosc2>=2.3.0->tables)
00:50:27 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:50:27 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:50:27 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
00:50:27 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (404 kB)
00:50:27 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
00:50:27 Using cached packaging-24.1-py3-none-any.whl (53 kB)
00:50:27 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:50:27 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (478 kB)
00:50:27 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB)
00:50:28 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
00:50:32 Successfully installed blosc2-2.5.1 msgpack-1.1.0 ndindex-1.9.2 numexpr-2.10.1 numpy-2.0.2 packaging-24.1 py-cpuinfo-9.0.0 tables-3.9.2
00:50:32 + pip install jinja2
00:50:33 Collecting jinja2
00:50:33 Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
00:50:33 Collecting MarkupSafe>=2.0 (from jinja2)
00:50:33 Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:50:33 Using cached jinja2-3.1.4-py3-none-any.whl (133 kB)
00:50:33 Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB)
00:50:33 Installing collected packages: MarkupSafe, jinja2
00:50:34 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.4
00:50:34 + pip install omero-py
00:50:34 Collecting omero-py
00:50:34 Using cached omero_py-5.19.5-py3-none-any.whl.metadata (6.3 kB)
00:50:34 Collecting urllib3<2 (from omero-py)
00:50:34 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:50:34 Collecting appdirs (from omero-py)
00:50:34 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:50:34 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
00:50:35 Collecting numpy<2 (from omero-py)
00:50:35 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
00:50:35 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (11.0.0)
00:50:35 Collecting PyYAML (from omero-py)
00:50:35 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:50:35 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
00:50:35 Collecting requests (from omero-py)
00:50:35 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
00:50:35 Collecting portalocker (from omero-py)
00:50:35 Using cached portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB)
00:50:35 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
00:50:35 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
00:50:35 Collecting idna<4,>=2.5 (from requests->omero-py)
00:50:35 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:50:36 Collecting certifi>=2017.4.17 (from requests->omero-py)
00:50:36 Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
00:50:36 Using cached omero_py-5.19.5-py3-none-any.whl (2.8 MB)
00:50:36 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
00:50:36 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:50:36 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:50:36 Using cached portalocker-2.10.1-py3-none-any.whl (18 kB)
00:50:36 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
00:50:36 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
00:50:36 Using cached certifi-2024.8.30-py3-none-any.whl (167 kB)
00:50:36 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (144 kB)
00:50:36 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:50:36 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, numpy, idna, charset-normalizer, certifi, requests, omero-py
00:50:37 Attempting uninstall: numpy
00:50:37 Found existing installation: numpy 2.0.2
00:50:37 Uninstalling numpy-2.0.2:
00:50:37 Successfully uninstalled numpy-2.0.2
00:50:42 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 certifi-2024.8.30 charset-normalizer-3.4.0 idna-3.10 numpy-1.26.4 omero-py-5.19.5 portalocker-2.10.1 requests-2.32.3 urllib3-1.26.20
00:50:42 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:50:43 Collecting omero-metadata
00:50:43 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-1f0b2l1p/omero-metadata_0111ce27ab9b493a98fbc33740a3ac07
00:50:43 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-1f0b2l1p/omero-metadata_0111ce27ab9b493a98fbc33740a3ac07
00:50:45 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit fcac1cad6ccb7975f08ee6b3bee5f3f17390620b
00:50:45 Installing build dependencies: started
00:50:47 Installing build dependencies: finished with status 'done'
00:50:47 Getting requirements to build wheel: started
00:50:47 Getting requirements to build wheel: finished with status 'done'
00:50:47 Preparing metadata (pyproject.toml): started
00:50:48 Preparing metadata (pyproject.toml): finished with status 'done'
00:50:48 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.5)
00:50:48 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.2)
00:50:48 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.4)
00:50:48 Collecting pandas (from omero-metadata)
00:50:48 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
00:50:48 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:50:48 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:50:48 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:50:48 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
00:50:48 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (11.0.0)
00:50:48 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
00:50:48 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
00:50:48 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.10.1)
00:50:48 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (3.0.2)
00:50:48 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
00:50:48 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:50:48 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:50:48 Using cached pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
00:50:48 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:50:48 Using cached tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:50:48 Requirement already satisfied: six>=1.5 in ./.venv3/lib/python3.9/site-packages (from python-dateutil>=2.8.2->pandas->omero-metadata) (1.16.0)
00:50:48 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.0)
00:50:48 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.10)
00:50:48 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2024.8.30)
00:50:48 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
00:50:49 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:50:49 Using cached pytz-2024.2-py2.py3-none-any.whl (508 kB)
00:50:49 Using cached tzdata-2024.2-py2.py3-none-any.whl (346 kB)
00:50:49 Building wheels for collected packages: omero-metadata
00:50:49 Building wheel for omero-metadata (pyproject.toml): started
00:50:49 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:50:49 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39187 sha256=b15dbeb5c86007ac06ca9079a3c3759000926887415e3988695481682abc793b
00:50:49 Stored in directory: /tmp/pip-ephem-wheel-cache-46rfbjna/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
00:50:49 Successfully built omero-metadata
00:50:50 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
00:50:55 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2024.2 tzdata-2024.2
00:50:55 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:50:55 Collecting omero-cli-render
00:50:55 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-q670c8c4/omero-cli-render_c24c0ca726cb4d4f9128081961c3f388
00:50:55 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-q670c8c4/omero-cli-render_c24c0ca726cb4d4f9128081961c3f388
00:50:56 Running command git checkout -b merge_ci --track origin/merge_ci
00:50:56 Switched to a new branch 'merge_ci'
00:50:56 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:50:56 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 1c99489987c04c759080dce3668605abe7417684
00:50:56 Installing build dependencies: started
00:50:58 Installing build dependencies: finished with status 'done'
00:50:58 Getting requirements to build wheel: started
00:50:58 Getting requirements to build wheel: finished with status 'done'
00:50:58 Preparing metadata (pyproject.toml): started
00:50:59 Preparing metadata (pyproject.toml): finished with status 'done'
00:50:59 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.2)
00:50:59 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.5)
00:50:59 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:50:59 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:50:59 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:50:59 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
00:50:59 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.0.0)
00:50:59 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
00:50:59 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
00:50:59 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.10.1)
00:50:59 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.0)
00:50:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.10)
00:50:59 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2024.8.30)
00:50:59 Building wheels for collected packages: omero-cli-render
00:50:59 Building wheel for omero-cli-render (pyproject.toml): started
00:50:59 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:50:59 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=18030 sha256=5b6d6608ce693ed9999f394fc1f674938ca82e8f32b50e00635c6d65afa1c711
00:50:59 Stored in directory: /tmp/pip-ephem-wheel-cache-c4igkxol/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
00:50:59 Successfully built omero-cli-render
00:50:59 Installing collected packages: omero-cli-render
00:50:59 Successfully installed omero-cli-render-0.8.2.dev0
00:50:59 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:51:00 Collecting omero-cli-duplicate
00:51:00 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-huzpblaj/omero-cli-duplicate_b010f3990daf4912be4244a2365d8662
00:51:00 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-huzpblaj/omero-cli-duplicate_b010f3990daf4912be4244a2365d8662
00:51:00 Running command git checkout -b merge_ci --track origin/merge_ci
00:51:01 Switched to a new branch 'merge_ci'
00:51:01 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:51:01 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 8438822c5351725fa14d38a532064785928011b0
00:51:01 Installing build dependencies: started
00:51:02 Installing build dependencies: finished with status 'done'
00:51:02 Getting requirements to build wheel: started
00:51:03 Getting requirements to build wheel: finished with status 'done'
00:51:03 Preparing metadata (pyproject.toml): started
00:51:03 Preparing metadata (pyproject.toml): finished with status 'done'
00:51:03 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.5)
00:51:03 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:51:03 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:51:03 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:51:03 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
00:51:03 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.0.0)
00:51:03 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:51:03 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5)
00:51:03 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
00:51:03 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.10.1)
00:51:03 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.0)
00:51:03 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.10)
00:51:03 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2024.8.30)
00:51:03 Building wheels for collected packages: omero-cli-duplicate
00:51:03 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:51:03 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:51:03 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11442 sha256=63f0f57d8eba2efce317419d710ad4cdaac115681dc1ac9913d6dec15dee8e82
00:51:03 Stored in directory: /tmp/pip-ephem-wheel-cache-rmhs1ztj/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
00:51:03 Successfully built omero-cli-duplicate
00:51:03 Installing collected packages: omero-cli-duplicate
00:51:03 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:51:03 + pip install omero-certificates
00:51:04 Collecting omero-certificates
00:51:04 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
00:51:04 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.5)
00:51:04 Collecting distro==1.8.0 (from omero-certificates)
00:51:04 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
00:51:04 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:51:04 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:51:04 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:51:04 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
00:51:04 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (11.0.0)
00:51:04 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:51:04 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
00:51:04 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
00:51:04 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.10.1)
00:51:04 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.0)
00:51:04 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
00:51:04 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2024.8.30)
00:51:04 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
00:51:04 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
00:51:05 Installing collected packages: distro, omero-certificates
00:51:05 Successfully installed distro-1.8.0 omero-certificates-0.3.2
00:51:05 + for x in *.tar.gz
00:51:05 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:51:05 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:51:05 Installing build dependencies: started
00:51:07 Installing build dependencies: finished with status 'done'
00:51:07 Getting requirements to build wheel: started
00:51:07 Getting requirements to build wheel: finished with status 'done'
00:51:07 Preparing metadata (pyproject.toml): started
00:51:07 Preparing metadata (pyproject.toml): finished with status 'done'
00:51:07 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.7.1.dev0) (5.19.5)
00:51:07 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
00:51:07 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:51:07 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:51:07 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.4)
00:51:07 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.0.0)
00:51:07 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:51:07 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5)
00:51:07 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3)
00:51:07 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.10.1)
00:51:07 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.0)
00:51:07 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10)
00:51:07 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2024.8.30)
00:51:07 Building wheels for collected packages: omero-dropbox
00:51:07 Building wheel for omero-dropbox (pyproject.toml): started
00:51:08 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:51:08 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49058 sha256=8c0d7f23abeaaa058ee47bc552298dba91021ef8b03a8a78202c4b3756f7f368
00:51:08 Stored in directory: /home/omero/.cache/pip/wheels/eb/76/85/58476368b176f793423899407c96293c22f9c9edc28cf54079
00:51:08 Successfully built omero-dropbox
00:51:08 Installing collected packages: omero-dropbox
00:51:08 Successfully installed omero-dropbox-5.7.1.dev0
00:51:08 + for x in *.tar.gz
00:51:08 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:51:08 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:51:08 Installing build dependencies: started
00:51:10 Installing build dependencies: finished with status 'done'
00:51:10 Getting requirements to build wheel: started
00:51:11 Getting requirements to build wheel: finished with status 'done'
00:51:11 Preparing metadata (pyproject.toml): started
00:51:11 Preparing metadata (pyproject.toml): finished with status 'done'
00:51:11 Building wheels for collected packages: omero_marshal
00:51:11 Building wheel for omero_marshal (pyproject.toml): started
00:51:11 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:51:11 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88031 sha256=34a1b040f4099e7c264aec46625c8a127665951f492f451969d461dbaf6b81ca
00:51:11 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
00:51:11 Successfully built omero_marshal
00:51:11 Installing collected packages: omero_marshal
00:51:11 Successfully installed omero_marshal-0.9.1.dev0
00:51:11 + for x in *.tar.gz
00:51:11 + pip install -U omero_py-5.19.6.dev0.tar.gz
00:51:12 Processing ./omero_py-5.19.6.dev0.tar.gz
00:51:12 Installing build dependencies: started
00:51:14 Installing build dependencies: finished with status 'done'
00:51:14 Getting requirements to build wheel: started
00:51:14 Getting requirements to build wheel: finished with status 'done'
00:51:14 Preparing metadata (pyproject.toml): started
00:51:15 Preparing metadata (pyproject.toml): finished with status 'done'
00:51:15 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.20)
00:51:15 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.4.4)
00:51:15 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.0.0)
00:51:15 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.4)
00:51:15 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (11.0.0)
00:51:15 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (6.0.2)
00:51:15 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (3.6.5)
00:51:15 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.32.3)
00:51:15 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.10.1)
00:51:15 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.4.0)
00:51:15 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.10)
00:51:15 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (2024.8.30)
00:51:15 Building wheels for collected packages: omero-py
00:51:15 Building wheel for omero-py (pyproject.toml): started
00:51:16 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:51:16 Created wheel for omero-py: filename=omero_py-5.19.6.dev0-py3-none-any.whl size=2783246 sha256=eb692e0bfc6e0aab126f8b1a41f1d8c3b8412b41c844353159608e85db270c28
00:51:16 Stored in directory: /home/omero/.cache/pip/wheels/80/e5/37/a3ff2b54d2fa16a058bb39e8eb6b77b050109520fb9f16931d
00:51:16 Successfully built omero-py
00:51:16 Installing collected packages: omero-py
00:51:16 Attempting uninstall: omero-py
00:51:16 Found existing installation: omero-py 5.19.5
00:51:16 Uninstalling omero-py-5.19.5:
00:51:16 Successfully uninstalled omero-py-5.19.5
00:51:18 Successfully installed omero-py-5.19.6.dev0
00:51:19 + for x in *.tar.gz
00:51:19 + pip install -U omero_scripts-5.8.4.dev0.tar.gz
00:51:19 Processing ./omero_scripts-5.8.4.dev0.tar.gz
00:51:19 Installing build dependencies: started
00:51:21 Installing build dependencies: finished with status 'done'
00:51:21 Getting requirements to build wheel: started
00:51:21 Getting requirements to build wheel: finished with status 'done'
00:51:21 Preparing metadata (pyproject.toml): started
00:51:21 Preparing metadata (pyproject.toml): finished with status 'done'
00:51:21 Building wheels for collected packages: omero-scripts
00:51:21 Building wheel for omero-scripts (pyproject.toml): started
00:51:21 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:51:21 Created wheel for omero-scripts: filename=omero_scripts-5.8.4.dev0-py3-none-any.whl size=116645 sha256=91f04fd8eb4c3c7ad1c0599611b29b9be9e31b42666aa75f7b0e199c89f6d1b3
00:51:21 Stored in directory: /home/omero/.cache/pip/wheels/50/80/aa/1e175e4f2a5b0a5343d01937a727d990d08c8e12000390ad9c
00:51:22 Successfully built omero-scripts
00:51:22 Installing collected packages: omero-scripts
00:51:22 Successfully installed omero-scripts-5.8.4.dev0
00:51:22 + for x in *.tar.gz
00:51:22 + pip install -U omero_web-5.27.3.dev0.tar.gz
00:51:22 Processing ./omero_web-5.27.3.dev0.tar.gz
00:51:23 Installing build dependencies: started
00:51:24 Installing build dependencies: finished with status 'done'
00:51:24 Getting requirements to build wheel: started
00:51:25 Getting requirements to build wheel: finished with status 'done'
00:51:25 Preparing metadata (pyproject.toml): started
00:51:25 Preparing metadata (pyproject.toml): finished with status 'done'
00:51:25 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (5.19.6.dev0)
00:51:25 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.27.3.dev0)
00:51:25 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
00:51:25 Collecting Django<4.3,>=4.2.3 (from omero-web==5.27.3.dev0)
00:51:25 Using cached Django-4.2.16-py3-none-any.whl.metadata (4.1 kB)
00:51:26 Collecting django-pipeline==2.1.0 (from omero-web==5.27.3.dev0)
00:51:26 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
00:51:26 Collecting django-cors-headers==3.7.0 (from omero-web==5.27.3.dev0)
00:51:26 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:51:26 Collecting django-csp (from omero-web==5.27.3.dev0)
00:51:26 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
00:51:26 Collecting whitenoise>=5.3.0 (from omero-web==5.27.3.dev0)
00:51:26 Using cached whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB)
00:51:26 Collecting gunicorn>=19.3 (from omero-web==5.27.3.dev0)
00:51:26 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:51:26 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (0.9.1.dev0)
00:51:26 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (11.0.0)
00:51:26 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2024.2)
00:51:26 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2.10.1)
00:51:26 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (24.1)
00:51:26 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
00:51:26 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
00:51:26 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
00:51:26 Using cached sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB)
00:51:26 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.26.20)
00:51:26 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.4.4)
00:51:26 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.0.0)
00:51:26 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.26.4)
00:51:26 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (6.0.2)
00:51:26 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.6.5)
00:51:26 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (2.32.3)
00:51:27 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
00:51:27 Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
00:51:27 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.4.0)
00:51:27 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.10)
00:51:27 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (2024.8.30)
00:51:27 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:51:27 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
00:51:27 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
00:51:27 Using cached Django-4.2.16-py3-none-any.whl (8.0 MB)
00:51:27 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:51:27 Using cached whitenoise-6.7.0-py3-none-any.whl (19 kB)
00:51:27 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
00:51:27 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
00:51:27 Using cached sqlparse-0.5.1-py3-none-any.whl (44 kB)
00:51:27 Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
00:51:27 Building wheels for collected packages: omero-web
00:51:27 Building wheel for omero-web (pyproject.toml): started
00:51:29 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:51:29 Created wheel for omero-web: filename=omero_web-5.27.3.dev0-py3-none-any.whl size=2766670 sha256=97f2a2ec9d32bfa1e62548f53472c4c4830e7936b5ee3bef74d95cede1f0a87c
00:51:29 Stored in directory: /home/omero/.cache/pip/wheels/ae/1e/5f/7127f5403b089e5e8280a504b3d30303e78d1102aa8854c22b
00:51:29 Successfully built omero-web
00:51:29 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
00:51:31 Successfully installed Django-4.2.16 asgiref-3.8.1 concurrent-log-handler-0.9.25 django-cors-headers-3.7.0 django-csp-3.8 django-pipeline-2.1.0 gunicorn-23.0.0 omero-web-5.27.3.dev0 sqlparse-0.5.1 typing-extensions-4.12.2 whitenoise-6.7.0
00:51:32 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:51:33 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:51:33 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:51:33 --2024-10-27 00:51:33-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:51:34 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.110.133, 185.199.109.133, ...
00:51:34 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
00:51:34 HTTP request sent, awaiting response... 200 OK
00:51:34 Length: 101739 (99K) [text/plain]
00:51:34 Saving to: ‘Figure_To_Pdf.py’
00:51:34
00:51:34 0K .......... .......... .......... .......... .......... 50% 1.68M 0s
00:51:34 50K .......... .......... .......... .......... ......... 100% 8.91M=0.03s
00:51:34
00:51:34 2024-10-27 00:51:34 (2.82 MB/s) - ‘Figure_To_Pdf.py’ saved [101739/101739]
00:51:34
00:51:34 + chmod 755 Figure_To_Pdf.py
00:51:34 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:51:34 + omero config set omero.db.name OMERO-server
00:51:36 + omero config set omero.db.host pg
00:51:38 + omero config set omero.db.user postgres
00:51:39 + omero config set omero.data.dir /home/omero/omero-server-data
00:51:41 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:51:42 + omero config set omero.db.poolsize 25
00:51:44 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:51:46 + omero config set omero.security.trustStorePassword changeit
00:51:47 + omero config set omero.mail.config true
00:51:49 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:51:50 + omero config set omero.mail.host smtp.dundee.ac.uk
00:51:52 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:51:53 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:51:55 + omero certificates
00:51:56 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
00:51:57 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:51:57 + '[' false = true ']'
00:51:57 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:51:57 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:51:57 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG dbcommand => upgrade
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG dbhost => localhost
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG dbname => OMERO-server
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG dbpass => omero
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG dbuser => omero
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG rootpass => omero
00:51:57 2024-10-27 00:51:57,598 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:51:57 2024-10-27 00:51:57,598 [omego.extern] INFO Executing : omero version
00:51:58 OMERO.py version:
00:51:59 OMERO.server version:
00:51:59 5.6.3-513-85571adcc5-ice36
00:51:59 5.19.6.dev0
00:51:59 2024-10-27 00:51:59,359 [omego.extern] INFO Completed [1.761 s]
00:51:59 2024-10-27 00:51:59,359 [omego.extern] DEBUG Using omero CLI from omero
00:51:59 2024-10-27 00:51:59,359 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:51:59 2024-10-27 00:51:59,360 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:51:59 2024-10-27 00:51:59,360 [omego.extern] INFO Executing : omero config get --show-password
00:52:00 2024-10-27 00:52:00,954 [omego.extern] INFO Completed [1.594 s]
00:52:00 2024-10-27 00:52:00,954 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:52:00 2024-10-27 00:52:00,954 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:52:01 2024-10-27 00:52:01,876 [omego.extern] INFO Completed [0.921 s]
00:52:01 2024-10-27 00:52:01,876 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.4\n'
00:52:01 2024-10-27 00:52:01,876 [ omego.db] INFO psql version: psql (PostgreSQL) 16.4
00:52:01
00:52:01 2024-10-27 00:52:01,876 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:52:01 2024-10-27 00:52:01,876 [omego.extern] INFO Executing : omero config get --show-password
00:52:03 2024-10-27 00:52:03,581 [omego.extern] INFO Completed [1.705 s]
00:52:03 2024-10-27 00:52:03,581 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:52:03 2024-10-27 00:52:03,582 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:52:03 2024-10-27 00:52:03,869 [omego.extern] INFO Completed [0.287 s]
00:52:03 2024-10-27 00:52:03,869 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.5") at port "5432".\n'
00:52:03 2024-10-27 00:52:03,869 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:52:03 2024-10-27 00:52:03,869 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:52:03 2024-10-27 00:52:03,869 [omego.extern] INFO Executing : omero config get --show-password
00:52:05 2024-10-27 00:52:05,501 [omego.extern] INFO Completed [1.632 s]
00:52:05 2024-10-27 00:52:05,501 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:52:05 2024-10-27 00:52:05,501 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:52:05 2024-10-27 00:52:05,738 [omego.extern] INFO Completed [0.237 s]
00:52:05 2024-10-27 00:52:05,739 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:52:05 2024-10-27 00:52:05,739 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:52:05 2024-10-27 00:52:05,741 [ omego.db] INFO Database is already at OMERO5.4__0
00:52:05 + export LANG=en_US.UTF-8
00:52:05 + LANG=en_US.UTF-8
00:52:05 + export LANGUAGE=en_US:en
00:52:05 + LANGUAGE=en_US:en
00:52:05 + export LC_ALL=en_US.UTF-8
00:52:05 + LC_ALL=en_US.UTF-8
00:52:05 + BUILD_ID=DONT_KILL_ME
00:52:05 + omero admin start
00:52:18 No descriptor given. Using etc/grid/default.xml
00:52:39 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:52:39 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:52:39 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:52:39 Waiting on startup. Use CTRL-C to exit
00:52:40 + omero admin waitup
00:52:41 Waiting on startup. Use CTRL-C to exit
00:52:41 + omero admin diagnostics
00:52:49 ERROR:omero.util.UpgradeCheck:HTTPConnectionPool(host='upgrade.openmicroscopy.org.uk', port=80): Max retries exceeded with url: /?version=5.19.6.dev0&os.name=Linux&os.arch=x86_64&os.version=Linux-5.14.0-427.40.1.el9_4.x86_64-x86_64-with-glibc2.34&python.version=3.9.18&python.compiler=GCC+11.4.1+20231218+%28Red+Hat+11.4.1-3%29&python.build=main&python.build=Aug+23+2024+00%3A00%3A00 (Caused by ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x7f915075f640>, 'Connection to upgrade.openmicroscopy.org.uk timed out. (connect timeout=6.0)'))
00:52:49
00:52:49 ================================================================================
00:52:49 OMERO Diagnostics (admin)
00:52:49 ================================================================================
00:52:49
00:52:49 Commands: java -version 11.0.24 (/usr/bin/java)
00:52:49 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:52:49 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:52:49 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:52:49 Commands: psql --version 16.4 (/usr/bin/psql)
00:52:49 Commands: openssl version 3.0.71 (/usr/bin/openssl)
00:52:49
00:52:49 Component: OMERO.py 5.19.6.dev0
00:52:49 Component: OMERO.server 5.6.3-513-85571adcc5-ice36
00:52:49
00:52:49 Server: icegridnode running
00:52:49 Server: Blitz-0 active (pid = 43841, enabled)
00:52:49 Server: Indexer-0 active (pid = 43861, enabled)
00:52:49 Server: OMERO.Glacier2 active (pid = 43863, enabled)
00:52:49 Server: OMERO.IceStorm active (pid = 43882, enabled)
00:52:49 Server: Processor-0 activating (enabled)
00:52:49 Server: Tables-0 activating (enabled)
00:52:49
00:52:49 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:52:49 Log files: Blitz-0.log 21.8 KB errors=1 warnings=0
00:52:49 Log files: DropBox.log n/a
00:52:49 Log files: FileServer.log n/a
00:52:49 Log files: Indexer-0.log 2.6 KB
00:52:49 Log files: MonitorServer.log n/a
00:52:49 Log files: Processor-0.log 592 B
00:52:49 Log files: Tables-0.log 841 B
00:52:49 Log files: TestDropBox.log n/a
00:52:49 Log files: master.err 180 B
00:52:49 Log files: master.out 30.1 KB
00:52:49 Log files: Total size 0.06 MB
00:52:49
00:52:49
00:52:49 Environment:OMERO_HOME=(unset)
00:52:49 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:52:49 Environment:OMERO_NODE=(unset)
00:52:49 Environment:OMERO_MASTER=(unset)
00:52:49 Environment:OMERO_USERDIR=(unset)
00:52:49 Environment:OMERO_TMPDIR=(unset)
00:52:49 Environment:PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:52:49 Environment:PYTHONPATH=(unset)
00:52:49 Environment:ICE_HOME=/opt/ice-3.6.5
00:52:49 Environment:LD_LIBRARY_PATH=(unset)
00:52:49 Environment:DYLD_LIBRARY_PATH=(unset)
00:52:49
00:52:49 OMERO SSL port:4064
00:52:49 OMERO TCP port:4063
00:52:49 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:52:49 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:52:49
00:52:49 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:52:49 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:52:49 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:52:49 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:52:49
00:52:49 Jar: lib/server/formats-api.jar Bio-Formats API 8.1.0-SNAPSHOT 27 October 2024 583016a8fb5118d0c2defeb87b80b78575f72f4f
00:52:49 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.1.0-SNAPSHOT 27 October 2024 583016a8fb5118d0c2defeb87b80b78575f72f4f
00:52:49 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.1.0-SNAPSHOT 27 October 2024 583016a8fb5118d0c2defeb87b80b78575f72f4f
00:52:49 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.4-SNAPSHOT 27 October 2024 857a3276c5e3744c713982a3b8585a17f7caaa60
00:52:49 Jar: lib/server/ome-common.jar OME Common Java 6.0.25-SNAPSHOT 27 October 2024 857a3276c5e3744c713982a3b8585a17f7caaa60
00:52:49 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 27 October 2024 857a3276c5e3744c713982a3b8585a17f7caaa60
00:52:49 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4-SNAPSHOT 27 October 2024 857a3276c5e3744c713982a3b8585a17f7caaa60
00:52:49 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 27 October 2024 857a3276c5e3744c713982a3b8585a17f7caaa60
00:52:49 Jar: lib/server/ome-xml.jar OME XML library 6.3.7-SNAPSHOT 27 October 2024 857a3276c5e3744c713982a3b8585a17f7caaa60
00:52:49 Jar: lib/server/omero-blitz.jar jar 5.7.5-SNAPSHOT
00:52:49 Jar: lib/server/omero-common.jar jar 5.6.8-SNAPSHOT
00:52:49 Jar: lib/server/omero-gateway.jar jar 5.9.4-SNAPSHOT
00:52:49 Jar: lib/server/omero-model.jar jar 5.6.16-SNAPSHOT
00:52:49 Jar: lib/server/omero-renderer.jar jar 5.5.18-SNAPSHOT
00:52:49 Jar: lib/server/omero-romio.jar jar 5.7.8-SNAPSHOT
00:52:49 Jar: lib/server/omero-server.jar jar 5.6.13-SNAPSHOT
00:52:49 + deactivate
00:52:49 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:52:49 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:52:49 + export PATH
00:52:49 + unset _OLD_VIRTUAL_PATH
00:52:49 + '[' -n '' ']'
00:52:49 + '[' -n /bin/bash -o -n '' ']'
00:52:49 + hash -r
00:52:49 + '[' -n '' ']'
00:52:49 + unset VIRTUAL_ENV
00:52:49 + '[' '!' '' = nondestructive ']'
00:52:49 + unset -f deactivate
00:52:49 Finished: SUCCESS
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