Console Output

09:03:52 Started by user devspace
09:03:52 Running as SYSTEM
09:03:53 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
09:03:53 [OMERO-server] $ /bin/bash -xe /tmp/jenkins7206315961402759188.sh
09:03:53 + source /home/settings.env
09:03:53 ++ OMERO_DB_HOST=pg
09:03:53 ++ OMERO_DB_USER=postgres
09:03:53 ++ OMERO_DB_PASS=
09:03:53 ++ OMERO_ROOT_PASS=omero
09:03:53 ++ OMERO_DATA_DIR=/OMERO
09:03:53 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:03:53 + OMERO_DB_NAME=OMERO-server
09:03:53 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:03:53 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:03:53 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:03:53 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:03:53 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
09:03:53 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:03:53 ++ deactivate nondestructive
09:03:53 ++ '[' -n '' ']'
09:03:53 ++ '[' -n '' ']'
09:03:53 ++ '[' -n /bin/bash -o -n '' ']'
09:03:53 ++ hash -r
09:03:53 ++ '[' -n '' ']'
09:03:53 ++ unset VIRTUAL_ENV
09:03:53 ++ '[' '!' nondestructive = nondestructive ']'
09:03:53 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:03:53 ++ export VIRTUAL_ENV
09:03:53 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:03:53 ++ 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
09:03:53 ++ export PATH
09:03:53 ++ '[' -n '' ']'
09:03:53 ++ '[' -z '' ']'
09:03:53 ++ _OLD_VIRTUAL_PS1=
09:03:53 ++ PS1='(.venv3) '
09:03:53 ++ export PS1
09:03:53 ++ '[' -n /bin/bash -o -n '' ']'
09:03:53 ++ hash -r
09:03:53 + omero admin stop
09:04:28 Server not running
09:04:29 + echo not running
09:04:29 not running
09:04:29 + sleep 5
09:04:34 + deactivate
09:04:34 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:04:34 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:04:34 + export PATH
09:04:34 + unset _OLD_VIRTUAL_PATH
09:04:34 + '[' -n '' ']'
09:04:34 + '[' -n /bin/bash -o -n '' ']'
09:04:34 + hash -r
09:04:34 + '[' -n '' ']'
09:04:34 + unset VIRTUAL_ENV
09:04:34 + '[' '!' '' = nondestructive ']'
09:04:34 + unset -f deactivate
09:04:34 + rm -rf /home/omero/workspace/OMERO-server/.venv3
09:04:34 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
09:04:38 + '[' false = true ']'
09:04:38 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
09:04:38 Skipping PURGE_DATA:CleanDbAndRepo
09:04:38 + 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-5.19.5.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-5.27.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
09:04:41 Copied 1 artifact from "OMERO-build" build number 145
09:04:41 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 143
09:04:41 Copied 2 artifacts from "OMERO-build-build" build number 149
09:04:41 [OMERO-server] $ /bin/bash -xe /tmp/jenkins3107835690787049738.sh
09:04:41 + source /home/settings.env
09:04:41 ++ OMERO_DB_HOST=pg
09:04:41 ++ OMERO_DB_USER=postgres
09:04:41 ++ OMERO_DB_PASS=
09:04:41 ++ OMERO_ROOT_PASS=omero
09:04:41 ++ OMERO_DATA_DIR=/OMERO
09:04:41 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
09:04:41 + OMERO_DB_NAME=OMERO-server
09:04:41 + OMERO_DATA_DIR=/home/omero/omero-server-data
09:04:41 + mkdir -p /home/omero/omero-server-data
09:04:41 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
09:04:41 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:04:41 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
09:04:41 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:04:41 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
09:04:41 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:04:41 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
09:04:41 ++ ls OMERO.server-5.6.3-496-880fc321e6-ice36.zip
09:04:41 + ZIP=OMERO.server-5.6.3-496-880fc321e6-ice36.zip
09:04:41 + '[' '!' -z '' ']'
09:04:41 + DIST=OMERO.server-5.6.3-496-880fc321e6-ice36
09:04:41 + unzip OMERO.server-5.6.3-496-880fc321e6-ice36.zip
09:04:41 Archive:  OMERO.server-5.6.3-496-880fc321e6-ice36.zip
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/blitz/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/grid/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/profiles/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/error/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/grid/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/luts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/luts/janelia/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/luts/ncsa_paledit/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/luts/wcif/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/analysis_scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/annotation_scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/export_scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/figure_scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/import_scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/scripts/omero/util_scripts/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/server/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/share/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/share/licenses/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/misc/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__1/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__10/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__11/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__2/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__3/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__4/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__5/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__6/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__7/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__8/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3A__9/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3__4/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3__5/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3__6/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO3__7/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO4.1__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO4.2__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO4.2__0/t/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO4.3__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO4.4__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO4__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.0__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.1__1/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.2__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.3__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.4DEV__1/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.4DEV__2/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.4DEV__3/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/sql/psql/OMERO5.4__0/
09:04:41    creating: OMERO.server-5.6.3-496-880fc321e6-ice36/var/
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/LICENSE.txt  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/backup.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/blitz/mail-senders.example  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/blitz/mail-server.example  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/build.properties  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/env.bat  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/env.sh  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/hibernate.properties  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/ice.config  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/logback-cli.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/logback-indexing-cli.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/logback-indexing.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/logback.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/mime.types  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/node1.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/node2.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/omero.properties  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/profiles/psql  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/rollover.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/Windows.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/error/maintainance.html  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/grid/README  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/grid/default.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/grid/templates.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/grid/windefault.xml  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/ice.config  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/internal.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/master.cfg  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/templates/robot.template  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/etc/testdropbox.config  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/history.rst  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/OMEZarrReader.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/activation.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/aggdesigner-algorithm.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/aircompressor.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/annotations.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/antlr.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/aopalliance.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/avatica-core.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/avatica-metrics.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/aws-java-sdk-core.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/aws-java-sdk-kms.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/aws-java-sdk-s3.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/base.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-all.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-anim.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-awt-util.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-bridge.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-codec.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-constants.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-css.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-dom.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-ext.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-extension.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-gui-util.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-gvt.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-i18n.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-parser.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-rasterizer-ext.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-rasterizer.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-script.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-slideshow.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-squiggle-ext.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-squiggle.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-svg-dom.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-svgbrowser.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-svggen.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-svgpp.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-svgrasterizer.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-swing.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-transcoder.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-ttf2svg.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-util.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/batik-xml.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/btm.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/bufr.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/c3p0.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/calcite-core.jar  
09:04:41   inflating: OMERO.server-5.6.3-496-880fc321e6-ice36/lib/client/calcite-linq4j.jar  
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09:04:43 + rm -f OMERO.server-5.6.3-496-880fc321e6-ice36.zip
09:04:44 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-496-880fc321e6-ice36 /home/omero/workspace/OMERO-server/OMERO.server
09:04:44 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
09:04:44 ++ deactivate nondestructive
09:04:44 ++ '[' -n '' ']'
09:04:44 ++ '[' -n '' ']'
09:04:44 ++ '[' -n /bin/bash -o -n '' ']'
09:04:44 ++ hash -r
09:04:44 ++ '[' -n '' ']'
09:04:44 ++ unset VIRTUAL_ENV
09:04:44 ++ '[' '!' nondestructive = nondestructive ']'
09:04:44 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
09:04:44 ++ export VIRTUAL_ENV
09:04:44 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:04:44 ++ 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
09:04:44 ++ export PATH
09:04:44 ++ '[' -n '' ']'
09:04:44 ++ '[' -z '' ']'
09:04:44 ++ _OLD_VIRTUAL_PS1=
09:04:44 ++ PS1='(.venv3) '
09:04:44 ++ export PS1
09:04:44 ++ '[' -n /bin/bash -o -n '' ']'
09:04:44 ++ hash -r
09:04:44 + 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
09:04:44 Collecting zeroc-ice==3.6.5
09:04:45   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)
09:04:46 Installing collected packages: zeroc-ice
09:04:47 Successfully installed zeroc-ice-3.6.5
09:04:47 + pip install -U pip future
09:04:47 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
09:04:47 Collecting pip
09:04:48   Using cached pip-24.2-py3-none-any.whl (1.8 MB)
09:04:48 Collecting future
09:04:48   Using cached future-1.0.0-py3-none-any.whl (491 kB)
09:04:48 Installing collected packages: pip, future
09:04:48   Attempting uninstall: pip
09:04:48     Found existing installation: pip 21.2.3
09:04:48     Uninstalling pip-21.2.3:
09:04:48       Successfully uninstalled pip-21.2.3
09:04:49 Successfully installed future-1.0.0 pip-24.2
09:04:49 + pip install markdown
09:04:50 Collecting markdown
09:04:50   Using cached Markdown-3.6-py3-none-any.whl.metadata (7.0 kB)
09:04:50 Collecting importlib-metadata>=4.4 (from markdown)
09:04:50   Using cached importlib_metadata-8.2.0-py3-none-any.whl.metadata (4.7 kB)
09:04:50 Collecting zipp>=0.5 (from importlib-metadata>=4.4->markdown)
09:04:50   Using cached zipp-3.20.0-py3-none-any.whl.metadata (3.6 kB)
09:04:50 Using cached Markdown-3.6-py3-none-any.whl (105 kB)
09:04:50 Using cached importlib_metadata-8.2.0-py3-none-any.whl (25 kB)
09:04:50 Using cached zipp-3.20.0-py3-none-any.whl (9.4 kB)
09:04:50 Installing collected packages: zipp, importlib-metadata, markdown
09:04:50 Successfully installed importlib-metadata-8.2.0 markdown-3.6 zipp-3.20.0
09:04:50 + pip install reportlab
09:04:51 Collecting reportlab
09:04:51   Using cached reportlab-4.2.2-py3-none-any.whl.metadata (1.4 kB)
09:04:52 Collecting pillow>=9.0.0 (from reportlab)
09:04:52   Using cached pillow-10.4.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.2 kB)
09:04:52 Collecting chardet (from reportlab)
09:04:52   Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
09:04:52 Using cached reportlab-4.2.2-py3-none-any.whl (1.9 MB)
09:04:52 Using cached pillow-10.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB)
09:04:52 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
09:04:52 Installing collected packages: pillow, chardet, reportlab
09:04:53 Successfully installed chardet-5.2.0 pillow-10.4.0 reportlab-4.2.2
09:04:53 + pip install omego
09:04:54 Collecting omego
09:04:54   Using cached omego-0.7.0-py3-none-any.whl
09:04:54 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
09:04:54 Collecting yaclifw>=0.1.1 (from omego)
09:04:54   Using cached yaclifw-0.2.0-py3-none-any.whl
09:04:54 Collecting six (from yaclifw>=0.1.1->omego)
09:04:54   Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
09:04:54 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
09:04:54 Installing collected packages: six, yaclifw, omego
09:04:55 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
09:04:55 + pip install tables
09:04:55 Collecting tables
09:04:55   Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
09:04:55 Collecting numpy>=1.19.0 (from tables)
09:04:55   Using cached numpy-2.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
09:04:56 Collecting numexpr>=2.6.2 (from tables)
09:04:56   Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.2 kB)
09:04:56 Collecting packaging (from tables)
09:04:56   Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
09:04:56 Collecting py-cpuinfo (from tables)
09:04:56   Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
09:04:56 Collecting blosc2>=2.3.0 (from tables)
09:04:56   Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
09:04:56 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
09:04:56   Using cached ndindex-1.8-py3-none-any.whl.metadata (3.4 kB)
09:04:56 Collecting msgpack (from blosc2>=2.3.0->tables)
09:04:56   Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.1 kB)
09:04:56 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
09:04:57 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
09:04:57 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (404 kB)
09:04:57 Using cached numpy-2.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
09:04:57 Using cached packaging-24.1-py3-none-any.whl (53 kB)
09:04:57 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
09:04:57 Using cached ndindex-1.8-py3-none-any.whl (91 kB)
09:04:57 Using cached msgpack-1.0.8-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (385 kB)
09:04:58 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
09:05:01 Successfully installed blosc2-2.5.1 msgpack-1.0.8 ndindex-1.8 numexpr-2.10.1 numpy-2.0.1 packaging-24.1 py-cpuinfo-9.0.0 tables-3.9.2
09:05:01 + pip install jinja2
09:05:01 Collecting jinja2
09:05:01   Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
09:05:01 Collecting MarkupSafe>=2.0 (from jinja2)
09:05:01   Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
09:05:01 Using cached jinja2-3.1.4-py3-none-any.whl (133 kB)
09:05:02 Using cached MarkupSafe-2.1.5-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (25 kB)
09:05:02 Installing collected packages: MarkupSafe, jinja2
09:05:02 Successfully installed MarkupSafe-2.1.5 jinja2-3.1.4
09:05:02 + pip install omero-py
09:05:02 Collecting omero-py
09:05:02   Using cached omero_py-5.19.4-py3-none-any.whl.metadata (6.3 kB)
09:05:03 Collecting urllib3<2 (from omero-py)
09:05:03   Using cached urllib3-1.26.19-py2.py3-none-any.whl.metadata (49 kB)
09:05:03 Collecting appdirs (from omero-py)
09:05:03   Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
09:05:03 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
09:05:03 Collecting numpy<2 (from omero-py)
09:05:03   Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
09:05:03 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (10.4.0)
09:05:03 Collecting PyYAML (from omero-py)
09:05:03   Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
09:05:03 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
09:05:04 Collecting requests (from omero-py)
09:05:04   Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
09:05:04 Collecting portalocker (from omero-py)
09:05:04   Using cached portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB)
09:05:04 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
09:05:04   Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
09:05:04 Collecting idna<4,>=2.5 (from requests->omero-py)
09:05:04   Using cached idna-3.7-py3-none-any.whl.metadata (9.9 kB)
09:05:04 Collecting certifi>=2017.4.17 (from requests->omero-py)
09:05:04   Using cached certifi-2024.7.4-py3-none-any.whl.metadata (2.2 kB)
09:05:04 Using cached omero_py-5.19.4-py3-none-any.whl (2.8 MB)
09:05:04 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
09:05:04 Using cached urllib3-1.26.19-py2.py3-none-any.whl (143 kB)
09:05:04 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
09:05:04 Using cached portalocker-2.10.1-py3-none-any.whl (18 kB)
09:05:04 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
09:05:05 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
09:05:05 Using cached certifi-2024.7.4-py3-none-any.whl (162 kB)
09:05:05 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
09:05:05 Using cached idna-3.7-py3-none-any.whl (66 kB)
09:05:05 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, numpy, idna, charset-normalizer, certifi, requests, omero-py
09:05:05   Attempting uninstall: numpy
09:05:05     Found existing installation: numpy 2.0.1
09:05:05     Uninstalling numpy-2.0.1:
09:05:05       Successfully uninstalled numpy-2.0.1
09:05:10 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 certifi-2024.7.4 charset-normalizer-3.3.2 idna-3.7 numpy-1.26.4 omero-py-5.19.4 portalocker-2.10.1 requests-2.32.3 urllib3-1.26.19
09:05:10 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
09:05:11 Collecting omero-metadata
09:05:11   Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-al5bqah_/omero-metadata_875145aab3fa4188a7ba0366a41981ff
09:05:11   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-al5bqah_/omero-metadata_875145aab3fa4188a7ba0366a41981ff
09:05:15   Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 574f225ed6efcd30d693c3923636dcbd21c73dd0
09:05:15   Installing build dependencies: started
09:05:17   Installing build dependencies: finished with status 'done'
09:05:17   Getting requirements to build wheel: started
09:05:17   Getting requirements to build wheel: finished with status 'done'
09:05:17   Preparing metadata (pyproject.toml): started
09:05:17   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:17 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.4)
09:05:17 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.2)
09:05:17 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.4)
09:05:17 Collecting pandas (from omero-metadata)
09:05:17   Using cached pandas-2.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (19 kB)
09:05:18 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.19)
09:05:18 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
09:05:18 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
09:05:18 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
09:05:18 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (10.4.0)
09:05:18 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)
09:05:18 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
09:05:18 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.10.1)
09:05:18 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (2.1.5)
09:05:18 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
09:05:18   Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
09:05:18 Collecting pytz>=2020.1 (from pandas->omero-metadata)
09:05:18   Using cached pytz-2024.1-py2.py3-none-any.whl.metadata (22 kB)
09:05:18 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
09:05:18   Using cached tzdata-2024.1-py2.py3-none-any.whl.metadata (1.4 kB)
09:05:18 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)
09:05:18 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)
09:05:18 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.7)
09:05:18 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2024.7.4)
09:05:18 Using cached pandas-2.2.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
09:05:18 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
09:05:18 Using cached pytz-2024.1-py2.py3-none-any.whl (505 kB)
09:05:18 Using cached tzdata-2024.1-py2.py3-none-any.whl (345 kB)
09:05:18 Building wheels for collected packages: omero-metadata
09:05:18   Building wheel for omero-metadata (pyproject.toml): started
09:05:19   Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
09:05:19   Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39111 sha256=3d3cc4556e137b12fd704bc7c2819e9ad2b4dc1ba7f969d1e1d21cbf60c7c578
09:05:19   Stored in directory: /tmp/pip-ephem-wheel-cache-rm9qnt_0/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
09:05:19 Successfully built omero-metadata
09:05:19 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
09:05:23 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.2 python-dateutil-2.9.0.post0 pytz-2024.1 tzdata-2024.1
09:05:24 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
09:05:24 Collecting omero-cli-render
09:05:24   Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-2rggz8pt/omero-cli-render_887108807f1f40af8a92741a935c6cd7
09:05:24   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-2rggz8pt/omero-cli-render_887108807f1f40af8a92741a935c6cd7
09:05:25   Running command git checkout -b merge_ci --track origin/merge_ci
09:05:25   Switched to a new branch 'merge_ci'
09:05:25   branch 'merge_ci' set up to track 'origin/merge_ci'.
09:05:25   Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit ff2de1c231af1fe1b1fbabbc1e2af103390042c3
09:05:25   Installing build dependencies: started
09:05:27   Installing build dependencies: finished with status 'done'
09:05:27   Getting requirements to build wheel: started
09:05:27   Getting requirements to build wheel: finished with status 'done'
09:05:27   Preparing metadata (pyproject.toml): started
09:05:27   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:27 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.2)
09:05:27 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.4)
09:05:27 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.19)
09:05:27 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
09:05:27 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
09:05:27 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
09:05:27 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (10.4.0)
09:05:27 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)
09:05:27 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
09:05:27 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.10.1)
09:05:27 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)
09:05:27 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.7)
09:05:27 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2024.7.4)
09:05:27 Building wheels for collected packages: omero-cli-render
09:05:27   Building wheel for omero-cli-render (pyproject.toml): started
09:05:27   Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
09:05:27   Created wheel for omero-cli-render: filename=omero_cli_render-0.8.1.dev0-py3-none-any.whl size=18032 sha256=46f6c6e2b45933f51447cc75ad9695cb5b4117b154284976f6eb8b327d8d1a16
09:05:27   Stored in directory: /tmp/pip-ephem-wheel-cache-mnrnqaj4/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
09:05:27 Successfully built omero-cli-render
09:05:28 Installing collected packages: omero-cli-render
09:05:28 Successfully installed omero-cli-render-0.8.1.dev0
09:05:28 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
09:05:28 Collecting omero-cli-duplicate
09:05:28   Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-okniykri/omero-cli-duplicate_58f6bbdbc5414d1ab8d8553982dcaa31
09:05:28   Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-okniykri/omero-cli-duplicate_58f6bbdbc5414d1ab8d8553982dcaa31
09:05:29   Running command git checkout -b merge_ci --track origin/merge_ci
09:05:29   Switched to a new branch 'merge_ci'
09:05:29   branch 'merge_ci' set up to track 'origin/merge_ci'.
09:05:29   Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit efb9f3e0f96e9550c1f652f17f517a8bc245cbc8
09:05:29   Installing build dependencies: started
09:05:31   Installing build dependencies: finished with status 'done'
09:05:31   Getting requirements to build wheel: started
09:05:31   Getting requirements to build wheel: finished with status 'done'
09:05:31   Preparing metadata (pyproject.toml): started
09:05:31   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:31 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.4)
09:05:31 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.19)
09:05:31 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
09:05:31 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
09:05:31 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
09:05:31 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (10.4.0)
09:05:31 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
09:05:31 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)
09:05:31 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
09:05:31 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.10.1)
09:05:31 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)
09:05:31 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.7)
09:05:31 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2024.7.4)
09:05:31 Building wheels for collected packages: omero-cli-duplicate
09:05:31   Building wheel for omero-cli-duplicate (pyproject.toml): started
09:05:31   Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
09:05:31   Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11444 sha256=f60d274b28c975f3bb2288fac12361d56ff0e3b71647fd5df82a3d42d2dafae9
09:05:31   Stored in directory: /tmp/pip-ephem-wheel-cache-zsd8c2gs/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
09:05:31 Successfully built omero-cli-duplicate
09:05:32 Installing collected packages: omero-cli-duplicate
09:05:32 Successfully installed omero-cli-duplicate-0.4.1.dev0
09:05:32 + pip install omero-certificates
09:05:32 Collecting omero-certificates
09:05:32   Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
09:05:32 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.4)
09:05:32 Collecting distro==1.8.0 (from omero-certificates)
09:05:32   Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
09:05:32 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.19)
09:05:32 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
09:05:32 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
09:05:32 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
09:05:32 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (10.4.0)
09:05:32 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
09:05:32 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)
09:05:32 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
09:05:32 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.10.1)
09:05:32 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)
09:05:32 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.7)
09:05:32 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2024.7.4)
09:05:32 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
09:05:32 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
09:05:32 Installing collected packages: distro, omero-certificates
09:05:32 Successfully installed distro-1.8.0 omero-certificates-0.3.2
09:05:32 + for x in *.tar.gz
09:05:32 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
09:05:33 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
09:05:33   Installing build dependencies: started
09:05:35   Installing build dependencies: finished with status 'done'
09:05:35   Getting requirements to build wheel: started
09:05:35   Getting requirements to build wheel: finished with status 'done'
09:05:35   Preparing metadata (pyproject.toml): started
09:05:35   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:35 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.7.1.dev0) (5.19.4)
09:05:35 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.19)
09:05:35 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
09:05:35 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
09:05:35 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.4)
09:05:35 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (10.4.0)
09:05:35 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
09:05:35 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)
09:05:35 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3)
09:05:35 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.10.1)
09:05:35 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.3.2)
09:05:35 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.7)
09:05:35 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2024.7.4)
09:05:35 Building wheels for collected packages: omero-dropbox
09:05:35   Building wheel for omero-dropbox (pyproject.toml): started
09:05:35   Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
09:05:35   Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49056 sha256=14d5d64fcfa5feef717c8f9ef18b8f0edecce7d318efc284a8f63dc87c0e2a79
09:05:35   Stored in directory: /home/omero/.cache/pip/wheels/eb/76/85/58476368b176f793423899407c96293c22f9c9edc28cf54079
09:05:35 Successfully built omero-dropbox
09:05:35 Installing collected packages: omero-dropbox
09:05:35 Successfully installed omero-dropbox-5.7.1.dev0
09:05:35 + for x in *.tar.gz
09:05:35 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
09:05:36 Processing ./omero_marshal-0.9.1.dev0.tar.gz
09:05:36   Installing build dependencies: started
09:05:38   Installing build dependencies: finished with status 'done'
09:05:38   Getting requirements to build wheel: started
09:05:38   Getting requirements to build wheel: finished with status 'done'
09:05:38   Preparing metadata (pyproject.toml): started
09:05:38   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:38 Building wheels for collected packages: omero_marshal
09:05:38   Building wheel for omero_marshal (pyproject.toml): started
09:05:39   Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
09:05:39   Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88029 sha256=0bb9626484b358f15f091461545eed993cc3358e4b5b9d3aad7e10fff1fe43ba
09:05:39   Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
09:05:39 Successfully built omero_marshal
09:05:39 Installing collected packages: omero_marshal
09:05:39 Successfully installed omero_marshal-0.9.1.dev0
09:05:39 + for x in *.tar.gz
09:05:39 + pip install -U omero_py-5.19.5.dev0.tar.gz
09:05:39 Processing ./omero_py-5.19.5.dev0.tar.gz
09:05:40   Installing build dependencies: started
09:05:42   Installing build dependencies: finished with status 'done'
09:05:42   Getting requirements to build wheel: started
09:05:42   Getting requirements to build wheel: finished with status 'done'
09:05:42   Preparing metadata (pyproject.toml): started
09:05:42   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:42 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (1.26.19)
09:05:42 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (1.4.4)
09:05:42 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (1.0.0)
09:05:42 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (1.26.4)
09:05:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (10.4.0)
09:05:42 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (6.0.2)
09:05:42 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (3.6.5)
09:05:42 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (2.32.3)
09:05:42 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.5.dev0) (2.10.1)
09:05:42 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.5.dev0) (3.3.2)
09:05:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.5.dev0) (3.7)
09:05:42 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.5.dev0) (2024.7.4)
09:05:42 Building wheels for collected packages: omero-py
09:05:42   Building wheel for omero-py (pyproject.toml): started
09:05:43   Building wheel for omero-py (pyproject.toml): finished with status 'done'
09:05:43   Created wheel for omero-py: filename=omero_py-5.19.5.dev0-py3-none-any.whl size=2782856 sha256=7a203e9fb07b52ff9b4fbb24e17ac38bda1d235b5613e86f9448b622f8d0a7b7
09:05:43   Stored in directory: /home/omero/.cache/pip/wheels/f8/22/3c/b4269ea2035cdd4c3f15d9990f88c807cd4a53e7b729c42a16
09:05:43 Successfully built omero-py
09:05:43 Installing collected packages: omero-py
09:05:43   Attempting uninstall: omero-py
09:05:43     Found existing installation: omero-py 5.19.4
09:05:44     Uninstalling omero-py-5.19.4:
09:05:44       Successfully uninstalled omero-py-5.19.4
09:05:46 Successfully installed omero-py-5.19.5.dev0
09:05:46 + for x in *.tar.gz
09:05:46 + pip install -U omero_scripts-5.8.4.dev0.tar.gz
09:05:46 Processing ./omero_scripts-5.8.4.dev0.tar.gz
09:05:46   Installing build dependencies: started
09:05:48   Installing build dependencies: finished with status 'done'
09:05:48   Getting requirements to build wheel: started
09:05:48   Getting requirements to build wheel: finished with status 'done'
09:05:48   Preparing metadata (pyproject.toml): started
09:05:48   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:48 Building wheels for collected packages: omero-scripts
09:05:48   Building wheel for omero-scripts (pyproject.toml): started
09:05:49   Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
09:05:49   Created wheel for omero-scripts: filename=omero_scripts-5.8.4.dev0-py3-none-any.whl size=116560 sha256=af42b9a8c722b9afa9f0220d8a853b8d2e67050261818cf3fdd0860d322e5f05
09:05:49   Stored in directory: /home/omero/.cache/pip/wheels/50/80/aa/1e175e4f2a5b0a5343d01937a727d990d08c8e12000390ad9c
09:05:49 Successfully built omero-scripts
09:05:49 Installing collected packages: omero-scripts
09:05:49 Successfully installed omero-scripts-5.8.4.dev0
09:05:49 + for x in *.tar.gz
09:05:49 + pip install -U omero_web-5.27.1.dev0.tar.gz
09:05:49 Processing ./omero_web-5.27.1.dev0.tar.gz
09:05:50   Installing build dependencies: started
09:05:52   Installing build dependencies: finished with status 'done'
09:05:52   Getting requirements to build wheel: started
09:05:52   Getting requirements to build wheel: finished with status 'done'
09:05:52   Preparing metadata (pyproject.toml): started
09:05:52   Preparing metadata (pyproject.toml): finished with status 'done'
09:05:52 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.1.dev0) (5.19.5.dev0)
09:05:52 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.27.1.dev0)
09:05:52   Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
09:05:53 Collecting Django<4.3,>=4.2.3 (from omero-web==5.27.1.dev0)
09:05:53   Using cached Django-4.2.15-py3-none-any.whl.metadata (4.1 kB)
09:05:53 Collecting django-pipeline==2.1.0 (from omero-web==5.27.1.dev0)
09:05:53   Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
09:05:53 Collecting django-cors-headers==3.7.0 (from omero-web==5.27.1.dev0)
09:05:53   Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
09:05:53 Collecting django-csp (from omero-web==5.27.1.dev0)
09:05:53   Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
09:05:53 Collecting whitenoise>=5.3.0 (from omero-web==5.27.1.dev0)
09:05:53   Using cached whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB)
09:05:53 Collecting gunicorn>=19.3 (from omero-web==5.27.1.dev0)
09:05:53   Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
09:05:53 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.1.dev0) (0.9.1.dev0)
09:05:53 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.1.dev0) (10.4.0)
09:05:53 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.1.dev0) (2024.1)
09:05:53 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.1.dev0) (2.10.1)
09:05:53 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.1.dev0) (24.1)
09:05:53 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.27.1.dev0)
09:05:53   Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
09:05:53 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.27.1.dev0)
09:05:53   Using cached sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB)
09:05:53 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.1.dev0) (1.26.19)
09:05:53 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.1.dev0) (1.4.4)
09:05:53 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.1.dev0) (1.0.0)
09:05:53 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.1.dev0) (1.26.4)
09:05:53 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.1.dev0) (6.0.2)
09:05:53 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==5.27.1.dev0) (3.6.5)
09:05:53 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.1.dev0) (2.32.3)
09:05:53 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.27.1.dev0)
09:05:53   Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
09:05:54 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.1.dev0) (3.3.2)
09:05:54 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.1.dev0) (3.7)
09:05:54 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.1.dev0) (2024.7.4)
09:05:54 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
09:05:54 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
09:05:54 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
09:05:54 Using cached Django-4.2.15-py3-none-any.whl (8.0 MB)
09:05:54 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
09:05:54 Using cached whitenoise-6.7.0-py3-none-any.whl (19 kB)
09:05:54 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
09:05:54 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
09:05:54 Using cached sqlparse-0.5.1-py3-none-any.whl (44 kB)
09:05:54 Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
09:05:54 Building wheels for collected packages: omero-web
09:05:54   Building wheel for omero-web (pyproject.toml): started
09:05:55   Building wheel for omero-web (pyproject.toml): finished with status 'done'
09:05:55   Created wheel for omero-web: filename=omero_web-5.27.1.dev0-py3-none-any.whl size=2766522 sha256=ecfdeb48fe761f2fdc43998afeeaed2b7e8ca6160a40a644ebbb3f801e093712
09:05:55   Stored in directory: /home/omero/.cache/pip/wheels/95/a2/6f/d45832b3b9dfb05411e1514f5c4953422c04f1662dacdfe59a
09:05:55 Successfully built omero-web
09:05:55 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
09:05:58 Successfully installed Django-4.2.15 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-5.27.1.dev0 sqlparse-0.5.1 typing-extensions-4.12.2 whitenoise-6.7.0
09:05:58 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
09:05:59 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
09:05:59 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
09:05:59 --2024-08-13 09:05:59--  https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
09:06:00 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.108.133, ...
09:06:00 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
09:06:00 HTTP request sent, awaiting response... 200 OK
09:06:00 Length: 95703 (93K) [text/plain]
09:06:00 Saving to: ‘Figure_To_Pdf.py’
09:06:00 
09:06:00      0K .......... .......... .......... .......... .......... 53% 2.31M 0s
09:06:00     50K .......... .......... .......... .......... ...       100% 23.1M=0.02s
09:06:00 
09:06:00 2024-08-13 09:06:00 (3.97 MB/s) - ‘Figure_To_Pdf.py’ saved [95703/95703]
09:06:00 
09:06:00 + chmod 755 Figure_To_Pdf.py
09:06:00 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
09:06:00 + omero config set omero.db.name OMERO-server
09:06:02 + omero config set omero.db.host pg
09:06:03 + omero config set omero.db.user postgres
09:06:04 + omero config set omero.data.dir /home/omero/omero-server-data
09:06:05 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
09:06:07 + omero config set omero.db.poolsize 25
09:06:08 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
09:06:09 + omero config set omero.security.trustStorePassword changeit
09:06:11 + omero config set omero.mail.config true
09:06:12 + omero config set omero.mail.from qa@openmicroscopy.org.uk
09:06:13 + omero config set omero.mail.host smtp.dundee.ac.uk
09:06:15 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
09:06:16 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
09:06:17 + omero certificates
09:06:19 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
09:06:19 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
09:06:19 + '[' false = true ']'
09:06:19 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
09:06:19 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
09:06:19 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
09:06:19 2024-08-13 09:06:19,680 [    omego.db] DEBUG            dbcommand => upgrade
09:06:19 2024-08-13 09:06:19,681 [    omego.db] DEBUG               dbhost => localhost
09:06:19 2024-08-13 09:06:19,681 [    omego.db] DEBUG               dbname => OMERO-server
09:06:19 2024-08-13 09:06:19,681 [    omego.db] DEBUG               dbpass => omero
09:06:19 2024-08-13 09:06:19,681 [    omego.db] DEBUG               dbuser => omero
09:06:19 2024-08-13 09:06:19,681 [    omego.db] DEBUG             rootpass => omero
09:06:19 2024-08-13 09:06:19,681 [    omego.db] DEBUG            serverdir => /home/omero/workspace/OMERO-server/OMERO.server
09:06:19 2024-08-13 09:06:19,681 [omego.extern] INFO  Executing : omero version
09:06:20 OMERO.py version:
09:06:20 OMERO.server version:
09:06:20 5.6.3-496-880fc321e6-ice36
09:06:20 5.19.5.dev0
09:06:21 2024-08-13 09:06:21,136 [omego.extern] INFO  Completed [1.455 s]
09:06:21 2024-08-13 09:06:21,136 [omego.extern] DEBUG Using omero CLI from omero
09:06:21 2024-08-13 09:06:21,136 [    omego.db] INFO  DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
09:06:21 2024-08-13 09:06:21,136 [omego.extern] INFO  Running [current environment]: omero config get --show-password
09:06:21 2024-08-13 09:06:21,136 [omego.extern] INFO  Executing : omero config get --show-password
09:06:22 2024-08-13 09:06:22,477 [omego.extern] INFO  Completed [1.341 s]
09:06:22 2024-08-13 09:06:22,478 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
09:06:22 2024-08-13 09:06:22,478 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
09:06:23 2024-08-13 09:06:23,017 [omego.extern] INFO  Completed [0.539 s]
09:06:23 2024-08-13 09:06:23,018 [    omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.2\n'
09:06:23 2024-08-13 09:06:23,018 [    omego.db] INFO  psql version: psql (PostgreSQL) 16.2
09:06:23 
09:06:23 2024-08-13 09:06:23,018 [omego.extern] INFO  Running [current environment]: omero config get --show-password
09:06:23 2024-08-13 09:06:23,018 [omego.extern] INFO  Executing : omero config get --show-password
09:06:24 2024-08-13 09:06:24,305 [omego.extern] INFO  Completed [1.287 s]
09:06:24 2024-08-13 09:06:24,305 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
09:06:24 2024-08-13 09:06:24,305 [omego.extern] INFO  Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
09:06:24 2024-08-13 09:06:24,633 [omego.extern] INFO  Completed [0.328 s]
09:06:24 2024-08-13 09:06:24,633 [    omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.19.0.6") at port "5432".\n'
09:06:24 2024-08-13 09:06:24,634 [    omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
09:06:24 2024-08-13 09:06:24,634 [omego.extern] INFO  Running [current environment]: omero config get --show-password
09:06:24 2024-08-13 09:06:24,634 [omego.extern] INFO  Executing : omero config get --show-password
09:06:25 2024-08-13 09:06:25,973 [omego.extern] INFO  Completed [1.339 s]
09:06:25 2024-08-13 09:06:25,973 [    omego.db] INFO  Failed to lookup parameter omero.db.pass, using omero
09:06:25 2024-08-13 09:06:25,973 [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
09:06:27 2024-08-13 09:06:27,005 [omego.extern] INFO  Completed [1.031 s]
09:06:27 2024-08-13 09:06:27,005 [    omego.db] DEBUG stdout: b'OMERO5.4|0\n'
09:06:27 2024-08-13 09:06:27,005 [    omego.db] INFO  Current omero db version: ('OMERO5.4', '0')
09:06:27 2024-08-13 09:06:27,007 [    omego.db] INFO  Database is already at OMERO5.4__0
09:06:27 + export LANG=en_US.UTF-8
09:06:27 + LANG=en_US.UTF-8
09:06:27 + export LANGUAGE=en_US:en
09:06:27 + LANGUAGE=en_US:en
09:06:27 + export LC_ALL=en_US.UTF-8
09:06:27 + LC_ALL=en_US.UTF-8
09:06:27 + BUILD_ID=DONT_KILL_ME
09:06:27 + omero admin start
09:06:37 No descriptor given. Using etc/grid/default.xml
09:06:47 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
09:06:47 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
09:06:47 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
09:06:47 Waiting on startup. Use CTRL-C to exit
09:06:47 + omero admin waitup
09:06:48 Waiting on startup. Use CTRL-C to exit
09:06:49 + omero admin diagnostics
09:06:50 
09:06:50 ================================================================================
09:06:50 OMERO Diagnostics (admin)
09:06:50 ================================================================================
09:06:50         
09:06:50 Commands:   java -version                  11.0.22   (/usr/bin/java)
09:06:50 Commands:   python -V                      3.9.18    (/home/omero/workspace/OMERO-server/.venv3/bin/python)
09:06:50 Commands:   icegridnode --version          3.6.5     (/opt/ice-3.6.5/bin/icegridnode)
09:06:50 Commands:   icegridadmin --version         3.6.5     (/opt/ice-3.6.5/bin/icegridadmin)
09:06:50 Commands:   psql --version                 16.2      (/usr/bin/psql)
09:06:50 Commands:   openssl version                3.0.71    (/usr/bin/openssl)
09:06:50 
09:06:50 Component:  OMERO.py                       5.19.5.dev0
09:06:50 Component:  OMERO.server                   5.6.3-496-880fc321e6-ice36
09:06:50 
09:06:50 Server:     icegridnode                    running
09:06:50 Server:     Blitz-0                        active (pid = 2612, enabled)
09:06:50 Server:     Indexer-0                      activating (enabled)
09:06:50 Server:     OMERO.Glacier2                 active (pid = 2639, enabled)
09:06:50 Server:     OMERO.IceStorm                 active (pid = 2661, enabled)
09:06:50 Server:     Processor-0                    activating (enabled)
09:06:50 Server:     Tables-0                       activating (enabled)
09:06:50 
09:06:50 Log dir:    /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
09:06:50 Log files:  Blitz-0.log                    12.8 KB       errors=0    warnings=1   
09:06:50 Log files:  DropBox.log                    n/a
09:06:50 Log files:  FileServer.log                 n/a
09:06:50 Log files:  Indexer-0.log                  598 B        
09:06:50 Log files:  MonitorServer.log              n/a
09:06:50 Log files:  Processor-0.log                281 B        
09:06:50 Log files:  Tables-0.log                   281 B        
09:06:50 Log files:  TestDropBox.log                n/a
09:06:50 Log files:  master.err                     180 B        
09:06:50 Log files:  master.out                     30.1 KB      
09:06:50 Log files:  Total size                     0.04 MB
09:06:50 
09:06:50 
09:06:50 Environment:OMERO_HOME=(unset)             
09:06:50 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 
09:06:50 Environment:OMERO_NODE=(unset)             
09:06:50 Environment:OMERO_MASTER=(unset)           
09:06:50 Environment:OMERO_USERDIR=(unset)          
09:06:50 Environment:OMERO_TMPDIR=(unset)           
09:06:50 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 
09:06:50 Environment:PYTHONPATH=(unset)             
09:06:50 Environment:ICE_HOME=/opt/ice-3.6.5        
09:06:50 Environment:LD_LIBRARY_PATH=(unset)        
09:06:50 Environment:DYLD_LIBRARY_PATH=(unset)      
09:06:50 
09:06:50 OMERO SSL port:4064                           
09:06:50 OMERO TCP port:4063                           
09:06:50 OMERO data dir:'/home/omero/omero-server-data' Exists? True	Is writable? True
09:06:50 OMERO temp dir:'/home/omero/omero/tmp'        Exists? True	Is writable? True   (Size: 0)
09:06:50 
09:06:50 JVM settings: Blitz-${index}                -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:06:50 JVM settings: Indexer-${index}              -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:06:50 JVM settings: PixelData-${index}            -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:06:50 JVM settings: Repository-${index}           -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
09:06:50 
09:06:50 Jar:        lib/server/formats-api.jar     Bio-Formats API	8.0.0-SNAPSHOT	13 August 2024	78145b4748cd1309eaaa39fb1e5cdbcb9a6d3f8b
09:06:50 Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers	8.0.0-SNAPSHOT	13 August 2024	78145b4748cd1309eaaa39fb1e5cdbcb9a6d3f8b
09:06:50 Jar:        lib/server/formats-gpl.jar     Bio-Formats library	8.0.0-SNAPSHOT	13 August 2024	78145b4748cd1309eaaa39fb1e5cdbcb9a6d3f8b
09:06:50 Jar:        lib/server/ome-codecs.jar      OME Codecs	1.0.4-SNAPSHOT	13 August 2024	ac9181f68e71cfc72aea7e86f5cbba3951807ca9
09:06:50 Jar:        lib/server/ome-common.jar      OME Common Java	6.0.23-SNAPSHOT	13 August 2024	ac9181f68e71cfc72aea7e86f5cbba3951807ca9
09:06:50 Jar:        lib/server/ome-jai.jar         OME JAI	0.1.5-SNAPSHOT	13 August 2024	ac9181f68e71cfc72aea7e86f5cbba3951807ca9
09:06:50 Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)	5.3.4-SNAPSHOT	13 August 2024	ac9181f68e71cfc72aea7e86f5cbba3951807ca9
09:06:50 Jar:        lib/server/ome-poi.jar         OME POI	5.3.10-SNAPSHOT	13 August 2024	ac9181f68e71cfc72aea7e86f5cbba3951807ca9
09:06:50 Jar:        lib/server/ome-xml.jar         OME XML library	6.3.7-SNAPSHOT	13 August 2024	ac9181f68e71cfc72aea7e86f5cbba3951807ca9
09:06:50 Jar:        lib/server/omero-blitz.jar     jar	5.7.5-SNAPSHOT		
09:06:50 Jar:        lib/server/omero-common.jar    jar	5.6.8-SNAPSHOT		
09:06:50 Jar:        lib/server/omero-gateway.jar   jar	5.9.3-SNAPSHOT		
09:06:50 Jar:        lib/server/omero-model.jar     jar	5.6.16-SNAPSHOT		
09:06:50 Jar:        lib/server/omero-renderer.jar  jar	5.5.18-SNAPSHOT		
09:06:50 Jar:        lib/server/omero-romio.jar     jar	5.7.8-SNAPSHOT		
09:06:50 Jar:        lib/server/omero-server.jar    jar	5.6.13-SNAPSHOT		
09:06:50 + deactivate
09:06:50 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
09:06:50 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
09:06:50 + export PATH
09:06:50 + unset _OLD_VIRTUAL_PATH
09:06:50 + '[' -n '' ']'
09:06:50 + '[' -n /bin/bash -o -n '' ']'
09:06:50 + hash -r
09:06:50 + '[' -n '' ']'
09:06:50 + unset VIRTUAL_ENV
09:06:50 + '[' '!' '' = nondestructive ']'
09:06:50 + unset -f deactivate
09:06:51 Finished: SUCCESS