08:08:16 Started by upstream project "Trigger" build number 241
08:08:16 originally caused by:
08:08:16 Started by user devspace
08:08:16 Running as SYSTEM
08:08:16 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
08:08:17 [OMERO-server] $ /bin/bash -xe /tmp/jenkins6910945793671464829.sh
08:08:17 + source /home/settings.env
08:08:17 ++ OMERO_DB_HOST=pg
08:08:17 ++ OMERO_DB_USER=postgres
08:08:17 ++ OMERO_DB_PASS=
08:08:17 ++ OMERO_ROOT_PASS=omero
08:08:17 ++ OMERO_DATA_DIR=/OMERO
08:08:17 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
08:08:17 + OMERO_DB_NAME=OMERO-server
08:08:17 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
08:08:17 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:08:17 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:08:17 + OMERO_DATA_DIR=/home/omero/omero-server-data
08:08:17 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
08:08:17 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
08:08:17 ++ deactivate nondestructive
08:08:17 ++ '[' -n '' ']'
08:08:17 ++ '[' -n '' ']'
08:08:17 ++ '[' -n /bin/bash -o -n '' ']'
08:08:17 ++ hash -r
08:08:17 ++ '[' -n '' ']'
08:08:17 ++ unset VIRTUAL_ENV
08:08:17 ++ '[' '!' nondestructive = nondestructive ']'
08:08:17 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
08:08:17 ++ export VIRTUAL_ENV
08:08:17 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:08:17 ++ 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
08:08:17 ++ export PATH
08:08:17 ++ '[' -n '' ']'
08:08:17 ++ '[' -z '' ']'
08:08:17 ++ _OLD_VIRTUAL_PS1=
08:08:17 ++ PS1='(.venv3) '
08:08:17 ++ export PS1
08:08:17 ++ '[' -n /bin/bash -o -n '' ']'
08:08:17 ++ hash -r
08:08:17 + omero admin stop
08:08:33 Server not running
08:08:34 + echo not running
08:08:34 not running
08:08:34 + sleep 5
08:08:39 + deactivate
08:08:39 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
08:08:39 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:08:39 + export PATH
08:08:39 + unset _OLD_VIRTUAL_PATH
08:08:39 + '[' -n '' ']'
08:08:39 + '[' -n /bin/bash -o -n '' ']'
08:08:39 + hash -r
08:08:39 + '[' -n '' ']'
08:08:39 + unset VIRTUAL_ENV
08:08:39 + '[' '!' '' = nondestructive ']'
08:08:39 + unset -f deactivate
08:08:39 + rm -rf /home/omero/workspace/OMERO-server/.venv3
08:08:39 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
08:08:43 + '[' false = true ']'
08:08:43 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
08:08:43 Skipping PURGE_DATA:CleanDbAndRepo
08:08:43 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.7.5-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.19.6.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.8.4.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.27.3.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
08:08:46 Copied 1 artifact from "OMERO-build" build number 198
08:08:46 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 195
08:08:46 Copied 2 artifacts from "OMERO-build-build" build number 206
08:08:46 [OMERO-server] $ /bin/bash -xe /tmp/jenkins8562868093482179587.sh
08:08:46 + source /home/settings.env
08:08:46 ++ OMERO_DB_HOST=pg
08:08:46 ++ OMERO_DB_USER=postgres
08:08:46 ++ OMERO_DB_PASS=
08:08:46 ++ OMERO_ROOT_PASS=omero
08:08:46 ++ OMERO_DATA_DIR=/OMERO
08:08:46 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
08:08:46 + OMERO_DB_NAME=OMERO-server
08:08:46 + OMERO_DATA_DIR=/home/omero/omero-server-data
08:08:46 + mkdir -p /home/omero/omero-server-data
08:08:46 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
08:08:46 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:08:46 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:08:46 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
08:08:46 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
08:08:46 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
08:08:46 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
08:08:46 ++ ls OMERO.server-5.6.3-513-77dcd6034a-ice36.zip
08:08:46 + ZIP=OMERO.server-5.6.3-513-77dcd6034a-ice36.zip
08:08:46 + '[' '!' -z '' ']'
08:08:46 + DIST=OMERO.server-5.6.3-513-77dcd6034a-ice36
08:08:46 + unzip OMERO.server-5.6.3-513-77dcd6034a-ice36.zip
08:08:46 Archive: OMERO.server-5.6.3-513-77dcd6034a-ice36.zip
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/blitz/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/grid/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/profiles/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/error/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/grid/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/luts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/luts/janelia/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/luts/ncsa_paledit/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/luts/wcif/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/analysis_scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/annotation_scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/export_scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/figure_scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/import_scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/scripts/omero/util_scripts/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/misc/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__1/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__10/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__11/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__2/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__3/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__4/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__5/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__6/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__7/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__8/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__9/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__4/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__5/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__6/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__7/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.1__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.2__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.2__0/t/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.3__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.4__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.0__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.1__1/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.2__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4DEV__1/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4DEV__2/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4DEV__3/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/
08:08:46 creating: OMERO.server-5.6.3-513-77dcd6034a-ice36/var/
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/LICENSE.txt
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/backup.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/blitz/mail-senders.example
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/blitz/mail-server.example
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/build.properties
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/env.bat
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/env.sh
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/hibernate.properties
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/ice.config
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/logback-cli.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/logback-indexing-cli.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/logback-indexing.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/logback.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/mime.types
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/node1.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/node2.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/omero.properties
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/profiles/psql
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/rollover.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/Windows.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/error/maintainance.html
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/grid/README
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/grid/default.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/grid/templates.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/grid/windefault.xml
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/ice.config
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/internal.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/master.cfg
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/templates/robot.template
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/etc/testdropbox.config
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/history.rst
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/OMEZarrReader.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/activation.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/aggdesigner-algorithm.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/aircompressor.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/annotations.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/antlr.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/aopalliance.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/avatica-core.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/avatica-metrics.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/aws-java-sdk-core.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/aws-java-sdk-kms.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/aws-java-sdk-s3.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/base.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-all.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-anim.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-awt-util.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-bridge.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-codec.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-constants.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-css.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-dom.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-ext.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-extension.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-gui-util.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-gvt.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-i18n.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-parser.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-rasterizer-ext.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-rasterizer.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-script.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-slideshow.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-squiggle-ext.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-squiggle.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-svg-dom.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-svgbrowser.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-svggen.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-svgpp.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-svgrasterizer.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-swing.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-transcoder.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-ttf2svg.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-util.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/batik-xml.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/btm.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/bufr.jar
08:08:46 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/c3p0.jar
08:08:47 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/calcite-core.jar
08:08:47 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/calcite-linq4j.jar
08:08:47 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/cdm-core.jar
08:08:47 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/client/checker-qual.jar
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08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/ome-jai.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/ome-mdbtools.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/ome-poi.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/ome-xml.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-blitz.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-common.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-gateway.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-model.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-renderer.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-romio.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/omero-server.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/pdfbox.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/perf4j.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/postgresql.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/protobuf-java.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/quartz.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/re2j.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/reflectasm.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/rhino.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/serializer.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/sketches-core.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/slf4j-api.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/snakeyaml.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/solr-analysis-extras.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/solr-commons-csv.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/solr-core.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/solr-solrj.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/specification.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-aop.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-beans.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-context-support.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-context.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-core.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-expression.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-jdbc.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-jms.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-ldap-core.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-messaging.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-orm.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-security-core.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-security-ldap.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/spring-tx.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/sqlite-jdbc.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/subethasmtp.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/turbojpeg.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/udunits.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xalan.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xercesImpl.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xml-apis-ext.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xml-apis.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xmlgraphics-commons.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xmpcore.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/lib/server/xpp3.jar
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/README
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/agpl.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/antlr.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/apache-v1.1.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/apache-v2.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/asm.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/bouncy_castle_license.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/bsd.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/cddl-v1.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/cpl-v10.html
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/crystalclear.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/django.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/dom4j.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/epl-v1.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/fbsd.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/freemarker.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/gpl-v2.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/gpl.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/gtest.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/iconsweets_license.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/jamon.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/jmock.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/jquery.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/jtidy.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/lgpl-3.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/lgpl-v2.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/lgpl-v2.1.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/lgpl-v3.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/lgpl.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/matplotlib.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/mit.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/mpl-v1_0.htm
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/npl-1_1.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/path.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/pil.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/postgresql.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/psf-v2.0.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/psf-v2.5.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/scons.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/slf4j.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/tablelayout.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/which.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/zlib-libpng.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/share/licenses/zpl-v2.1.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/README.txt
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/misc/Makefile
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/misc/current.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/misc/enums.py
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__1/OMERO3__7.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__10/OMERO3A__9.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__11/OMERO3A__10.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__11/OMERO3A__5.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__2/OMERO3A__1.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__3/OMERO3A__2.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__3/OMERO3__5.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__4/OMERO3A__3.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__4/OMERO3__5.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__5/OMERO3A__4.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__6/OMERO3A__5.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__7/OMERO3A__6.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__8/OMERO3A__6.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3A__9/OMERO3A__8.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__4/OMERO3__1.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__5/OMERO3__4.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__6/OMERO3__5.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO3__7/OMERO3__6.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.1__0/OMERO4__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.2__0/OMERO4.1__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO4__0/OMERO3A__11.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/psql-footer.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/psql-header.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/schema.sql
08:08:49 inflating: OMERO.server-5.6.3-513-77dcd6034a-ice36/sql/psql/OMERO5.4__0/views.sql
08:08:49 + rm -f OMERO.server-5.6.3-513-77dcd6034a-ice36.zip
08:08:49 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-513-77dcd6034a-ice36 /home/omero/workspace/OMERO-server/OMERO.server
08:08:49 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
08:08:49 ++ deactivate nondestructive
08:08:49 ++ '[' -n '' ']'
08:08:49 ++ '[' -n '' ']'
08:08:49 ++ '[' -n /bin/bash -o -n '' ']'
08:08:49 ++ hash -r
08:08:49 ++ '[' -n '' ']'
08:08:49 ++ unset VIRTUAL_ENV
08:08:49 ++ '[' '!' nondestructive = nondestructive ']'
08:08:49 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
08:08:49 ++ export VIRTUAL_ENV
08:08:49 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:08:49 ++ 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
08:08:49 ++ export PATH
08:08:49 ++ '[' -n '' ']'
08:08:49 ++ '[' -z '' ']'
08:08:49 ++ _OLD_VIRTUAL_PS1=
08:08:49 ++ PS1='(.venv3) '
08:08:49 ++ export PS1
08:08:49 ++ '[' -n /bin/bash -o -n '' ']'
08:08:49 ++ hash -r
08:08:49 + 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
08:08:49 Collecting zeroc-ice==3.6.5
08:08:50 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)
08:08:52 Installing collected packages: zeroc-ice
08:08:52 Successfully installed zeroc-ice-3.6.5
08:08:53 + pip install -U pip future
08:08:53 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
08:08:53 Collecting pip
08:08:53 Using cached pip-24.2-py3-none-any.whl (1.8 MB)
08:08:53 Collecting future
08:08:53 Using cached future-1.0.0-py3-none-any.whl (491 kB)
08:08:53 Installing collected packages: pip, future
08:08:53 Attempting uninstall: pip
08:08:53 Found existing installation: pip 21.2.3
08:08:54 Uninstalling pip-21.2.3:
08:08:54 Successfully uninstalled pip-21.2.3
08:08:55 Successfully installed future-1.0.0 pip-24.2
08:08:55 + pip install markdown
08:08:56 Collecting markdown
08:08:56 Using cached Markdown-3.7-py3-none-any.whl.metadata (7.0 kB)
08:08:56 Collecting importlib-metadata>=4.4 (from markdown)
08:08:56 Using cached importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
08:08:56 Collecting zipp>=3.20 (from importlib-metadata>=4.4->markdown)
08:08:56 Using cached zipp-3.20.2-py3-none-any.whl.metadata (3.7 kB)
08:08:56 Using cached Markdown-3.7-py3-none-any.whl (106 kB)
08:08:56 Using cached importlib_metadata-8.5.0-py3-none-any.whl (26 kB)
08:08:56 Using cached zipp-3.20.2-py3-none-any.whl (9.2 kB)
08:08:56 Installing collected packages: zipp, importlib-metadata, markdown
08:08:56 Successfully installed importlib-metadata-8.5.0 markdown-3.7 zipp-3.20.2
08:08:56 + pip install reportlab
08:08:57 Collecting reportlab
08:08:57 Using cached reportlab-4.2.5-py3-none-any.whl.metadata (1.5 kB)
08:08:57 Collecting pillow>=9.0.0 (from reportlab)
08:08:58 Using cached pillow-10.4.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.2 kB)
08:08:58 Collecting chardet (from reportlab)
08:08:58 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
08:08:58 Using cached reportlab-4.2.5-py3-none-any.whl (1.9 MB)
08:08:58 Using cached pillow-10.4.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.5 MB)
08:08:58 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
08:08:58 Installing collected packages: pillow, chardet, reportlab
08:08:59 Successfully installed chardet-5.2.0 pillow-10.4.0 reportlab-4.2.5
08:08:59 + pip install omego
08:09:01 Collecting omego
08:09:01 Using cached omego-0.7.0-py3-none-any.whl
08:09:01 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
08:09:01 Collecting yaclifw>=0.1.1 (from omego)
08:09:01 Using cached yaclifw-0.2.0-py3-none-any.whl
08:09:01 Collecting six (from yaclifw>=0.1.1->omego)
08:09:01 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
08:09:01 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
08:09:01 Installing collected packages: six, yaclifw, omego
08:09:01 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
08:09:01 + pip install tables
08:09:02 Collecting tables
08:09:02 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
08:09:02 Collecting numpy>=1.19.0 (from tables)
08:09:02 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
08:09:02 Collecting numexpr>=2.6.2 (from tables)
08:09:02 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.2 kB)
08:09:02 Collecting packaging (from tables)
08:09:02 Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
08:09:02 Collecting py-cpuinfo (from tables)
08:09:02 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
08:09:02 Collecting blosc2>=2.3.0 (from tables)
08:09:02 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
08:09:02 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
08:09:02 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB)
08:09:02 Collecting msgpack (from blosc2>=2.3.0->tables)
08:09:02 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
08:09:03 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
08:09:03 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
08:09:03 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (404 kB)
08:09:03 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
08:09:03 Using cached packaging-24.1-py3-none-any.whl (53 kB)
08:09:03 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
08:09:03 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (478 kB)
08:09:03 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB)
08:09:03 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
08:09:07 Successfully installed blosc2-2.5.1 msgpack-1.1.0 ndindex-1.9.2 numexpr-2.10.1 numpy-2.0.2 packaging-24.1 py-cpuinfo-9.0.0 tables-3.9.2
08:09:07 + pip install jinja2
08:09:07 Collecting jinja2
08:09:07 Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
08:09:08 Collecting MarkupSafe>=2.0 (from jinja2)
08:09:08 Downloading MarkupSafe-3.0.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
08:09:08 Using cached jinja2-3.1.4-py3-none-any.whl (133 kB)
08:09:08 Downloading MarkupSafe-3.0.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB)
08:09:08 Installing collected packages: MarkupSafe, jinja2
08:09:08 Successfully installed MarkupSafe-3.0.0 jinja2-3.1.4
08:09:08 + pip install omero-py
08:09:09 Collecting omero-py
08:09:09 Using cached omero_py-5.19.5-py3-none-any.whl.metadata (6.3 kB)
08:09:09 Collecting urllib3<2 (from omero-py)
08:09:09 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
08:09:09 Collecting appdirs (from omero-py)
08:09:09 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
08:09:09 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
08:09:09 Collecting numpy<2 (from omero-py)
08:09:09 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
08:09:09 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (10.4.0)
08:09:09 Collecting PyYAML (from omero-py)
08:09:09 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
08:09:09 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
08:09:10 Collecting requests (from omero-py)
08:09:10 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
08:09:10 Collecting portalocker (from omero-py)
08:09:10 Using cached portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB)
08:09:10 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
08:09:10 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
08:09:10 Collecting idna<4,>=2.5 (from requests->omero-py)
08:09:10 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
08:09:10 Collecting certifi>=2017.4.17 (from requests->omero-py)
08:09:10 Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
08:09:10 Using cached omero_py-5.19.5-py3-none-any.whl (2.8 MB)
08:09:10 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
08:09:10 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
08:09:10 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
08:09:10 Using cached portalocker-2.10.1-py3-none-any.whl (18 kB)
08:09:10 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
08:09:10 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
08:09:10 Using cached certifi-2024.8.30-py3-none-any.whl (167 kB)
08:09:10 Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
08:09:10 Using cached idna-3.10-py3-none-any.whl (70 kB)
08:09:11 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, numpy, idna, charset-normalizer, certifi, requests, omero-py
08:09:11 Attempting uninstall: numpy
08:09:11 Found existing installation: numpy 2.0.2
08:09:11 Uninstalling numpy-2.0.2:
08:09:11 Successfully uninstalled numpy-2.0.2
08:09:15 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 certifi-2024.8.30 charset-normalizer-3.3.2 idna-3.10 numpy-1.26.4 omero-py-5.19.5 portalocker-2.10.1 requests-2.32.3 urllib3-1.26.20
08:09:15 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
08:09:16 Collecting omero-metadata
08:09:16 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-y10g5gfn/omero-metadata_ff0ee2f9a7314c03993438e153fee61b
08:09:16 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-y10g5gfn/omero-metadata_ff0ee2f9a7314c03993438e153fee61b
08:09:17 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit fd2adc1820d9896e2bf6b46b8bc4f261cb01c6dc
08:09:17 Installing build dependencies: started
08:09:21 Installing build dependencies: finished with status 'done'
08:09:21 Getting requirements to build wheel: started
08:09:21 Getting requirements to build wheel: finished with status 'done'
08:09:21 Preparing metadata (pyproject.toml): started
08:09:21 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:21 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.5)
08:09:21 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.2)
08:09:21 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.4)
08:09:21 Collecting pandas (from omero-metadata)
08:09:21 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
08:09:22 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
08:09:22 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
08:09:22 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
08:09:22 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
08:09:22 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)
08:09:22 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)
08:09:22 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
08:09:22 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.10.1)
08:09:22 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (3.0.0)
08:09:22 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
08:09:22 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
08:09:22 Collecting pytz>=2020.1 (from pandas->omero-metadata)
08:09:22 Using cached pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
08:09:22 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
08:09:22 Using cached tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
08:09:22 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)
08:09:22 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)
08:09:22 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.10)
08:09:22 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2024.8.30)
08:09:22 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
08:09:22 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
08:09:22 Using cached pytz-2024.2-py2.py3-none-any.whl (508 kB)
08:09:22 Using cached tzdata-2024.2-py2.py3-none-any.whl (346 kB)
08:09:23 Building wheels for collected packages: omero-metadata
08:09:23 Building wheel for omero-metadata (pyproject.toml): started
08:09:23 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
08:09:23 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39187 sha256=fd00a2112089d5e27fd5c6e49f2b2cf78c93c2ec33c0b5c922a4a6a64eb74175
08:09:23 Stored in directory: /tmp/pip-ephem-wheel-cache-3_ld1xmf/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
08:09:23 Successfully built omero-metadata
08:09:23 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
08:09:28 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2024.2 tzdata-2024.2
08:09:28 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
08:09:28 Collecting omero-cli-render
08:09:28 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-x6r6mr7b/omero-cli-render_d4b90a7ea99d43be98dcdf3f6683ff9c
08:09:28 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-x6r6mr7b/omero-cli-render_d4b90a7ea99d43be98dcdf3f6683ff9c
08:09:29 Running command git checkout -b merge_ci --track origin/merge_ci
08:09:30 Switched to a new branch 'merge_ci'
08:09:30 branch 'merge_ci' set up to track 'origin/merge_ci'.
08:09:30 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 63d0ce1dbc40506e24f6775d66ea62350b4afb7f
08:09:30 Installing build dependencies: started
08:09:32 Installing build dependencies: finished with status 'done'
08:09:32 Getting requirements to build wheel: started
08:09:32 Getting requirements to build wheel: finished with status 'done'
08:09:32 Preparing metadata (pyproject.toml): started
08:09:32 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:32 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.2)
08:09:32 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.5)
08:09:32 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
08:09:32 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
08:09:32 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
08:09:32 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
08:09:32 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)
08:09:32 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
08:09:32 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
08:09:32 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.10.1)
08:09:32 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)
08:09:32 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.10)
08:09:32 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2024.8.30)
08:09:32 Building wheels for collected packages: omero-cli-render
08:09:32 Building wheel for omero-cli-render (pyproject.toml): started
08:09:32 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
08:09:32 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=18031 sha256=4f9d74d96f54556ee084663ecd344d294ede8bcee29119b56e45d27689ad594b
08:09:32 Stored in directory: /tmp/pip-ephem-wheel-cache-qayf4wow/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
08:09:32 Successfully built omero-cli-render
08:09:32 Installing collected packages: omero-cli-render
08:09:32 Successfully installed omero-cli-render-0.8.2.dev0
08:09:32 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
08:09:33 Collecting omero-cli-duplicate
08:09:33 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-giwxrs5u/omero-cli-duplicate_a2f56beaa28342fbbd4867cc0238813b
08:09:33 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-giwxrs5u/omero-cli-duplicate_a2f56beaa28342fbbd4867cc0238813b
08:09:34 Running command git checkout -b merge_ci --track origin/merge_ci
08:09:34 Switched to a new branch 'merge_ci'
08:09:34 branch 'merge_ci' set up to track 'origin/merge_ci'.
08:09:34 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit d281e97fff0ea4db207ad2566b5ba299af157619
08:09:34 Installing build dependencies: started
08:09:36 Installing build dependencies: finished with status 'done'
08:09:36 Getting requirements to build wheel: started
08:09:36 Getting requirements to build wheel: finished with status 'done'
08:09:36 Preparing metadata (pyproject.toml): started
08:09:36 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:36 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.5)
08:09:36 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
08:09:36 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
08:09:36 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
08:09:36 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
08:09:36 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)
08:09:36 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
08:09:36 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)
08:09:36 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
08:09:36 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.10.1)
08:09:36 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)
08:09:36 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.10)
08:09:36 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2024.8.30)
08:09:36 Building wheels for collected packages: omero-cli-duplicate
08:09:36 Building wheel for omero-cli-duplicate (pyproject.toml): started
08:09:36 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
08:09:36 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11442 sha256=7ac2dc8a2bcafa5e14d0fbbac3233d7be01b31e77f60b6f76f0b67aeb1901761
08:09:36 Stored in directory: /tmp/pip-ephem-wheel-cache-kpy7qvlj/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
08:09:36 Successfully built omero-cli-duplicate
08:09:36 Installing collected packages: omero-cli-duplicate
08:09:36 Successfully installed omero-cli-duplicate-0.4.1.dev0
08:09:37 + pip install omero-certificates
08:09:37 Collecting omero-certificates
08:09:37 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
08:09:37 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.5)
08:09:37 Collecting distro==1.8.0 (from omero-certificates)
08:09:37 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
08:09:37 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
08:09:37 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
08:09:37 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
08:09:37 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
08:09:37 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)
08:09:37 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
08:09:37 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)
08:09:37 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
08:09:37 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.10.1)
08:09:37 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)
08:09:37 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
08:09:37 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2024.8.30)
08:09:37 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
08:09:37 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
08:09:37 Installing collected packages: distro, omero-certificates
08:09:37 Successfully installed distro-1.8.0 omero-certificates-0.3.2
08:09:37 + for x in *.tar.gz
08:09:37 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
08:09:38 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
08:09:38 Installing build dependencies: started
08:09:40 Installing build dependencies: finished with status 'done'
08:09:40 Getting requirements to build wheel: started
08:09:40 Getting requirements to build wheel: finished with status 'done'
08:09:40 Preparing metadata (pyproject.toml): started
08:09:40 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:40 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.7.1.dev0) (5.19.5)
08:09:40 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
08:09:40 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
08:09:40 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
08:09:40 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.4)
08:09:40 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)
08:09:40 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
08:09:40 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)
08:09:40 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3)
08:09:40 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.10.1)
08:09:40 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)
08:09:40 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10)
08:09:40 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2024.8.30)
08:09:40 Building wheels for collected packages: omero-dropbox
08:09:40 Building wheel for omero-dropbox (pyproject.toml): started
08:09:40 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
08:09:40 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49056 sha256=acf13902574d8243b58827ad82a18d36e8614f79be01d51149964c78681b2534
08:09:40 Stored in directory: /home/omero/.cache/pip/wheels/eb/76/85/58476368b176f793423899407c96293c22f9c9edc28cf54079
08:09:40 Successfully built omero-dropbox
08:09:40 Installing collected packages: omero-dropbox
08:09:40 Successfully installed omero-dropbox-5.7.1.dev0
08:09:40 + for x in *.tar.gz
08:09:40 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
08:09:41 Processing ./omero_marshal-0.9.1.dev0.tar.gz
08:09:41 Installing build dependencies: started
08:09:43 Installing build dependencies: finished with status 'done'
08:09:43 Getting requirements to build wheel: started
08:09:43 Getting requirements to build wheel: finished with status 'done'
08:09:43 Preparing metadata (pyproject.toml): started
08:09:43 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:43 Building wheels for collected packages: omero_marshal
08:09:43 Building wheel for omero_marshal (pyproject.toml): started
08:09:43 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
08:09:43 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88030 sha256=77ccd2ebe12c40c689a50f7425fe183d1fbd2e8d6533d66c2344666a6a57d976
08:09:44 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
08:09:44 Successfully built omero_marshal
08:09:44 Installing collected packages: omero_marshal
08:09:44 Successfully installed omero_marshal-0.9.1.dev0
08:09:44 + for x in *.tar.gz
08:09:44 + pip install -U omero_py-5.19.6.dev0.tar.gz
08:09:44 Processing ./omero_py-5.19.6.dev0.tar.gz
08:09:45 Installing build dependencies: started
08:09:47 Installing build dependencies: finished with status 'done'
08:09:47 Getting requirements to build wheel: started
08:09:47 Getting requirements to build wheel: finished with status 'done'
08:09:47 Preparing metadata (pyproject.toml): started
08:09:47 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:47 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.20)
08:09:47 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.4.4)
08:09:47 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.0.0)
08:09:47 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.4)
08:09:47 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (10.4.0)
08:09:47 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (6.0.2)
08:09:47 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (3.6.5)
08:09:47 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.32.3)
08:09:47 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.10.1)
08:09:47 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.3.2)
08:09:47 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.10)
08:09:47 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (2024.8.30)
08:09:47 Building wheels for collected packages: omero-py
08:09:47 Building wheel for omero-py (pyproject.toml): started
08:09:48 Building wheel for omero-py (pyproject.toml): finished with status 'done'
08:09:48 Created wheel for omero-py: filename=omero_py-5.19.6.dev0-py3-none-any.whl size=2783245 sha256=678b51fa38bc15daf0b8aa91539f665c57c16c82fbcd8ccbd967bea8f2f79f58
08:09:48 Stored in directory: /home/omero/.cache/pip/wheels/80/e5/37/a3ff2b54d2fa16a058bb39e8eb6b77b050109520fb9f16931d
08:09:48 Successfully built omero-py
08:09:49 Installing collected packages: omero-py
08:09:49 Attempting uninstall: omero-py
08:09:49 Found existing installation: omero-py 5.19.5
08:09:49 Uninstalling omero-py-5.19.5:
08:09:49 Successfully uninstalled omero-py-5.19.5
08:09:51 Successfully installed omero-py-5.19.6.dev0
08:09:51 + for x in *.tar.gz
08:09:51 + pip install -U omero_scripts-5.8.4.dev0.tar.gz
08:09:51 Processing ./omero_scripts-5.8.4.dev0.tar.gz
08:09:51 Installing build dependencies: started
08:09:53 Installing build dependencies: finished with status 'done'
08:09:53 Getting requirements to build wheel: started
08:09:53 Getting requirements to build wheel: finished with status 'done'
08:09:53 Preparing metadata (pyproject.toml): started
08:09:54 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:54 Building wheels for collected packages: omero-scripts
08:09:54 Building wheel for omero-scripts (pyproject.toml): started
08:09:54 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
08:09:54 Created wheel for omero-scripts: filename=omero_scripts-5.8.4.dev0-py3-none-any.whl size=116644 sha256=d1c83f86c96c6bd29c287c4fb5ac8f6030f26db3531715134f800d0bfe5a5ab7
08:09:54 Stored in directory: /home/omero/.cache/pip/wheels/50/80/aa/1e175e4f2a5b0a5343d01937a727d990d08c8e12000390ad9c
08:09:54 Successfully built omero-scripts
08:09:54 Installing collected packages: omero-scripts
08:09:54 Successfully installed omero-scripts-5.8.4.dev0
08:09:54 + for x in *.tar.gz
08:09:54 + pip install -U omero_web-5.27.3.dev0.tar.gz
08:09:55 Processing ./omero_web-5.27.3.dev0.tar.gz
08:09:55 Installing build dependencies: started
08:09:57 Installing build dependencies: finished with status 'done'
08:09:57 Getting requirements to build wheel: started
08:09:57 Getting requirements to build wheel: finished with status 'done'
08:09:57 Preparing metadata (pyproject.toml): started
08:09:57 Preparing metadata (pyproject.toml): finished with status 'done'
08:09:57 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (5.19.6.dev0)
08:09:58 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.27.3.dev0)
08:09:58 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
08:09:58 Collecting Django<4.3,>=4.2.3 (from omero-web==5.27.3.dev0)
08:09:58 Using cached Django-4.2.16-py3-none-any.whl.metadata (4.1 kB)
08:09:58 Collecting django-pipeline==2.1.0 (from omero-web==5.27.3.dev0)
08:09:58 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
08:09:58 Collecting django-cors-headers==3.7.0 (from omero-web==5.27.3.dev0)
08:09:58 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
08:09:58 Collecting django-csp (from omero-web==5.27.3.dev0)
08:09:58 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
08:09:58 Collecting whitenoise>=5.3.0 (from omero-web==5.27.3.dev0)
08:09:58 Using cached whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB)
08:09:58 Collecting gunicorn>=19.3 (from omero-web==5.27.3.dev0)
08:09:58 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
08:09:58 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (0.9.1.dev0)
08:09:58 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (10.4.0)
08:09:58 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2024.2)
08:09:58 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2.10.1)
08:09:58 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (24.1)
08:09:58 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
08:09:58 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
08:09:58 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
08:09:58 Using cached sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB)
08:09:58 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.26.20)
08:09:58 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.4.4)
08:09:58 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.0.0)
08:09:58 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.26.4)
08:09:58 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (6.0.2)
08:09:58 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.6.5)
08:09:58 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (2.32.3)
08:09:59 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
08:09:59 Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
08:09:59 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.3.2)
08:09:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.10)
08:09:59 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (2024.8.30)
08:09:59 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
08:09:59 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
08:09:59 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
08:09:59 Using cached Django-4.2.16-py3-none-any.whl (8.0 MB)
08:09:59 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
08:09:59 Using cached whitenoise-6.7.0-py3-none-any.whl (19 kB)
08:09:59 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
08:09:59 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
08:09:59 Using cached sqlparse-0.5.1-py3-none-any.whl (44 kB)
08:09:59 Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
08:09:59 Building wheels for collected packages: omero-web
08:09:59 Building wheel for omero-web (pyproject.toml): started
08:10:00 Building wheel for omero-web (pyproject.toml): finished with status 'done'
08:10:00 Created wheel for omero-web: filename=omero_web-5.27.3.dev0-py3-none-any.whl size=2766671 sha256=7ba48337df4535fb0f30d9b11ccd4f1a1a8e267b8be74d9d9f6d37b54e5a537b
08:10:00 Stored in directory: /home/omero/.cache/pip/wheels/ae/1e/5f/7127f5403b089e5e8280a504b3d30303e78d1102aa8854c22b
08:10:00 Successfully built omero-web
08:10:00 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
08:10:03 Successfully installed Django-4.2.16 asgiref-3.8.1 concurrent-log-handler-0.9.25 django-cors-headers-3.7.0 django-csp-3.8 django-pipeline-2.1.0 gunicorn-23.0.0 omero-web-5.27.3.dev0 sqlparse-0.5.1 typing-extensions-4.12.2 whitenoise-6.7.0
08:10:03 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
08:10:04 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
08:10:04 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
08:10:04 --2024-10-08 08:10:04-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
08:10:04 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.109.133, 185.199.108.133, ...
08:10:04 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.
08:10:04 HTTP request sent, awaiting response... 200 OK
08:10:04 Length: 98962 (97K) [text/plain]
08:10:04 Saving to: ‘Figure_To_Pdf.py’
08:10:04
08:10:04 0K .......... .......... .......... .......... .......... 51% 3.07M 0s
08:10:04 50K .......... .......... .......... .......... ...... 100% 6.08M=0.02s
08:10:04
08:10:04 2024-10-08 08:10:04 (4.03 MB/s) - ‘Figure_To_Pdf.py’ saved [98962/98962]
08:10:04
08:10:04 + chmod 755 Figure_To_Pdf.py
08:10:04 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
08:10:04 + omero config set omero.db.name OMERO-server
08:10:06 + omero config set omero.db.host pg
08:10:07 + omero config set omero.db.user postgres
08:10:09 + omero config set omero.data.dir /home/omero/omero-server-data
08:10:10 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
08:10:12 + omero config set omero.db.poolsize 25
08:10:13 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
08:10:15 + omero config set omero.security.trustStorePassword changeit
08:10:16 + omero config set omero.mail.config true
08:10:17 + omero config set omero.mail.from qa@openmicroscopy.org.uk
08:10:19 + omero config set omero.mail.host smtp.dundee.ac.uk
08:10:21 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
08:10:22 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
08:10:24 + omero certificates
08:10:25 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
08:10:25 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
08:10:25 + '[' false = true ']'
08:10:25 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
08:10:25 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
08:10:25 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
08:10:25 2024-10-08 08:10:25,746 [ omego.db] DEBUG dbcommand => upgrade
08:10:25 2024-10-08 08:10:25,746 [ omego.db] DEBUG dbhost => localhost
08:10:25 2024-10-08 08:10:25,746 [ omego.db] DEBUG dbname => OMERO-server
08:10:25 2024-10-08 08:10:25,746 [ omego.db] DEBUG dbpass => omero
08:10:25 2024-10-08 08:10:25,746 [ omego.db] DEBUG dbuser => omero
08:10:25 2024-10-08 08:10:25,746 [ omego.db] DEBUG rootpass => omero
08:10:25 2024-10-08 08:10:25,747 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
08:10:25 2024-10-08 08:10:25,747 [omego.extern] INFO Executing : omero version
08:10:26 OMERO.py version:
08:10:27 OMERO.server version:
08:10:27 5.6.3-513-77dcd6034a-ice36
08:10:27 5.19.6.dev0
08:10:27 2024-10-08 08:10:27,223 [omego.extern] INFO Completed [1.476 s]
08:10:27 2024-10-08 08:10:27,223 [omego.extern] DEBUG Using omero CLI from omero
08:10:27 2024-10-08 08:10:27,223 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
08:10:27 2024-10-08 08:10:27,223 [omego.extern] INFO Running [current environment]: omero config get --show-password
08:10:27 2024-10-08 08:10:27,223 [omego.extern] INFO Executing : omero config get --show-password
08:10:28 2024-10-08 08:10:28,611 [omego.extern] INFO Completed [1.388 s]
08:10:28 2024-10-08 08:10:28,612 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
08:10:28 2024-10-08 08:10:28,612 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
08:10:29 2024-10-08 08:10:29,035 [omego.extern] INFO Completed [0.424 s]
08:10:29 2024-10-08 08:10:29,036 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.4\n'
08:10:29 2024-10-08 08:10:29,036 [ omego.db] INFO psql version: psql (PostgreSQL) 16.4
08:10:29
08:10:29 2024-10-08 08:10:29,036 [omego.extern] INFO Running [current environment]: omero config get --show-password
08:10:29 2024-10-08 08:10:29,036 [omego.extern] INFO Executing : omero config get --show-password
08:10:30 2024-10-08 08:10:30,527 [omego.extern] INFO Completed [1.491 s]
08:10:30 2024-10-08 08:10:30,527 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
08:10:30 2024-10-08 08:10:30,527 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
08:10:30 2024-10-08 08:10:30,659 [omego.extern] INFO Completed [0.131 s]
08:10:30 2024-10-08 08:10:30,659 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.6") at port "5432".\n'
08:10:30 2024-10-08 08:10:30,659 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
08:10:30 2024-10-08 08:10:30,659 [omego.extern] INFO Running [current environment]: omero config get --show-password
08:10:30 2024-10-08 08:10:30,659 [omego.extern] INFO Executing : omero config get --show-password
08:10:32 2024-10-08 08:10:32,079 [omego.extern] INFO Completed [1.420 s]
08:10:32 2024-10-08 08:10:32,080 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
08:10:32 2024-10-08 08:10:32,080 [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
08:10:33 2024-10-08 08:10:33,178 [omego.extern] INFO Completed [1.098 s]
08:10:33 2024-10-08 08:10:33,178 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
08:10:33 2024-10-08 08:10:33,178 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
08:10:33 2024-10-08 08:10:33,180 [ omego.db] INFO Database is already at OMERO5.4__0
08:10:33 + export LANG=en_US.UTF-8
08:10:33 + LANG=en_US.UTF-8
08:10:33 + export LANGUAGE=en_US:en
08:10:33 + LANGUAGE=en_US:en
08:10:33 + export LC_ALL=en_US.UTF-8
08:10:33 + LC_ALL=en_US.UTF-8
08:10:33 + BUILD_ID=DONT_KILL_ME
08:10:33 + omero admin start
08:10:43 No descriptor given. Using etc/grid/default.xml
08:10:55 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
08:10:55 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
08:10:55 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
08:10:55 Waiting on startup. Use CTRL-C to exit
08:10:56 + omero admin waitup
08:10:57 Waiting on startup. Use CTRL-C to exit
08:10:57 + omero admin diagnostics
08:10:59
08:10:59 ================================================================================
08:10:59 OMERO Diagnostics (admin)
08:10:59 ================================================================================
08:10:59
08:10:59 Commands: java -version 11.0.24 (/usr/bin/java)
08:10:59 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
08:10:59 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
08:10:59 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
08:10:59 Commands: psql --version 16.4 (/usr/bin/psql)
08:10:59 Commands: openssl version 3.0.71 (/usr/bin/openssl)
08:10:59
08:10:59 Component: OMERO.py 5.19.6.dev0
08:10:59 Component: OMERO.server 5.6.3-513-77dcd6034a-ice36
08:10:59
08:10:59 Server: icegridnode running
08:10:59 Server: Blitz-0 active (pid = 2586, enabled)
08:10:59 Server: Indexer-0 activating (enabled)
08:10:59 Server: OMERO.Glacier2 active (pid = 2634, enabled)
08:10:59 Server: OMERO.IceStorm active (pid = 2628, enabled)
08:10:59 Server: Processor-0 activating (enabled)
08:10:59 Server: Tables-0 activating (enabled)
08:10:59
08:10:59 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
08:10:59 Log files: Blitz-0.log 21.7 KB errors=0 warnings=1
08:10:59 Log files: DropBox.log n/a
08:10:59 Log files: FileServer.log n/a
08:10:59 Log files: Indexer-0.log 598 B
08:10:59 Log files: MonitorServer.log n/a
08:10:59 Log files: Processor-0.log 592 B
08:10:59 Log files: Tables-0.log 841 B
08:10:59 Log files: TestDropBox.log n/a
08:10:59 Log files: master.err 180 B
08:10:59 Log files: master.out 30.1 KB
08:10:59 Log files: Total size 0.05 MB
08:10:59
08:10:59
08:10:59 Environment:OMERO_HOME=(unset)
08:10:59 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
08:10:59 Environment:OMERO_NODE=(unset)
08:10:59 Environment:OMERO_MASTER=(unset)
08:10:59 Environment:OMERO_USERDIR=(unset)
08:10:59 Environment:OMERO_TMPDIR=(unset)
08:10:59 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
08:10:59 Environment:PYTHONPATH=(unset)
08:10:59 Environment:ICE_HOME=/opt/ice-3.6.5
08:10:59 Environment:LD_LIBRARY_PATH=(unset)
08:10:59 Environment:DYLD_LIBRARY_PATH=(unset)
08:10:59
08:10:59 OMERO SSL port:4064
08:10:59 OMERO TCP port:4063
08:10:59 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
08:10:59 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
08:10:59
08:10:59 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
08:10:59 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
08:10:59 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
08:10:59 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
08:10:59
08:10:59 Jar: lib/server/formats-api.jar Bio-Formats API 8.0.0-SNAPSHOT 8 October 2024 188d49c0ebb3c4fe2e8f6dc31c5cadb47fd3e357
08:10:59 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.0.0-SNAPSHOT 8 October 2024 188d49c0ebb3c4fe2e8f6dc31c5cadb47fd3e357
08:10:59 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.0.0-SNAPSHOT 8 October 2024 188d49c0ebb3c4fe2e8f6dc31c5cadb47fd3e357
08:10:59 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.4-SNAPSHOT 8 October 2024 ca1c86546c3c6797a1264a42535ce79d52d1a102
08:10:59 Jar: lib/server/ome-common.jar OME Common Java 6.0.24-SNAPSHOT 8 October 2024 ca1c86546c3c6797a1264a42535ce79d52d1a102
08:10:59 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 8 October 2024 ca1c86546c3c6797a1264a42535ce79d52d1a102
08:10:59 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4-SNAPSHOT 8 October 2024 ca1c86546c3c6797a1264a42535ce79d52d1a102
08:10:59 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 8 October 2024 ca1c86546c3c6797a1264a42535ce79d52d1a102
08:10:59 Jar: lib/server/ome-xml.jar OME XML library 6.3.7-SNAPSHOT 8 October 2024 ca1c86546c3c6797a1264a42535ce79d52d1a102
08:10:59 Jar: lib/server/omero-blitz.jar jar 5.7.5-SNAPSHOT
08:10:59 Jar: lib/server/omero-common.jar jar 5.6.8-SNAPSHOT
08:10:59 Jar: lib/server/omero-gateway.jar jar 5.9.4-SNAPSHOT
08:10:59 Jar: lib/server/omero-model.jar jar 5.6.16-SNAPSHOT
08:10:59 Jar: lib/server/omero-renderer.jar jar 5.5.18-SNAPSHOT
08:10:59 Jar: lib/server/omero-romio.jar jar 5.7.8-SNAPSHOT
08:10:59 Jar: lib/server/omero-server.jar jar 5.6.13-SNAPSHOT
08:10:59 + deactivate
08:10:59 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
08:10:59 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
08:10:59 + export PATH
08:10:59 + unset _OLD_VIRTUAL_PATH
08:10:59 + '[' -n '' ']'
08:10:59 + '[' -n /bin/bash -o -n '' ']'
08:10:59 + hash -r
08:10:59 + '[' -n '' ']'
08:10:59 + unset VIRTUAL_ENV
08:10:59 + '[' '!' '' = nondestructive ']'
08:10:59 + unset -f deactivate
08:11:00 Finished: SUCCESS
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