09:54:35 Started by user devspace
09:54:35 Running as SYSTEM
09:54:35 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
09:54:35 [OMERO-server] $ /bin/bash -xe /tmp/jenkins123916965571503889.sh
09:54:35 + source /home/settings.env
09:54:35 ++ OMERO_DB_HOST=pg
09:54:35 ++ OMERO_DB_USER=postgres
09:54:35 ++ OMERO_DB_PASS=
09:54:35 ++ OMERO_ROOT_PASS=omero
09:54:35 ++ OMERO_DATA_DIR=/OMERO
09:54:35 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:54:35 + OMERO_DB_NAME=OMERO-server
09:54:35 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:54:35 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:54:35 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:54:35 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:54:35 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
09:54:35 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:54:35 ++ deactivate nondestructive
09:54:35 ++ '[' -n '' ']'
09:54:35 ++ '[' -n '' ']'
09:54:35 ++ '[' -n /bin/bash -o -n '' ']'
09:54:35 ++ hash -r
09:54:35 ++ '[' -n '' ']'
09:54:35 ++ unset VIRTUAL_ENV
09:54:35 ++ '[' '!' nondestructive = nondestructive ']'
09:54:35 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:54:35 ++ export VIRTUAL_ENV
09:54:35 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:54:35 ++ 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
09:54:35 ++ export PATH
09:54:35 ++ '[' -n '' ']'
09:54:35 ++ '[' -z '' ']'
09:54:35 ++ _OLD_VIRTUAL_PS1=
09:54:35 ++ PS1='(.venv3) '
09:54:35 ++ export PS1
09:54:35 ++ '[' -n /bin/bash -o -n '' ']'
09:54:35 ++ hash -r
09:54:35 + omero admin stop
09:54:49 Server not running
09:54:50 + echo not running
09:54:50 not running
09:54:50 + sleep 5
09:54:55 + deactivate
09:54:55 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:54:55 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:54:55 + export PATH
09:54:55 + unset _OLD_VIRTUAL_PATH
09:54:55 + '[' -n '' ']'
09:54:55 + '[' -n /bin/bash -o -n '' ']'
09:54:55 + hash -r
09:54:55 + '[' -n '' ']'
09:54:55 + unset VIRTUAL_ENV
09:54:55 + '[' '!' '' = nondestructive ']'
09:54:55 + unset -f deactivate
09:54:55 + rm -rf /home/omero/workspace/OMERO-server/.venv3
09:54:59 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
09:55:02 + '[' false = true ']'
09:55:02 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
09:55:02 Skipping PURGE_DATA:CleanDbAndRepo
09:55:02 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.7.3-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero-dropbox-5.6.3.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero-py-5.19.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero-scripts-5.8.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero-web-5.25.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
09:55:06 Copied 1 artifact from "OMERO-build" build number 7
09:55:06 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 7
09:55:07 Copied 2 artifacts from "OMERO-build-build" build number 7
09:55:07 [OMERO-server] $ /bin/bash -xe /tmp/jenkins8177324086523070660.sh
09:55:07 + source /home/settings.env
09:55:07 ++ OMERO_DB_HOST=pg
09:55:07 ++ OMERO_DB_USER=postgres
09:55:07 ++ OMERO_DB_PASS=
09:55:07 ++ OMERO_ROOT_PASS=omero
09:55:07 ++ OMERO_DATA_DIR=/OMERO
09:55:07 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:55:07 + OMERO_DB_NAME=OMERO-server
09:55:07 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:55:07 + mkdir -p /home/omero/omero-server-data
09:55:07 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:55:07 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:55:07 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:55:07 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:55:07 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:55:07 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:55:07 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:55:07 ++ ls OMERO.server-5.6.3-437-854b934e23-ice36.zip
09:55:07 + ZIP=OMERO.server-5.6.3-437-854b934e23-ice36.zip
09:55:07 + '[' '!' -z '' ']'
09:55:07 + DIST=OMERO.server-5.6.3-437-854b934e23-ice36
09:55:07 + unzip OMERO.server-5.6.3-437-854b934e23-ice36.zip
09:55:07 Archive: OMERO.server-5.6.3-437-854b934e23-ice36.zip
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/blitz/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/grid/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/profiles/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/error/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/janelia/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/ncsa_paledit/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/luts/wcif/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/analysis_scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/annotation_scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/export_scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/figure_scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/import_scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/scripts/omero/util_scripts/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/server/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/share/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/share/licenses/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/misc/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__1/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__10/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__11/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__2/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__3/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__4/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__5/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__6/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__7/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__8/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3A__9/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__4/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__5/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__6/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO3__7/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.1__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.2__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.2__0/t/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.3__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4.4__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO4__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.0__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__1/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__2/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__3/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/
09:55:07 creating: OMERO.server-5.6.3-437-854b934e23-ice36/var/
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/LICENSE.txt
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/backup.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/blitz/mail-senders.example
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/blitz/mail-server.example
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/build.properties
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/env.bat
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/env.sh
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/hibernate.properties
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/ice.config
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback-cli.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback-indexing-cli.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback-indexing.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/logback.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/mime.types
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/node1.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/node2.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/omero.properties
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/profiles/psql
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/rollover.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/Windows.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/error/maintainance.html
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/README
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/default.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/templates.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/grid/windefault.xml
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/ice.config
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/internal.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/master.cfg
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/templates/robot.template
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/etc/testdropbox.config
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/history.rst
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/OMEZarrReader.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/activation.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aggdesigner-algorithm.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aircompressor.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/annotations.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/antlr.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aopalliance.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/apache-client.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/arns.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/auth.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/avatica-core.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/avatica-metrics.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aws-core.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aws-query-protocol.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/aws-xml-protocol.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/base.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-all.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-anim.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-awt-util.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-bridge.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-codec.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-constants.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-css.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-dom.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-ext.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-extension.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-gui-util.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-gvt.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-i18n.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-parser.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-rasterizer-ext.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-rasterizer.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-script.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-slideshow.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-squiggle-ext.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-squiggle.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svg-dom.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svgbrowser.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svggen.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svgpp.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-svgrasterizer.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-swing.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-transcoder.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-ttf2svg.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-util.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/batik-xml.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/btm.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/bufr.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/c3p0.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/calcite-core.jar
09:55:07 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/lib/client/calcite-linq4j.jar
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09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/psql-footer.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/psql-header.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/schema.sql
09:55:09 inflating: OMERO.server-5.6.3-437-854b934e23-ice36/sql/psql/OMERO5.4__0/views.sql
09:55:09 + rm -f OMERO.server-5.6.3-437-854b934e23-ice36.zip
09:55:09 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-437-854b934e23-ice36 /home/omero/workspace/OMERO-server/OMERO.server
09:55:09 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:55:09 ++ deactivate nondestructive
09:55:09 ++ '[' -n '' ']'
09:55:09 ++ '[' -n '' ']'
09:55:09 ++ '[' -n /bin/bash -o -n '' ']'
09:55:09 ++ hash -r
09:55:09 ++ '[' -n '' ']'
09:55:09 ++ unset VIRTUAL_ENV
09:55:09 ++ '[' '!' nondestructive = nondestructive ']'
09:55:09 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:55:09 ++ export VIRTUAL_ENV
09:55:09 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:55:09 ++ 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
09:55:09 ++ export PATH
09:55:09 ++ '[' -n '' ']'
09:55:09 ++ '[' -z '' ']'
09:55:09 ++ _OLD_VIRTUAL_PS1=
09:55:09 ++ PS1='(.venv3) '
09:55:09 ++ export PS1
09:55:09 ++ '[' -n /bin/bash -o -n '' ']'
09:55:09 ++ hash -r
09:55:09 + 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
09:55:10 Collecting zeroc-ice==3.6.5
09:55:11 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)
09:55:13 Installing collected packages: zeroc-ice
09:55:14 Successfully installed zeroc-ice-3.6.5
09:55:14 WARNING: You are using pip version 21.2.3; however, version 24.0 is available.
09:55:14 You should consider upgrading via the '/home/omero/workspace/OMERO-server/.venv3/bin/python3 -m pip install --upgrade pip' command.
09:55:14 + pip install -U pip future
09:55:14 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
09:55:15 Collecting pip
09:55:15 Using cached pip-24.0-py3-none-any.whl (2.1 MB)
09:55:15 Collecting future
09:55:15 Using cached future-1.0.0-py3-none-any.whl (491 kB)
09:55:15 Installing collected packages: pip, future
09:55:15 Attempting uninstall: pip
09:55:15 Found existing installation: pip 21.2.3
09:55:15 Uninstalling pip-21.2.3:
09:55:15 Successfully uninstalled pip-21.2.3
09:55:17 Successfully installed future-1.0.0 pip-24.0
09:55:17 + pip install markdown
09:55:18 Collecting markdown
09:55:18 Using cached Markdown-3.6-py3-none-any.whl.metadata (7.0 kB)
09:55:18 Collecting importlib-metadata>=4.4 (from markdown)
09:55:18 Using cached importlib_metadata-7.1.0-py3-none-any.whl.metadata (4.7 kB)
09:55:18 Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown)
09:55:18 Using cached zipp-3.18.1-py3-none-any.whl.metadata (3.5 kB)
09:55:18 Using cached Markdown-3.6-py3-none-any.whl (105 kB)
09:55:18 Using cached importlib_metadata-7.1.0-py3-none-any.whl (24 kB)
09:55:18 Using cached zipp-3.18.1-py3-none-any.whl (8.2 kB)
09:55:18 Installing collected packages: zipp, importlib-metadata, markdown
09:55:18 Successfully installed importlib-metadata-7.1.0 markdown-3.6 zipp-3.18.1
09:55:18 + pip install reportlab
09:55:19 Collecting reportlab
09:55:19 Using cached reportlab-4.1.0-py3-none-any.whl.metadata (1.4 kB)
09:55:20 Collecting pillow>=9.0.0 (from reportlab)
09:55:20 Using cached pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.7 kB)
09:55:20 Collecting chardet (from reportlab)
09:55:20 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
09:55:20 Using cached reportlab-4.1.0-py3-none-any.whl (1.9 MB)
09:55:20 Using cached pillow-10.2.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB)
09:55:20 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
09:55:20 Installing collected packages: pillow, chardet, reportlab
09:55:21 Successfully installed chardet-5.2.0 pillow-10.2.0 reportlab-4.1.0
09:55:21 + pip install omego
09:55:22 Collecting omego
09:55:22 Using cached omego-0.7.0-py3-none-any.whl
09:55:22 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
09:55:22 Collecting yaclifw>=0.1.1 (from omego)
09:55:22 Using cached yaclifw-0.2.0-py3-none-any.whl
09:55:22 Collecting six (from yaclifw>=0.1.1->omego)
09:55:22 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
09:55:22 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
09:55:22 Installing collected packages: six, yaclifw, omego
09:55:23 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
09:55:23 + pip install tables
09:55:23 Collecting tables
09:55:23 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
09:55:24 Collecting numpy>=1.19.0 (from tables)
09:55:24 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
09:55:24 Collecting numexpr>=2.6.2 (from tables)
09:55:24 Using cached numexpr-2.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (7.9 kB)
09:55:24 Collecting packaging (from tables)
09:55:24 Using cached packaging-24.0-py3-none-any.whl.metadata (3.2 kB)
09:55:24 Collecting py-cpuinfo (from tables)
09:55:24 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
09:55:24 Collecting blosc2>=2.3.0 (from tables)
09:55:24 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
09:55:24 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
09:55:24 Using cached ndindex-1.8-py3-none-any.whl.metadata (3.4 kB)
09:55:24 Collecting msgpack (from blosc2>=2.3.0->tables)
09:55:24 Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
09:55:24 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
09:55:25 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
09:55:25 Using cached numexpr-2.9.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (374 kB)
09:55:25 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
09:55:25 Using cached packaging-24.0-py3-none-any.whl (53 kB)
09:55:25 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
09:55:25 Using cached ndindex-1.8-py3-none-any.whl (91 kB)
09:55:25 Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (385 kB)
09:55:25 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
09:55:28 Successfully installed blosc2-2.5.1 msgpack-1.0.8 ndindex-1.8 numexpr-2.9.0 numpy-1.26.4 packaging-24.0 py-cpuinfo-9.0.0 tables-3.9.2
09:55:28 + pip install jinja2
09:55:29 Collecting jinja2
09:55:29 Using cached Jinja2-3.1.3-py3-none-any.whl.metadata (3.3 kB)
09:55:29 Collecting MarkupSafe>=2.0 (from jinja2)
09:55:29 Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
09:55:29 Using cached Jinja2-3.1.3-py3-none-any.whl (133 kB)
09:55:29 Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
09:55:29 Installing collected packages: MarkupSafe, jinja2
09:55:29 Successfully installed MarkupSafe-2.1.5 jinja2-3.1.3
09:55:29 + pip install omero-py
09:55:30 Collecting omero-py
09:55:30 Using cached omero_py-5.19.0-py3-none-any.whl.metadata (6.6 kB)
09:55:30 Collecting urllib3<2 (from omero-py)
09:55:30 Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB)
09:55:30 Collecting appdirs (from omero-py)
09:55:30 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
09:55:30 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
09:55:30 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.26.4)
09:55:30 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (10.2.0)
09:55:30 Collecting PyYAML (from omero-py)
09:55:30 Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
09:55:30 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
09:55:30 Collecting requests (from omero-py)
09:55:30 Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
09:55:30 Collecting portalocker (from omero-py)
09:55:30 Using cached portalocker-2.8.2-py3-none-any.whl.metadata (8.5 kB)
09:55:31 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
09:55:31 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
09:55:31 Collecting idna<4,>=2.5 (from requests->omero-py)
09:55:31 Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)
09:55:31 Collecting certifi>=2017.4.17 (from requests->omero-py)
09:55:31 Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
09:55:31 Using cached omero_py-5.19.0-py3-none-any.whl (2.8 MB)
09:55:31 Using cached urllib3-1.26.18-py2.py3-none-any.whl (143 kB)
09:55:31 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
09:55:31 Using cached portalocker-2.8.2-py3-none-any.whl (17 kB)
09:55:31 Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
09:55:31 Using cached requests-2.31.0-py3-none-any.whl (62 kB)
09:55:31 Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)
09:55:31 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
09:55:31 Using cached idna-3.6-py3-none-any.whl (61 kB)
09:55:31 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, idna, charset-normalizer, certifi, requests, omero-py
09:55:33 Successfully installed PyYAML-6.0.1 appdirs-1.4.4 certifi-2024.2.2 charset-normalizer-3.3.2 idna-3.6 omero-py-5.19.0 portalocker-2.8.2 requests-2.31.0 urllib3-1.26.18
09:55:33 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
09:55:34 Collecting omero-metadata
09:55:34 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-kdxgmzze/omero-metadata_bcfe42bb3a2d40cb83c352463c998230
09:55:34 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-kdxgmzze/omero-metadata_bcfe42bb3a2d40cb83c352463c998230
09:55:35 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 1d3d76cb73401efbb04e5efafc7c7e04aa91a5bc
09:55:35 Installing build dependencies: started
09:55:37 Installing build dependencies: finished with status 'done'
09:55:37 Getting requirements to build wheel: started
09:55:37 Getting requirements to build wheel: finished with status 'done'
09:55:37 Installing backend dependencies: started
09:55:38 Installing backend dependencies: finished with status 'done'
09:55:38 Preparing metadata (pyproject.toml): started
09:55:38 Preparing metadata (pyproject.toml): finished with status 'done'
09:55:38 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.0)
09:55:38 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.1)
09:55:38 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.3)
09:55:38 Collecting pandas (from omero-metadata)
09:55:38 Using cached pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
09:55:38 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.18)
09:55:38 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
09:55:38 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
09:55:38 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
09:55:38 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (10.2.0)
09:55:38 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)
09:55:38 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.31.0)
09:55:38 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.8.2)
09:55:38 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (2.1.5)
09:55:39 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
09:55:39 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
09:55:39 Collecting pytz>=2020.1 (from pandas->omero-metadata)
09:55:39 Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
09:55:39 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
09:55:39 Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
09:55:39 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)
09:55:39 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.3.2)
09:55:39 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.6)
09:55:39 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2024.2.2)
09:55:39 Using cached pandas-2.2.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.0 MB)
09:55:39 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
09:55:39 Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
09:55:39 Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)
09:55:39 Building wheels for collected packages: omero-metadata
09:55:39 Building wheel for omero-metadata (pyproject.toml): started
09:55:39 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
09:55:39 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39111 sha256=8d18dedab40076eada8a4db5d38089efbec1708e9fd19b124e46f996f46ddd44
09:55:39 Stored in directory: /tmp/pip-ephem-wheel-cache-8wgtzshw/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
09:55:39 Successfully built omero-metadata
09:55:40 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
09:55:45 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.1 python-dateutil-2.9.0.post0 pytz-2024.1 tzdata-2024.1
09:55:45 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
09:55:45 Collecting omero-cli-render
09:55:45 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-ehlcdxzr/omero-cli-render_29211caecc1d4fe98911cfa7fd378123
09:55:45 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-ehlcdxzr/omero-cli-render_29211caecc1d4fe98911cfa7fd378123
09:55:46 Running command git checkout -b merge_ci --track origin/merge_ci
09:55:47 Switched to a new branch 'merge_ci'
09:55:47 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:55:47 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit c9d362b6f278aecfcdf112f038624c6b0dae202d
09:55:47 Installing build dependencies: started
09:55:48 Installing build dependencies: finished with status 'done'
09:55:48 Getting requirements to build wheel: started
09:55:49 Getting requirements to build wheel: finished with status 'done'
09:55:49 Installing backend dependencies: started
09:55:49 Installing backend dependencies: finished with status 'done'
09:55:49 Preparing metadata (pyproject.toml): started
09:55:50 Preparing metadata (pyproject.toml): finished with status 'done'
09:55:50 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.1)
09:55:50 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.0)
09:55:50 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (1.0.0)
09:55:50 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.18)
09:55:50 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
09:55:50 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
09:55:50 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (10.2.0)
09:55:50 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)
09:55:50 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.31.0)
09:55:50 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.8.2)
09:55:50 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.3.2)
09:55:50 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.6)
09:55:50 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2024.2.2)
09:55:50 Building wheels for collected packages: omero-cli-render
09:55:50 Building wheel for omero-cli-render (pyproject.toml): started
09:55:50 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
09:55:50 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.1.dev0-py3-none-any.whl size=18018 sha256=a96bf29ea233e7dd011ef726f4e781f27581460d7c3ea1f54b7a300f70a26bd9
09:55:50 Stored in directory: /tmp/pip-ephem-wheel-cache-7mtkwahf/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
09:55:50 Successfully built omero-cli-render
09:55:50 Installing collected packages: omero-cli-render
09:55:50 Successfully installed omero-cli-render-0.8.1.dev0
09:55:50 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
09:55:51 Collecting omero-cli-duplicate
09:55:51 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-_wj4c3s1/omero-cli-duplicate_07a15faf3e9f4d2db384bd07df5aa6cd
09:55:51 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-_wj4c3s1/omero-cli-duplicate_07a15faf3e9f4d2db384bd07df5aa6cd
09:55:52 Running command git checkout -b merge_ci --track origin/merge_ci
09:55:52 Switched to a new branch 'merge_ci'
09:55:52 branch 'merge_ci' set up to track 'origin/merge_ci'.
09:55:52 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 6a0c1d0cb6c23071709dfe245393cb37747601b9
09:55:52 Installing build dependencies: started
09:55:54 Installing build dependencies: finished with status 'done'
09:55:54 Getting requirements to build wheel: started
09:55:54 Getting requirements to build wheel: finished with status 'done'
09:55:54 Installing backend dependencies: started
09:55:55 Installing backend dependencies: finished with status 'done'
09:55:55 Preparing metadata (pyproject.toml): started
09:55:55 Preparing metadata (pyproject.toml): finished with status 'done'
09:55:55 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.0)
09:55:55 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.18)
09:55:55 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
09:55:55 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
09:55:55 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
09:55:55 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (10.2.0)
09:55:55 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.1)
09:55:55 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)
09:55:55 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.31.0)
09:55:55 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.8.2)
09:55:55 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.3.2)
09:55:55 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.6)
09:55:55 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2024.2.2)
09:55:55 Building wheels for collected packages: omero-cli-duplicate
09:55:55 Building wheel for omero-cli-duplicate (pyproject.toml): started
09:55:56 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
09:55:56 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11443 sha256=d817f7fddc6554e237bdaa1be5d5942308801cd08da5fc0be10ba3b709c98f9d
09:55:56 Stored in directory: /tmp/pip-ephem-wheel-cache-09z_uhf1/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
09:55:56 Successfully built omero-cli-duplicate
09:55:56 Installing collected packages: omero-cli-duplicate
09:55:56 Successfully installed omero-cli-duplicate-0.4.1.dev0
09:55:56 + pip install omero-certificates
09:55:57 Collecting omero-certificates
09:55:57 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
09:55:57 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.0)
09:55:57 Collecting distro==1.8.0 (from omero-certificates)
09:55:57 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
09:55:57 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.18)
09:55:57 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
09:55:57 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
09:55:57 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
09:55:57 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (10.2.0)
09:55:57 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.1)
09:55:57 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)
09:55:57 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.31.0)
09:55:57 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.8.2)
09:55:57 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.3.2)
09:55:57 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.6)
09:55:57 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2024.2.2)
09:55:57 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
09:55:57 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
09:55:57 Installing collected packages: distro, omero-certificates
09:55:59 Successfully installed distro-1.8.0 omero-certificates-0.3.2
09:55:59 + for x in *.tar.gz
09:55:59 + pip install -U omero-dropbox-5.6.3.dev0.tar.gz
09:55:59 Processing ./omero-dropbox-5.6.3.dev0.tar.gz
09:55:59 Installing build dependencies: started
09:56:01 Installing build dependencies: finished with status 'done'
09:56:01 Getting requirements to build wheel: started
09:56:01 Getting requirements to build wheel: finished with status 'done'
09:56:01 Installing backend dependencies: started
09:56:02 Installing backend dependencies: finished with status 'done'
09:56:02 Preparing metadata (pyproject.toml): started
09:56:02 Preparing metadata (pyproject.toml): finished with status 'done'
09:56:02 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.6.3.dev0) (5.19.0)
09:56:02 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.26.18)
09:56:02 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.4.4)
09:56:02 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.0.0)
09:56:02 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (1.26.4)
09:56:02 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (10.2.0)
09:56:02 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (6.0.1)
09:56:02 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (3.6.5)
09:56:02 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (2.31.0)
09:56:02 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.6.3.dev0) (2.8.2)
09:56:02 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.6.3.dev0) (3.3.2)
09:56:02 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.6.3.dev0) (3.6)
09:56:02 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.6.3.dev0) (2024.2.2)
09:56:02 Building wheels for collected packages: omero-dropbox
09:56:02 Building wheel for omero-dropbox (pyproject.toml): started
09:56:03 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
09:56:03 Created wheel for omero-dropbox: filename=omero_dropbox-5.6.3.dev0-py3-none-any.whl size=49057 sha256=dedaf73e2ab7ac89363c0679bd9df20c45cfa52eb4ee8ba6914d85da83833c07
09:56:03 Stored in directory: /home/omero/.cache/pip/wheels/a5/63/29/4452e52704e5ad491f397a0013b20ebb9d413ceb110f8101d1
09:56:03 Successfully built omero-dropbox
09:56:03 Installing collected packages: omero-dropbox
09:56:03 Successfully installed omero-dropbox-5.6.3.dev0
09:56:03 + for x in *.tar.gz
09:56:03 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
09:56:03 Processing ./omero_marshal-0.9.1.dev0.tar.gz
09:56:03 Installing build dependencies: started
09:56:05 Installing build dependencies: finished with status 'done'
09:56:05 Getting requirements to build wheel: started
09:56:05 Getting requirements to build wheel: finished with status 'done'
09:56:05 Installing backend dependencies: started
09:56:06 Installing backend dependencies: finished with status 'done'
09:56:06 Preparing metadata (pyproject.toml): started
09:56:07 Preparing metadata (pyproject.toml): finished with status 'done'
09:56:07 Building wheels for collected packages: omero_marshal
09:56:07 Building wheel for omero_marshal (pyproject.toml): started
09:56:07 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
09:56:07 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88031 sha256=f32729e76fac4ad686294db4491a961b280ed221ae670fce10c400e525ffcff0
09:56:07 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
09:56:07 Successfully built omero_marshal
09:56:07 Installing collected packages: omero_marshal
09:56:07 Successfully installed omero_marshal-0.9.1.dev0
09:56:07 + for x in *.tar.gz
09:56:07 + pip install -U omero-py-5.19.1.dev0.tar.gz
09:56:08 Processing ./omero-py-5.19.1.dev0.tar.gz
09:56:08 Installing build dependencies: started
09:56:10 Installing build dependencies: finished with status 'done'
09:56:10 Getting requirements to build wheel: started
09:56:10 Getting requirements to build wheel: finished with status 'done'
09:56:10 Installing backend dependencies: started
09:56:11 Installing backend dependencies: finished with status 'done'
09:56:11 Preparing metadata (pyproject.toml): started
09:56:11 Preparing metadata (pyproject.toml): finished with status 'done'
09:56:11 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.26.18)
09:56:11 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.4.4)
09:56:11 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.0.0)
09:56:11 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (1.26.4)
09:56:11 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (10.2.0)
09:56:11 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (6.0.1)
09:56:11 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (3.6.5)
09:56:11 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (2.31.0)
09:56:11 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.1.dev0) (2.8.2)
09:56:11 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.1.dev0) (3.3.2)
09:56:11 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.1.dev0) (3.6)
09:56:11 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.1.dev0) (2024.2.2)
09:56:11 Building wheels for collected packages: omero-py
09:56:11 Building wheel for omero-py (pyproject.toml): started
09:56:12 Building wheel for omero-py (pyproject.toml): finished with status 'done'
09:56:12 Created wheel for omero-py: filename=omero_py-5.19.1.dev0-py3-none-any.whl size=2781680 sha256=02a7dacf2d71826cd1cb21fcff114210d7c181cc5d2f1cbe19ab3b667cfd2d5c
09:56:12 Stored in directory: /home/omero/.cache/pip/wheels/52/ce/ea/f5d1427ab67c2783e3f124f0ebf8311109c5ac331893a591ad
09:56:12 Successfully built omero-py
09:56:13 Installing collected packages: omero-py
09:56:13 Attempting uninstall: omero-py
09:56:13 Found existing installation: omero-py 5.19.0
09:56:13 Uninstalling omero-py-5.19.0:
09:56:13 Successfully uninstalled omero-py-5.19.0
09:56:15 Successfully installed omero-py-5.19.1.dev0
09:56:15 + for x in *.tar.gz
09:56:15 + pip install -U omero-scripts-5.8.1.dev0.tar.gz
09:56:16 Processing ./omero-scripts-5.8.1.dev0.tar.gz
09:56:16 Installing build dependencies: started
09:56:17 Installing build dependencies: finished with status 'done'
09:56:17 Getting requirements to build wheel: started
09:56:18 Getting requirements to build wheel: finished with status 'done'
09:56:18 Installing backend dependencies: started
09:56:18 Installing backend dependencies: finished with status 'done'
09:56:18 Preparing metadata (pyproject.toml): started
09:56:19 Preparing metadata (pyproject.toml): finished with status 'done'
09:56:19 Building wheels for collected packages: omero-scripts
09:56:19 Building wheel for omero-scripts (pyproject.toml): started
09:56:19 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
09:56:19 Created wheel for omero-scripts: filename=omero_scripts-5.8.1.dev0-py3-none-any.whl size=116570 sha256=b1ee712731c43e1644feaf37e06959c42a3eee97909a3976b101185919818f90
09:56:19 Stored in directory: /home/omero/.cache/pip/wheels/ef/a0/80/e3393129cedc64a3ad2b8c2fa437d83a3d318cba65d425f5cf
09:56:19 Successfully built omero-scripts
09:56:19 Installing collected packages: omero-scripts
09:56:19 Successfully installed omero-scripts-5.8.1.dev0
09:56:19 + for x in *.tar.gz
09:56:19 + pip install -U omero-web-5.25.1.dev0.tar.gz
09:56:20 Processing ./omero-web-5.25.1.dev0.tar.gz
09:56:20 Installing build dependencies: started
09:56:22 Installing build dependencies: finished with status 'done'
09:56:22 Getting requirements to build wheel: started
09:56:22 Getting requirements to build wheel: finished with status 'done'
09:56:22 Installing backend dependencies: started
09:56:23 Installing backend dependencies: finished with status 'done'
09:56:23 Preparing metadata (pyproject.toml): started
09:56:24 Preparing metadata (pyproject.toml): finished with status 'done'
09:56:24 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (5.19.1.dev0)
09:56:24 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.25.1.dev0)
09:56:24 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
09:56:24 Collecting Django<4.3,>=4.2.3 (from omero-web==5.25.1.dev0)
09:56:24 Using cached Django-4.2.11-py3-none-any.whl.metadata (4.2 kB)
09:56:24 Collecting django-pipeline==2.1.0 (from omero-web==5.25.1.dev0)
09:56:24 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
09:56:24 Collecting django-cors-headers==3.7.0 (from omero-web==5.25.1.dev0)
09:56:24 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
09:56:24 Collecting django-csp (from omero-web==5.25.1.dev0)
09:56:24 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
09:56:24 Collecting whitenoise>=5.3.0 (from omero-web==5.25.1.dev0)
09:56:24 Using cached whitenoise-6.6.0-py3-none-any.whl.metadata (3.7 kB)
09:56:24 Collecting gunicorn>=19.3 (from omero-web==5.25.1.dev0)
09:56:24 Using cached gunicorn-21.2.0-py3-none-any.whl.metadata (4.1 kB)
09:56:24 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (0.9.1.dev0)
09:56:24 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (10.2.0)
09:56:24 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (2024.1)
09:56:24 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (2.8.2)
09:56:24 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.25.1.dev0) (24.0)
09:56:24 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
09:56:24 Using cached asgiref-3.8.0-py3-none-any.whl.metadata (9.3 kB)
09:56:24 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
09:56:24 Using cached sqlparse-0.4.4-py3-none-any.whl.metadata (4.0 kB)
09:56:24 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.26.18)
09:56:24 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.4.4)
09:56:24 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.0.0)
09:56:24 Requirement already satisfied: numpy in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (1.26.4)
09:56:24 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (6.0.1)
09:56:24 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==5.25.1.dev0) (3.6.5)
09:56:24 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.25.1.dev0) (2.31.0)
09:56:25 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.25.1.dev0)
09:56:25 Using cached typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB)
09:56:25 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.25.1.dev0) (3.3.2)
09:56:25 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.25.1.dev0) (3.6)
09:56:25 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.25.1.dev0) (2024.2.2)
09:56:25 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
09:56:25 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
09:56:25 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
09:56:25 Using cached Django-4.2.11-py3-none-any.whl (8.0 MB)
09:56:25 Using cached gunicorn-21.2.0-py3-none-any.whl (80 kB)
09:56:25 Using cached whitenoise-6.6.0-py3-none-any.whl (19 kB)
09:56:25 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
09:56:25 Using cached asgiref-3.8.0-py3-none-any.whl (23 kB)
09:56:25 Using cached sqlparse-0.4.4-py3-none-any.whl (41 kB)
09:56:25 Using cached typing_extensions-4.10.0-py3-none-any.whl (33 kB)
09:56:25 Building wheels for collected packages: omero-web
09:56:25 Building wheel for omero-web (pyproject.toml): started
09:56:26 Building wheel for omero-web (pyproject.toml): finished with status 'done'
09:56:26 Created wheel for omero-web: filename=omero_web-5.25.1.dev0-py3-none-any.whl size=2769903 sha256=614de995a62c388c294a82ec938898b90ea46c3275c3f2f201590c1c3b0e149a
09:56:26 Stored in directory: /home/omero/.cache/pip/wheels/c5/4f/aa/011f4ecfdcda915571d213b068a736fbddf1b36b2e590de11a
09:56:26 Successfully built omero-web
09:56:26 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
09:56:29 Successfully installed Django-4.2.11 asgiref-3.8.0 concurrent-log-handler-0.9.25 django-cors-headers-3.7.0 django-csp-3.8 django-pipeline-2.1.0 gunicorn-21.2.0 omero-web-5.25.1.dev0 sqlparse-0.4.4 typing-extensions-4.10.0 whitenoise-6.6.0
09:56:29 + omero config set omero.db.name OMERO-server
09:56:31 + omero config set omero.db.host pg
09:56:32 + omero config set omero.db.user postgres
09:56:34 + omero config set omero.data.dir /home/omero/omero-server-data
09:56:35 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
09:56:36 + omero config set omero.db.poolsize 25
09:56:38 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
09:56:39 + omero config set omero.security.trustStorePassword changeit
09:56:41 + omero config set omero.mail.config true
09:56:42 + omero config set omero.mail.from qa@openmicroscopy.org.uk
09:56:43 + omero config set omero.mail.host smtp.dundee.ac.uk
09:56:45 + omero certificates
09:56:46 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
09:56:46 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
09:56:46 + '[' false = true ']'
09:56:46 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
09:56:46 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
09:56:46 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
09:56:47 2024-03-21 09:56:47,021 [ omego.db] DEBUG dbcommand => upgrade
09:56:47 2024-03-21 09:56:47,021 [ omego.db] DEBUG dbhost => localhost
09:56:47 2024-03-21 09:56:47,021 [ omego.db] DEBUG dbname => OMERO-server
09:56:47 2024-03-21 09:56:47,022 [ omego.db] DEBUG dbpass => omero
09:56:47 2024-03-21 09:56:47,022 [ omego.db] DEBUG dbuser => omero
09:56:47 2024-03-21 09:56:47,022 [ omego.db] DEBUG rootpass => omero
09:56:47 2024-03-21 09:56:47,022 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
09:56:47 2024-03-21 09:56:47,022 [omego.extern] INFO Executing : omero version
09:56:48 OMERO.py version:
09:56:48 OMERO.server version:
09:56:48 5.6.3-437-854b934e23-ice36
09:56:48 5.19.1.dev0
09:56:48 2024-03-21 09:56:48,595 [omego.extern] INFO Completed [1.573 s]
09:56:48 2024-03-21 09:56:48,595 [omego.extern] DEBUG Using omero CLI from omero
09:56:48 2024-03-21 09:56:48,595 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
09:56:48 2024-03-21 09:56:48,596 [omego.extern] INFO Running [current environment]: omero config get --show-password
09:56:48 2024-03-21 09:56:48,596 [omego.extern] INFO Executing : omero config get --show-password
09:56:49 2024-03-21 09:56:49,981 [omego.extern] INFO Completed [1.385 s]
09:56:49 2024-03-21 09:56:49,981 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
09:56:49 2024-03-21 09:56:49,981 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
09:56:50 2024-03-21 09:56:50,079 [omego.extern] INFO Completed [0.098 s]
09:56:50 2024-03-21 09:56:50,080 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.2\n'
09:56:50 2024-03-21 09:56:50,080 [ omego.db] INFO psql version: psql (PostgreSQL) 16.2
09:56:50
09:56:50 2024-03-21 09:56:50,080 [omego.extern] INFO Running [current environment]: omero config get --show-password
09:56:50 2024-03-21 09:56:50,080 [omego.extern] INFO Executing : omero config get --show-password
09:56:51 2024-03-21 09:56:51,501 [omego.extern] INFO Completed [1.421 s]
09:56:51 2024-03-21 09:56:51,502 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
09:56:51 2024-03-21 09:56:51,502 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
09:56:51 2024-03-21 09:56:51,772 [omego.extern] INFO Completed [0.270 s]
09:56:51 2024-03-21 09:56:51,772 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.29.0.4") at port "5432".\n'
09:56:51 2024-03-21 09:56:51,772 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
09:56:51 2024-03-21 09:56:51,772 [omego.extern] INFO Running [current environment]: omero config get --show-password
09:56:51 2024-03-21 09:56:51,772 [omego.extern] INFO Executing : omero config get --show-password
09:56:53 2024-03-21 09:56:53,199 [omego.extern] INFO Completed [1.426 s]
09:56:53 2024-03-21 09:56:53,199 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
09:56:53 2024-03-21 09:56:53,199 [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
09:56:54 2024-03-21 09:56:54,271 [omego.extern] INFO Completed [1.071 s]
09:56:54 2024-03-21 09:56:54,271 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
09:56:54 2024-03-21 09:56:54,271 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
09:56:54 2024-03-21 09:56:54,273 [ omego.db] INFO Database is already at OMERO5.4__0
09:56:54 + export LANG=en_US.UTF-8
09:56:54 + LANG=en_US.UTF-8
09:56:54 + export LANGUAGE=en_US:en
09:56:54 + LANGUAGE=en_US:en
09:56:54 + export LC_ALL=en_US.UTF-8
09:56:54 + LC_ALL=en_US.UTF-8
09:56:54 + BUILD_ID=DONT_KILL_ME
09:56:54 + omero admin start
09:57:07 WARNING: lock files in /home/omero/omero-server-data
09:57:07 ----------------------------------------
09:57:07 /home/omero/omero-server-data/.omero/repository/7097ab62-1c9f-4ba2-a5e5-d5b1f868081e/.lock
09:57:07 ----------------------------------------
09:57:07
09:57:07 You may want to stop all server processes and remove
09:57:07 these files manually. Lock files can remain after an
09:57:07 abrupt server outage and are especially frequent on
09:57:07 remotely mounted filesystems like NFS.
09:57:07
09:57:07 No descriptor given. Using etc/grid/default.xml
09:57:17 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
09:57:17 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
09:57:17 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
09:57:17 Waiting on startup. Use CTRL-C to exit
09:57:17 + omero admin waitup
09:57:18 Waiting on startup. Use CTRL-C to exit
09:57:18 + omero admin diagnostics
09:57:20
09:57:20 ================================================================================
09:57:20 OMERO Diagnostics (admin)
09:57:20 ================================================================================
09:57:20
09:57:20 Commands: java -version 11.0.22 (/usr/bin/java)
09:57:20 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
09:57:20 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
09:57:20 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
09:57:20 Commands: psql --version 16.2 (/usr/bin/psql)
09:57:20 Commands: openssl version 3.0.71 (/usr/bin/openssl)
09:57:20
09:57:20 Component: OMERO.py 5.19.1.dev0
09:57:20 Component: OMERO.server 5.6.3-437-854b934e23-ice36
09:57:20
09:57:20 Server: icegridnode running
09:57:20 Server: Blitz-0 active (pid = 2379, enabled)
09:57:20 Server: DropBox activating (enabled)
09:57:20 Server: FileServer active (pid = 2409, enabled)
09:57:20 Server: Indexer-0 activating (enabled)
09:57:20 Server: MonitorServer active (pid = 2413, enabled)
09:57:20 Server: OMERO.Glacier2 active (pid = 2423, enabled)
09:57:20 Server: OMERO.IceStorm active (pid = 2438, enabled)
09:57:20 Server: PixelData-0 activating (enabled)
09:57:20 Server: Processor-0 active (pid = 2456, enabled)
09:57:20 Server: Tables-0 activating (enabled)
09:57:20 Server: TestDropBox inactive (enabled)
09:57:20
09:57:20 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
09:57:20 Log files: Blitz-0.log 33.1 KB errors=0 warnings=1
09:57:20 Log files: DropBox.log 1.2 KB
09:57:20 Log files: FileServer.log 114 B
09:57:20 Log files: Indexer-0.log 598 B
09:57:20 Log files: MonitorServer.log 1.1 KB
09:57:20 Log files: PixelData-0.log 599 B
09:57:20 Log files: Processor-0.log 735 B
09:57:20 Log files: Tables-0.log 856 B
09:57:20 Log files: TestDropBox.log n/a
09:57:20 Log files: master.err 2.1 KB
09:57:20 Log files: master.out 41.5 KB
09:57:20 Log files: Total size 0.08 MB
09:57:20
09:57:20
09:57:20 Environment:OMERO_HOME=(unset)
09:57:20 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:57:20 Environment:OMERO_NODE=(unset)
09:57:20 Environment:OMERO_MASTER=(unset)
09:57:20 Environment:OMERO_USERDIR=(unset)
09:57:20 Environment:OMERO_TMPDIR=(unset)
09:57:20 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
09:57:20 Environment:PYTHONPATH=(unset)
09:57:20 Environment:ICE_HOME=/opt/ice-3.6.5
09:57:20 Environment:LD_LIBRARY_PATH=(unset)
09:57:20 Environment:DYLD_LIBRARY_PATH=(unset)
09:57:20
09:57:20 OMERO SSL port:4064
09:57:20 OMERO TCP port:4063
09:57:20 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
09:57:20 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
09:57:20
09:57:20 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:57:20 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:57:20 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:57:20 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:57:20
09:57:20 Jar: lib/server/formats-api.jar Bio-Formats API 8.0.0-SNAPSHOT 21 March 2024 5c6c3e1ca3aac5f8e55dd5c5693604d128be5965
09:57:20 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.0.0-SNAPSHOT 21 March 2024 5c6c3e1ca3aac5f8e55dd5c5693604d128be5965
09:57:20 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.0.0-SNAPSHOT 21 March 2024 5c6c3e1ca3aac5f8e55dd5c5693604d128be5965
09:57:20 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.1 8 December 2023 4f6bf7551ed2d1dfe8e74c857f6a694da40d1d97
09:57:20 Jar: lib/server/ome-common.jar OME Common Java 6.0.21 7 December 2023 fdace3279d4f6b682c5ba47ae4c49daac687459b
09:57:20 Jar: lib/server/ome-jai.jar OME JAI 0.1.3 3 August 2018 489959cb7d24c279249bc08181aa9f734158ca4e
09:57:20 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.2 7 August 2018 68ffca2a95750cbb96f0d11785851aa4a554c0a4
09:57:20 Jar: lib/server/ome-poi.jar OME POI 5.3.7 5 July 2022 79a44040fa896a7c78b4e25da6ba7f4dda204c8e
09:57:20 Jar: lib/server/ome-xml.jar OME XML library 6.3.4 7 December 2023 b4c6f4490d762138453225e0499346a6334f00e5
09:57:20 Jar: lib/server/omero-blitz.jar jar 5.7.3-SNAPSHOT
09:57:20 Jar: lib/server/omero-common.jar jar 5.6.5-SNAPSHOT
09:57:20 Jar: lib/server/omero-gateway.jar jar 5.9.1-SNAPSHOT
09:57:20 Jar: lib/server/omero-model.jar jar 5.6.14-SNAPSHOT
09:57:20 Jar: lib/server/omero-renderer.jar jar 5.5.16-SNAPSHOT
09:57:20 Jar: lib/server/omero-romio.jar jar 5.7.6-SNAPSHOT
09:57:20 Jar: lib/server/omero-server.jar jar 5.6.11-SNAPSHOT
09:57:21 + deactivate
09:57:21 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:57:21 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:57:21 + export PATH
09:57:21 + unset _OLD_VIRTUAL_PATH
09:57:21 + '[' -n '' ']'
09:57:21 + '[' -n /bin/bash -o -n '' ']'
09:57:21 + hash -r
09:57:21 + '[' -n '' ']'
09:57:21 + unset VIRTUAL_ENV
09:57:21 + '[' '!' '' = nondestructive ']'
09:57:21 + unset -f deactivate
09:57:21 Finished: SUCCESS
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