07:03:59 Started by upstream project "Trigger" build number 252
07:03:59 originally caused by:
07:03:59 Started by user devspace
07:03:59 Running as SYSTEM
07:04:00 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
07:04:00 [OMERO-server] $ /bin/bash -xe /tmp/jenkins9649649222495013546.sh
07:04:01 + source /home/settings.env
07:04:01 ++ OMERO_DB_HOST=pg
07:04:01 ++ OMERO_DB_USER=postgres
07:04:01 ++ OMERO_DB_PASS=
07:04:01 ++ OMERO_ROOT_PASS=omero
07:04:01 ++ OMERO_DATA_DIR=/OMERO
07:04:01 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
07:04:01 + OMERO_DB_NAME=OMERO-server
07:04:01 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
07:04:01 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:04:01 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:04:01 + OMERO_DATA_DIR=/home/omero/omero-server-data
07:04:01 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
07:04:01 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
07:04:01 ++ deactivate nondestructive
07:04:01 ++ '[' -n '' ']'
07:04:01 ++ '[' -n '' ']'
07:04:01 ++ '[' -n /bin/bash -o -n '' ']'
07:04:01 ++ hash -r
07:04:01 ++ '[' -n '' ']'
07:04:01 ++ unset VIRTUAL_ENV
07:04:01 ++ '[' '!' nondestructive = nondestructive ']'
07:04:01 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
07:04:01 ++ export VIRTUAL_ENV
07:04:01 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:04:01 ++ 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
07:04:01 ++ export PATH
07:04:01 ++ '[' -n '' ']'
07:04:01 ++ '[' -z '' ']'
07:04:01 ++ _OLD_VIRTUAL_PS1=
07:04:01 ++ PS1='(.venv3) '
07:04:01 ++ export PS1
07:04:01 ++ '[' -n /bin/bash -o -n '' ']'
07:04:01 ++ hash -r
07:04:01 + omero admin stop
07:04:31 Server not running
07:04:31 + echo not running
07:04:31 not running
07:04:31 + sleep 5
07:04:36 + deactivate
07:04:36 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
07:04:36 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:04:36 + export PATH
07:04:36 + unset _OLD_VIRTUAL_PATH
07:04:36 + '[' -n '' ']'
07:04:36 + '[' -n /bin/bash -o -n '' ']'
07:04:36 + hash -r
07:04:36 + '[' -n '' ']'
07:04:36 + unset VIRTUAL_ENV
07:04:36 + '[' '!' '' = nondestructive ']'
07:04:36 + unset -f deactivate
07:04:36 + rm -rf /home/omero/workspace/OMERO-server/.venv3
07:04:37 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
07:04:41 + '[' false = true ']'
07:04:41 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
07:04:41 Skipping PURGE_DATA:CleanDbAndRepo
07:04:41 + 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
07:04:43 Copied 1 artifact from "OMERO-build" build number 208
07:04:43 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 205
07:04:43 Copied 2 artifacts from "OMERO-build-build" build number 216
07:04:43 [OMERO-server] $ /bin/bash -xe /tmp/jenkins18188082787518048627.sh
07:04:43 + source /home/settings.env
07:04:43 ++ OMERO_DB_HOST=pg
07:04:43 ++ OMERO_DB_USER=postgres
07:04:43 ++ OMERO_DB_PASS=
07:04:43 ++ OMERO_ROOT_PASS=omero
07:04:43 ++ OMERO_DATA_DIR=/OMERO
07:04:43 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
07:04:43 + OMERO_DB_NAME=OMERO-server
07:04:43 + OMERO_DATA_DIR=/home/omero/omero-server-data
07:04:43 + mkdir -p /home/omero/omero-server-data
07:04:44 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
07:04:44 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:04:44 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:04:44 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
07:04:44 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
07:04:44 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
07:04:44 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
07:04:44 ++ ls OMERO.server-5.6.3-513-ae72da0f50-ice36.zip
07:04:44 + ZIP=OMERO.server-5.6.3-513-ae72da0f50-ice36.zip
07:04:44 + '[' '!' -z '' ']'
07:04:44 + DIST=OMERO.server-5.6.3-513-ae72da0f50-ice36
07:04:44 + unzip OMERO.server-5.6.3-513-ae72da0f50-ice36.zip
07:04:44 Archive: OMERO.server-5.6.3-513-ae72da0f50-ice36.zip
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/blitz/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/grid/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/profiles/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/error/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/grid/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/luts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/luts/janelia/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/luts/ncsa_paledit/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/luts/wcif/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/analysis_scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/annotation_scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/export_scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/figure_scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/import_scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/scripts/omero/util_scripts/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/misc/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__1/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__10/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__11/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__2/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__3/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__4/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__5/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__6/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__7/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__8/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__9/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__4/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__5/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__6/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__7/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.1__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.2__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.2__0/t/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.3__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.4__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.0__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.1__1/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.2__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4DEV__1/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4DEV__2/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4DEV__3/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/
07:04:44 creating: OMERO.server-5.6.3-513-ae72da0f50-ice36/var/
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/LICENSE.txt
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/backup.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/blitz/mail-senders.example
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/blitz/mail-server.example
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/build.properties
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/env.bat
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/env.sh
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/hibernate.properties
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/ice.config
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/logback-cli.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/logback-indexing-cli.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/logback-indexing.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/logback.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/mime.types
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/node1.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/node2.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/omero.properties
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/profiles/psql
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/rollover.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/Windows.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/error/maintainance.html
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/grid/README
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/grid/default.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/grid/templates.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/grid/windefault.xml
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/ice.config
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/internal.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/master.cfg
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/templates/robot.template
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/etc/testdropbox.config
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/history.rst
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/OMEZarrReader.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/activation.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/aggdesigner-algorithm.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/aircompressor.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/annotations.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/antlr.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/aopalliance.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/avatica-core.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/avatica-metrics.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/aws-java-sdk-core.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/aws-java-sdk-kms.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/aws-java-sdk-s3.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/base.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-all.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-anim.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-awt-util.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-bridge.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-codec.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-constants.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-css.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-dom.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-ext.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-extension.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-gui-util.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-gvt.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-i18n.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-parser.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-rasterizer-ext.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-rasterizer.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-script.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-slideshow.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-squiggle-ext.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-squiggle.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-svg-dom.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-svgbrowser.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-svggen.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-svgpp.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-svgrasterizer.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-swing.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-transcoder.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-ttf2svg.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-util.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/batik-xml.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/btm.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/bufr.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/c3p0.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/calcite-core.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/calcite-linq4j.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/cdm-core.jar
07:04:44 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/client/checker-qual.jar
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07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/ome-jai.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/ome-mdbtools.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/ome-poi.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/ome-xml.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-blitz.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-common.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-gateway.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-model.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-renderer.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-romio.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/omero-server.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/pdfbox.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/perf4j.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/postgresql.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/protobuf-java.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/quartz.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/re2j.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/reflectasm.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/rhino.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/serializer.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/sketches-core.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/slf4j-api.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/snakeyaml.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/solr-analysis-extras.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/solr-commons-csv.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/solr-core.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/solr-solrj.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/specification.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-aop.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-beans.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-context-support.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-context.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-core.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-expression.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-jdbc.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-jms.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-ldap-core.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-messaging.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-orm.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-security-core.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-security-ldap.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/spring-tx.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/sqlite-jdbc.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/subethasmtp.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/turbojpeg.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/udunits.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xalan.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xercesImpl.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xml-apis-ext.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xml-apis.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xmlgraphics-commons.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xmpcore.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/lib/server/xpp3.jar
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/README
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/agpl.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/antlr.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/apache-v1.1.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/apache-v2.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/asm.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/bouncy_castle_license.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/bsd.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/cddl-v1.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/cpl-v10.html
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/crystalclear.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/django.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/dom4j.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/epl-v1.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/fbsd.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/freemarker.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/gpl-v2.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/gpl.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/gtest.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/iconsweets_license.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/jamon.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/jmock.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/jquery.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/jtidy.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/lgpl-3.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/lgpl-v2.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/lgpl-v2.1.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/lgpl-v3.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/lgpl.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/matplotlib.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/mit.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/mpl-v1_0.htm
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/npl-1_1.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/path.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/pil.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/postgresql.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/psf-v2.0.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/psf-v2.5.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/scons.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/slf4j.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/tablelayout.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/which.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/zlib-libpng.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/share/licenses/zpl-v2.1.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/README.txt
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/misc/Makefile
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/misc/current.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/misc/enums.py
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__1/OMERO3__7.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__10/OMERO3A__9.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__11/OMERO3A__10.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__11/OMERO3A__5.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__2/OMERO3A__1.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__3/OMERO3A__2.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__3/OMERO3__5.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__4/OMERO3A__3.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__4/OMERO3__5.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__5/OMERO3A__4.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__6/OMERO3A__5.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__7/OMERO3A__6.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__8/OMERO3A__6.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3A__9/OMERO3A__8.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__4/OMERO3__1.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__5/OMERO3__4.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__6/OMERO3__5.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO3__7/OMERO3__6.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.1__0/OMERO4__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.2__0/OMERO4.1__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO4__0/OMERO3A__11.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/psql-footer.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/psql-header.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/schema.sql
07:04:46 inflating: OMERO.server-5.6.3-513-ae72da0f50-ice36/sql/psql/OMERO5.4__0/views.sql
07:04:46 + rm -f OMERO.server-5.6.3-513-ae72da0f50-ice36.zip
07:04:46 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-513-ae72da0f50-ice36 /home/omero/workspace/OMERO-server/OMERO.server
07:04:46 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
07:04:46 ++ deactivate nondestructive
07:04:46 ++ '[' -n '' ']'
07:04:46 ++ '[' -n '' ']'
07:04:46 ++ '[' -n /bin/bash -o -n '' ']'
07:04:46 ++ hash -r
07:04:46 ++ '[' -n '' ']'
07:04:46 ++ unset VIRTUAL_ENV
07:04:46 ++ '[' '!' nondestructive = nondestructive ']'
07:04:46 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
07:04:46 ++ export VIRTUAL_ENV
07:04:46 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:04:46 ++ 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
07:04:46 ++ export PATH
07:04:46 ++ '[' -n '' ']'
07:04:46 ++ '[' -z '' ']'
07:04:46 ++ _OLD_VIRTUAL_PS1=
07:04:46 ++ PS1='(.venv3) '
07:04:46 ++ export PS1
07:04:46 ++ '[' -n /bin/bash -o -n '' ']'
07:04:46 ++ hash -r
07:04:46 + 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
07:04:47 Collecting zeroc-ice==3.6.5
07:04:47 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)
07:04:50 Installing collected packages: zeroc-ice
07:04:50 Successfully installed zeroc-ice-3.6.5
07:04:51 + pip install -U pip future
07:04:51 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
07:04:51 Collecting pip
07:04:51 Using cached pip-24.2-py3-none-any.whl (1.8 MB)
07:04:52 Collecting future
07:04:52 Using cached future-1.0.0-py3-none-any.whl (491 kB)
07:04:52 Installing collected packages: pip, future
07:04:52 Attempting uninstall: pip
07:04:52 Found existing installation: pip 21.2.3
07:04:52 Uninstalling pip-21.2.3:
07:04:52 Successfully uninstalled pip-21.2.3
07:04:53 Successfully installed future-1.0.0 pip-24.2
07:04:53 + pip install markdown
07:04:54 Collecting markdown
07:04:54 Using cached Markdown-3.7-py3-none-any.whl.metadata (7.0 kB)
07:04:54 Collecting importlib-metadata>=4.4 (from markdown)
07:04:54 Using cached importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
07:04:54 Collecting zipp>=3.20 (from importlib-metadata>=4.4->markdown)
07:04:54 Using cached zipp-3.20.2-py3-none-any.whl.metadata (3.7 kB)
07:04:54 Using cached Markdown-3.7-py3-none-any.whl (106 kB)
07:04:54 Using cached importlib_metadata-8.5.0-py3-none-any.whl (26 kB)
07:04:54 Using cached zipp-3.20.2-py3-none-any.whl (9.2 kB)
07:04:54 Installing collected packages: zipp, importlib-metadata, markdown
07:04:54 Successfully installed importlib-metadata-8.5.0 markdown-3.7 zipp-3.20.2
07:04:54 + pip install reportlab
07:04:55 Collecting reportlab
07:04:55 Using cached reportlab-4.2.5-py3-none-any.whl.metadata (1.5 kB)
07:04:56 Collecting pillow>=9.0.0 (from reportlab)
07:04:56 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
07:04:56 Collecting chardet (from reportlab)
07:04:56 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
07:04:56 Using cached reportlab-4.2.5-py3-none-any.whl (1.9 MB)
07:04:56 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.4 MB)
07:04:56 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
07:04:56 Installing collected packages: pillow, chardet, reportlab
07:04:57 Successfully installed chardet-5.2.0 pillow-11.0.0 reportlab-4.2.5
07:04:57 + pip install omego
07:04:58 Collecting omego
07:04:58 Using cached omego-0.7.0-py3-none-any.whl
07:04:58 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
07:04:58 Collecting yaclifw>=0.1.1 (from omego)
07:04:58 Using cached yaclifw-0.2.0-py3-none-any.whl
07:04:58 Collecting six (from yaclifw>=0.1.1->omego)
07:04:58 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
07:04:58 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
07:04:58 Installing collected packages: six, yaclifw, omego
07:04:58 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
07:04:58 + pip install tables
07:04:59 Collecting tables
07:04:59 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
07:05:00 Collecting numpy>=1.19.0 (from tables)
07:05:00 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
07:05:00 Collecting numexpr>=2.6.2 (from tables)
07:05:00 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.2 kB)
07:05:00 Collecting packaging (from tables)
07:05:00 Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
07:05:00 Collecting py-cpuinfo (from tables)
07:05:00 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
07:05:00 Collecting blosc2>=2.3.0 (from tables)
07:05:00 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
07:05:01 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
07:05:01 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB)
07:05:01 Collecting msgpack (from blosc2>=2.3.0->tables)
07:05:01 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
07:05:01 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
07:05:01 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
07:05:01 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (404 kB)
07:05:01 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
07:05:02 Using cached packaging-24.1-py3-none-any.whl (53 kB)
07:05:02 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
07:05:02 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (478 kB)
07:05:02 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB)
07:05:02 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
07:05:07 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
07:05:07 + pip install jinja2
07:05:08 Collecting jinja2
07:05:08 Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
07:05:08 Collecting MarkupSafe>=2.0 (from jinja2)
07:05:08 Using cached MarkupSafe-3.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
07:05:08 Using cached jinja2-3.1.4-py3-none-any.whl (133 kB)
07:05:08 Using cached MarkupSafe-3.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB)
07:05:08 Installing collected packages: MarkupSafe, jinja2
07:05:08 Successfully installed MarkupSafe-3.0.1 jinja2-3.1.4
07:05:08 + pip install omero-py
07:05:09 Collecting omero-py
07:05:09 Using cached omero_py-5.19.5-py3-none-any.whl.metadata (6.3 kB)
07:05:09 Collecting urllib3<2 (from omero-py)
07:05:09 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
07:05:09 Collecting appdirs (from omero-py)
07:05:09 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
07:05:09 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
07:05:09 Collecting numpy<2 (from omero-py)
07:05:09 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
07:05:09 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (11.0.0)
07:05:09 Collecting PyYAML (from omero-py)
07:05:09 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
07:05:09 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
07:05:09 Collecting requests (from omero-py)
07:05:09 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
07:05:09 Collecting portalocker (from omero-py)
07:05:09 Using cached portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB)
07:05:10 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
07:05:10 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
07:05:10 Collecting idna<4,>=2.5 (from requests->omero-py)
07:05:10 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
07:05:10 Collecting certifi>=2017.4.17 (from requests->omero-py)
07:05:10 Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
07:05:10 Using cached omero_py-5.19.5-py3-none-any.whl (2.8 MB)
07:05:10 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
07:05:10 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
07:05:11 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
07:05:11 Using cached portalocker-2.10.1-py3-none-any.whl (18 kB)
07:05:11 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
07:05:11 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
07:05:11 Using cached certifi-2024.8.30-py3-none-any.whl (167 kB)
07:05:11 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (144 kB)
07:05:11 Using cached idna-3.10-py3-none-any.whl (70 kB)
07:05:11 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, numpy, idna, charset-normalizer, certifi, requests, omero-py
07:05:11 Attempting uninstall: numpy
07:05:11 Found existing installation: numpy 2.0.2
07:05:11 Uninstalling numpy-2.0.2:
07:05:11 Successfully uninstalled numpy-2.0.2
07:05:16 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 certifi-2024.8.30 charset-normalizer-3.4.0 idna-3.10 numpy-1.26.4 omero-py-5.19.5 portalocker-2.10.1 requests-2.32.3 urllib3-1.26.20
07:05:16 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
07:05:16 Collecting omero-metadata
07:05:16 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-xutp0bza/omero-metadata_4dedf3917e0a4453a8e3d9c0e6b5f13f
07:05:16 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-xutp0bza/omero-metadata_4dedf3917e0a4453a8e3d9c0e6b5f13f
07:05:17 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 46439a38104e538279e15b4eeae17af5adffb49e
07:05:17 Installing build dependencies: started
07:05:20 Installing build dependencies: finished with status 'done'
07:05:20 Getting requirements to build wheel: started
07:05:20 Getting requirements to build wheel: finished with status 'done'
07:05:20 Preparing metadata (pyproject.toml): started
07:05:21 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:21 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.5)
07:05:21 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.2)
07:05:21 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.4)
07:05:21 Collecting pandas (from omero-metadata)
07:05:21 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
07:05:21 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
07:05:21 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
07:05:21 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
07:05:21 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
07:05:21 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (11.0.0)
07:05:21 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)
07:05:21 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
07:05:21 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.10.1)
07:05:21 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (3.0.1)
07:05:21 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
07:05:21 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
07:05:21 Collecting pytz>=2020.1 (from pandas->omero-metadata)
07:05:21 Using cached pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
07:05:21 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
07:05:21 Using cached tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
07:05:21 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)
07:05:21 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.0)
07:05:21 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)
07:05:21 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)
07:05:21 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
07:05:21 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
07:05:21 Using cached pytz-2024.2-py2.py3-none-any.whl (508 kB)
07:05:22 Using cached tzdata-2024.2-py2.py3-none-any.whl (346 kB)
07:05:22 Building wheels for collected packages: omero-metadata
07:05:22 Building wheel for omero-metadata (pyproject.toml): started
07:05:22 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
07:05:22 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39187 sha256=dbc44dbf7c53e06b9bc0700ccfbde4eda092d6637cf55c2a72840a515bd4be71
07:05:22 Stored in directory: /tmp/pip-ephem-wheel-cache-24i2_wx9/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
07:05:22 Successfully built omero-metadata
07:05:22 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
07:05:27 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2024.2 tzdata-2024.2
07:05:28 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
07:05:28 Collecting omero-cli-render
07:05:28 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-gbc6lzr1/omero-cli-render_cf56c66bae86421f820d2ecd27c830fd
07:05:28 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-gbc6lzr1/omero-cli-render_cf56c66bae86421f820d2ecd27c830fd
07:05:29 Running command git checkout -b merge_ci --track origin/merge_ci
07:05:29 Switched to a new branch 'merge_ci'
07:05:29 branch 'merge_ci' set up to track 'origin/merge_ci'.
07:05:29 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit d5b237d8a543edc295c95357c9b8157ff50051a4
07:05:29 Installing build dependencies: started
07:05:31 Installing build dependencies: finished with status 'done'
07:05:31 Getting requirements to build wheel: started
07:05:31 Getting requirements to build wheel: finished with status 'done'
07:05:31 Preparing metadata (pyproject.toml): started
07:05:31 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:31 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.2)
07:05:31 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.5)
07:05:31 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
07:05:31 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
07:05:31 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
07:05:31 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
07:05:31 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.0.0)
07:05:31 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)
07:05:31 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
07:05:31 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.10.1)
07:05:31 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.0)
07:05:31 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)
07:05:31 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)
07:05:31 Building wheels for collected packages: omero-cli-render
07:05:31 Building wheel for omero-cli-render (pyproject.toml): started
07:05:32 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
07:05:32 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=18030 sha256=a11b9d9b667116291d3f44d6acf85583390f243467e82ae975c409f7cd641248
07:05:32 Stored in directory: /tmp/pip-ephem-wheel-cache-39anr4xm/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
07:05:32 Successfully built omero-cli-render
07:05:32 Installing collected packages: omero-cli-render
07:05:32 Successfully installed omero-cli-render-0.8.2.dev0
07:05:32 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
07:05:32 Collecting omero-cli-duplicate
07:05:32 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-uzf7bj7i/omero-cli-duplicate_fcbd27a77cf64b14925dbfbdcd1c0391
07:05:32 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-uzf7bj7i/omero-cli-duplicate_fcbd27a77cf64b14925dbfbdcd1c0391
07:05:33 Running command git checkout -b merge_ci --track origin/merge_ci
07:05:33 Switched to a new branch 'merge_ci'
07:05:33 branch 'merge_ci' set up to track 'origin/merge_ci'.
07:05:33 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit acd5d6bbef73644c6785f476cd1294c819d9ff72
07:05:33 Installing build dependencies: started
07:05:35 Installing build dependencies: finished with status 'done'
07:05:35 Getting requirements to build wheel: started
07:05:35 Getting requirements to build wheel: finished with status 'done'
07:05:35 Preparing metadata (pyproject.toml): started
07:05:35 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:35 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.5)
07:05:35 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
07:05:35 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
07:05:35 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
07:05:35 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
07:05:35 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.0.0)
07:05:35 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
07:05:35 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)
07:05:35 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
07:05:35 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.10.1)
07:05:35 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.0)
07:05:35 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)
07:05:35 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)
07:05:35 Building wheels for collected packages: omero-cli-duplicate
07:05:35 Building wheel for omero-cli-duplicate (pyproject.toml): started
07:05:36 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
07:05:36 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11442 sha256=4f4a641889601a9337516d8655ecc5c9e92e83538aa456f81519df6f95357af1
07:05:36 Stored in directory: /tmp/pip-ephem-wheel-cache-r9m8rg8n/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
07:05:36 Successfully built omero-cli-duplicate
07:05:36 Installing collected packages: omero-cli-duplicate
07:05:36 Successfully installed omero-cli-duplicate-0.4.1.dev0
07:05:36 + pip install omero-certificates
07:05:36 Collecting omero-certificates
07:05:36 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
07:05:36 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.5)
07:05:36 Collecting distro==1.8.0 (from omero-certificates)
07:05:36 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
07:05:36 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
07:05:36 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
07:05:36 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
07:05:36 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
07:05:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (11.0.0)
07:05:37 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
07:05:37 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)
07:05:37 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
07:05:37 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.10.1)
07:05:37 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.0)
07:05:37 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)
07:05:37 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)
07:05:37 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
07:05:37 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
07:05:37 Installing collected packages: distro, omero-certificates
07:05:37 Successfully installed distro-1.8.0 omero-certificates-0.3.2
07:05:37 + for x in *.tar.gz
07:05:37 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
07:05:37 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
07:05:37 Installing build dependencies: started
07:05:39 Installing build dependencies: finished with status 'done'
07:05:39 Getting requirements to build wheel: started
07:05:39 Getting requirements to build wheel: finished with status 'done'
07:05:39 Preparing metadata (pyproject.toml): started
07:05:39 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:39 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.7.1.dev0) (5.19.5)
07:05:39 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
07:05:39 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
07:05:39 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
07:05:39 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.4)
07:05:39 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.0.0)
07:05:39 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
07:05:39 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)
07:05:39 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3)
07:05:39 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.10.1)
07:05:39 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.0)
07:05:39 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)
07:05:39 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)
07:05:39 Building wheels for collected packages: omero-dropbox
07:05:39 Building wheel for omero-dropbox (pyproject.toml): started
07:05:40 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
07:05:40 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49058 sha256=a3f7cc3f191dcf09070b04714936a03c9b076dd829e6945cf4b6bfdf00bd1ff8
07:05:40 Stored in directory: /home/omero/.cache/pip/wheels/eb/76/85/58476368b176f793423899407c96293c22f9c9edc28cf54079
07:05:40 Successfully built omero-dropbox
07:05:40 Installing collected packages: omero-dropbox
07:05:40 Successfully installed omero-dropbox-5.7.1.dev0
07:05:40 + for x in *.tar.gz
07:05:40 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
07:05:40 Processing ./omero_marshal-0.9.1.dev0.tar.gz
07:05:40 Installing build dependencies: started
07:05:43 Installing build dependencies: finished with status 'done'
07:05:43 Getting requirements to build wheel: started
07:05:43 Getting requirements to build wheel: finished with status 'done'
07:05:43 Preparing metadata (pyproject.toml): started
07:05:44 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:44 Building wheels for collected packages: omero_marshal
07:05:44 Building wheel for omero_marshal (pyproject.toml): started
07:05:44 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
07:05:44 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88031 sha256=b91bce35db5001731a3866116b4b3a586fdfd7cfcb0edc2316b603807ba1024e
07:05:44 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
07:05:44 Successfully built omero_marshal
07:05:44 Installing collected packages: omero_marshal
07:05:44 Successfully installed omero_marshal-0.9.1.dev0
07:05:44 + for x in *.tar.gz
07:05:44 + pip install -U omero_py-5.19.6.dev0.tar.gz
07:05:45 Processing ./omero_py-5.19.6.dev0.tar.gz
07:05:45 Installing build dependencies: started
07:05:47 Installing build dependencies: finished with status 'done'
07:05:47 Getting requirements to build wheel: started
07:05:47 Getting requirements to build wheel: finished with status 'done'
07:05:47 Preparing metadata (pyproject.toml): started
07:05:47 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:47 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.20)
07:05:47 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.4.4)
07:05:47 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.0.0)
07:05:47 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.4)
07:05:47 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (11.0.0)
07:05:47 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (6.0.2)
07:05:47 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)
07:05:47 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.32.3)
07:05:47 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.10.1)
07:05:47 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.4.0)
07:05:47 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.10)
07:05:47 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)
07:05:47 Building wheels for collected packages: omero-py
07:05:47 Building wheel for omero-py (pyproject.toml): started
07:05:48 Building wheel for omero-py (pyproject.toml): finished with status 'done'
07:05:48 Created wheel for omero-py: filename=omero_py-5.19.6.dev0-py3-none-any.whl size=2783246 sha256=a594fa4202883448f567bde99e1484c2ab577cd7de599f9ecaf21077698313d7
07:05:48 Stored in directory: /home/omero/.cache/pip/wheels/80/e5/37/a3ff2b54d2fa16a058bb39e8eb6b77b050109520fb9f16931d
07:05:48 Successfully built omero-py
07:05:48 Installing collected packages: omero-py
07:05:48 Attempting uninstall: omero-py
07:05:48 Found existing installation: omero-py 5.19.5
07:05:49 Uninstalling omero-py-5.19.5:
07:05:49 Successfully uninstalled omero-py-5.19.5
07:05:51 Successfully installed omero-py-5.19.6.dev0
07:05:51 + for x in *.tar.gz
07:05:51 + pip install -U omero_scripts-5.8.4.dev0.tar.gz
07:05:51 Processing ./omero_scripts-5.8.4.dev0.tar.gz
07:05:51 Installing build dependencies: started
07:05:53 Installing build dependencies: finished with status 'done'
07:05:53 Getting requirements to build wheel: started
07:05:53 Getting requirements to build wheel: finished with status 'done'
07:05:53 Preparing metadata (pyproject.toml): started
07:05:54 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:54 Building wheels for collected packages: omero-scripts
07:05:54 Building wheel for omero-scripts (pyproject.toml): started
07:05:54 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
07:05:54 Created wheel for omero-scripts: filename=omero_scripts-5.8.4.dev0-py3-none-any.whl size=116645 sha256=30139acaf37d907af9693fc00885c1335219a736c2d8e4d202182cbc3e3c65d4
07:05:54 Stored in directory: /home/omero/.cache/pip/wheels/50/80/aa/1e175e4f2a5b0a5343d01937a727d990d08c8e12000390ad9c
07:05:54 Successfully built omero-scripts
07:05:54 Installing collected packages: omero-scripts
07:05:54 Successfully installed omero-scripts-5.8.4.dev0
07:05:54 + for x in *.tar.gz
07:05:54 + pip install -U omero_web-5.27.3.dev0.tar.gz
07:05:55 Processing ./omero_web-5.27.3.dev0.tar.gz
07:05:55 Installing build dependencies: started
07:05:57 Installing build dependencies: finished with status 'done'
07:05:57 Getting requirements to build wheel: started
07:05:57 Getting requirements to build wheel: finished with status 'done'
07:05:57 Preparing metadata (pyproject.toml): started
07:05:57 Preparing metadata (pyproject.toml): finished with status 'done'
07:05:57 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)
07:05:57 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.27.3.dev0)
07:05:57 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
07:05:58 Collecting Django<4.3,>=4.2.3 (from omero-web==5.27.3.dev0)
07:05:58 Using cached Django-4.2.16-py3-none-any.whl.metadata (4.1 kB)
07:05:58 Collecting django-pipeline==2.1.0 (from omero-web==5.27.3.dev0)
07:05:58 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
07:05:58 Collecting django-cors-headers==3.7.0 (from omero-web==5.27.3.dev0)
07:05:58 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
07:05:58 Collecting django-csp (from omero-web==5.27.3.dev0)
07:05:58 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
07:05:58 Collecting whitenoise>=5.3.0 (from omero-web==5.27.3.dev0)
07:05:58 Using cached whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB)
07:05:58 Collecting gunicorn>=19.3 (from omero-web==5.27.3.dev0)
07:05:58 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
07:05:58 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)
07:05:58 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (11.0.0)
07:05:58 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2024.2)
07:05:58 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2.10.1)
07:05:58 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (24.1)
07:05:58 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
07:05:58 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
07:05:58 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
07:05:58 Using cached sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB)
07:05:58 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)
07:05:58 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)
07:05:58 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)
07:05:58 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)
07:05:58 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)
07:05:58 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)
07:05:58 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)
07:05:58 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
07:05:58 Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
07:05:58 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.4.0)
07:05:58 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)
07:05:58 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)
07:05:59 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
07:05:59 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
07:05:59 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
07:05:59 Using cached Django-4.2.16-py3-none-any.whl (8.0 MB)
07:05:59 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
07:05:59 Using cached whitenoise-6.7.0-py3-none-any.whl (19 kB)
07:05:59 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
07:05:59 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
07:05:59 Using cached sqlparse-0.5.1-py3-none-any.whl (44 kB)
07:05:59 Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
07:05:59 Building wheels for collected packages: omero-web
07:05:59 Building wheel for omero-web (pyproject.toml): started
07:06:00 Building wheel for omero-web (pyproject.toml): finished with status 'done'
07:06:00 Created wheel for omero-web: filename=omero_web-5.27.3.dev0-py3-none-any.whl size=2766670 sha256=0c381323001a1e1d8771deb4be2ec0ce340da13025c6fa8f5d0e3594f2750a6d
07:06:00 Stored in directory: /home/omero/.cache/pip/wheels/ae/1e/5f/7127f5403b089e5e8280a504b3d30303e78d1102aa8854c22b
07:06:00 Successfully built omero-web
07:06:00 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
07:06:03 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
07:06:03 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
07:06:04 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
07:06:04 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
07:06:04 --2024-10-18 07:06:04-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
07:06:04 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.111.133, 185.199.110.133, ...
07:06:04 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
07:06:04 HTTP request sent, awaiting response... 200 OK
07:06:04 Length: 99504 (97K) [text/plain]
07:06:04 Saving to: ‘Figure_To_Pdf.py’
07:06:04
07:06:04 0K .......... .......... .......... .......... .......... 51% 3.83M 0s
07:06:04 50K .......... .......... .......... .......... ....... 100% 3.83M=0.02s
07:06:04
07:06:04 2024-10-18 07:06:04 (3.83 MB/s) - ‘Figure_To_Pdf.py’ saved [99504/99504]
07:06:04
07:06:04 + chmod 755 Figure_To_Pdf.py
07:06:04 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
07:06:04 + omero config set omero.db.name OMERO-server
07:06:06 + omero config set omero.db.host pg
07:06:07 + omero config set omero.db.user postgres
07:06:08 + omero config set omero.data.dir /home/omero/omero-server-data
07:06:10 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
07:06:11 + omero config set omero.db.poolsize 25
07:06:13 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
07:06:14 + omero config set omero.security.trustStorePassword changeit
07:06:15 + omero config set omero.mail.config true
07:06:17 + omero config set omero.mail.from qa@openmicroscopy.org.uk
07:06:18 + omero config set omero.mail.host smtp.dundee.ac.uk
07:06:19 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
07:06:21 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
07:06:22 + omero certificates
07:06:24 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
07:06:24 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
07:06:24 + '[' false = true ']'
07:06:24 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
07:06:24 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
07:06:24 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG dbcommand => upgrade
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG dbhost => localhost
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG dbname => OMERO-server
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG dbpass => omero
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG dbuser => omero
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG rootpass => omero
07:06:24 2024-10-18 07:06:24,720 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
07:06:24 2024-10-18 07:06:24,720 [omego.extern] INFO Executing : omero version
07:06:25 OMERO.py version:
07:06:25 OMERO.server version:
07:06:25 5.6.3-513-ae72da0f50-ice36
07:06:25 5.19.6.dev0
07:06:26 2024-10-18 07:06:26,235 [omego.extern] INFO Completed [1.515 s]
07:06:26 2024-10-18 07:06:26,235 [omego.extern] DEBUG Using omero CLI from omero
07:06:26 2024-10-18 07:06:26,235 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
07:06:26 2024-10-18 07:06:26,235 [omego.extern] INFO Running [current environment]: omero config get --show-password
07:06:26 2024-10-18 07:06:26,236 [omego.extern] INFO Executing : omero config get --show-password
07:06:27 2024-10-18 07:06:27,698 [omego.extern] INFO Completed [1.462 s]
07:06:27 2024-10-18 07:06:27,698 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
07:06:27 2024-10-18 07:06:27,698 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
07:06:27 2024-10-18 07:06:27,808 [omego.extern] INFO Completed [0.110 s]
07:06:27 2024-10-18 07:06:27,809 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.4\n'
07:06:27 2024-10-18 07:06:27,809 [ omego.db] INFO psql version: psql (PostgreSQL) 16.4
07:06:27
07:06:27 2024-10-18 07:06:27,809 [omego.extern] INFO Running [current environment]: omero config get --show-password
07:06:27 2024-10-18 07:06:27,809 [omego.extern] INFO Executing : omero config get --show-password
07:06:29 2024-10-18 07:06:29,240 [omego.extern] INFO Completed [1.431 s]
07:06:29 2024-10-18 07:06:29,240 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
07:06:29 2024-10-18 07:06:29,240 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
07:06:29 2024-10-18 07:06:29,384 [omego.extern] INFO Completed [0.143 s]
07:06:29 2024-10-18 07:06:29,384 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.4") at port "5432".\n'
07:06:29 2024-10-18 07:06:29,384 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
07:06:29 2024-10-18 07:06:29,384 [omego.extern] INFO Running [current environment]: omero config get --show-password
07:06:29 2024-10-18 07:06:29,384 [omego.extern] INFO Executing : omero config get --show-password
07:06:30 2024-10-18 07:06:30,737 [omego.extern] INFO Completed [1.353 s]
07:06:30 2024-10-18 07:06:30,737 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
07:06:30 2024-10-18 07:06:30,737 [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
07:06:31 2024-10-18 07:06:31,934 [omego.extern] INFO Completed [1.197 s]
07:06:31 2024-10-18 07:06:31,934 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
07:06:31 2024-10-18 07:06:31,934 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
07:06:31 2024-10-18 07:06:31,936 [ omego.db] INFO Database is already at OMERO5.4__0
07:06:31 + export LANG=en_US.UTF-8
07:06:31 + LANG=en_US.UTF-8
07:06:31 + export LANGUAGE=en_US:en
07:06:31 + LANGUAGE=en_US:en
07:06:31 + export LC_ALL=en_US.UTF-8
07:06:31 + LC_ALL=en_US.UTF-8
07:06:31 + BUILD_ID=DONT_KILL_ME
07:06:31 + omero admin start
07:06:42 WARNING: lock files in /home/omero/omero-server-data
07:06:42 ----------------------------------------
07:06:42 /home/omero/omero-server-data/.omero/repository/7097ab62-1c9f-4ba2-a5e5-d5b1f868081e/.lock
07:06:42 ----------------------------------------
07:06:42
07:06:42 You may want to stop all server processes and remove
07:06:42 these files manually. Lock files can remain after an
07:06:42 abrupt server outage and are especially frequent on
07:06:42 remotely mounted filesystems like NFS.
07:06:42
07:06:42 No descriptor given. Using etc/grid/default.xml
07:06:55 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
07:06:55 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
07:06:55 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
07:06:55 Waiting on startup. Use CTRL-C to exit
07:06:56 + omero admin waitup
07:06:57 Waiting on startup. Use CTRL-C to exit
07:06:57 + omero admin diagnostics
07:06:59
07:06:59 ================================================================================
07:06:59 OMERO Diagnostics (admin)
07:06:59 ================================================================================
07:06:59
07:06:59 Commands: java -version 11.0.24 (/usr/bin/java)
07:06:59 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
07:06:59 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
07:06:59 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
07:06:59 Commands: psql --version 16.4 (/usr/bin/psql)
07:06:59 Commands: openssl version 3.0.71 (/usr/bin/openssl)
07:06:59
07:06:59 Component: OMERO.py 5.19.6.dev0
07:06:59 Component: OMERO.server 5.6.3-513-ae72da0f50-ice36
07:06:59
07:06:59 Server: icegridnode running
07:06:59 Server: Blitz-0 active (pid = 2582, enabled)
07:06:59 Server: Indexer-0 activating (enabled)
07:06:59 Server: OMERO.Glacier2 active (pid = 2630, enabled)
07:06:59 Server: OMERO.IceStorm active (pid = 2619, enabled)
07:06:59 Server: Processor-0 activating (enabled)
07:06:59 Server: Tables-0 activating (enabled)
07:06:59
07:06:59 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
07:06:59 Log files: Blitz-0.log 21.7 KB errors=0 warnings=1
07:06:59 Log files: DropBox.log n/a
07:06:59 Log files: FileServer.log n/a
07:06:59 Log files: Indexer-0.log 2.4 KB
07:06:59 Log files: MonitorServer.log n/a
07:06:59 Log files: Processor-0.log 592 B
07:06:59 Log files: Tables-0.log 841 B
07:06:59 Log files: TestDropBox.log n/a
07:06:59 Log files: master.err 180 B
07:06:59 Log files: master.out 30.1 KB
07:06:59 Log files: Total size 0.06 MB
07:06:59
07:06:59
07:06:59 Environment:OMERO_HOME=(unset)
07:06:59 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
07:06:59 Environment:OMERO_NODE=(unset)
07:06:59 Environment:OMERO_MASTER=(unset)
07:06:59 Environment:OMERO_USERDIR=(unset)
07:06:59 Environment:OMERO_TMPDIR=(unset)
07:06:59 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
07:06:59 Environment:PYTHONPATH=(unset)
07:06:59 Environment:ICE_HOME=/opt/ice-3.6.5
07:06:59 Environment:LD_LIBRARY_PATH=(unset)
07:06:59 Environment:DYLD_LIBRARY_PATH=(unset)
07:06:59
07:06:59 OMERO SSL port:4064
07:06:59 OMERO TCP port:4063
07:06:59 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
07:06:59 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
07:06:59
07:06:59 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
07:06:59 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
07:06:59 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
07:06:59 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
07:06:59
07:06:59 Jar: lib/server/formats-api.jar Bio-Formats API 8.0.0-SNAPSHOT 18 October 2024 2c119e22073df2e269e72a0d5f39bc862268ca69
07:06:59 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.0.0-SNAPSHOT 18 October 2024 2c119e22073df2e269e72a0d5f39bc862268ca69
07:06:59 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.0.0-SNAPSHOT 18 October 2024 2c119e22073df2e269e72a0d5f39bc862268ca69
07:06:59 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.4-SNAPSHOT 18 October 2024 1bf7027180f3fef832719d38b0da9ae42172559f
07:06:59 Jar: lib/server/ome-common.jar OME Common Java 6.0.25-SNAPSHOT 18 October 2024 1bf7027180f3fef832719d38b0da9ae42172559f
07:06:59 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 18 October 2024 1bf7027180f3fef832719d38b0da9ae42172559f
07:06:59 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4-SNAPSHOT 18 October 2024 1bf7027180f3fef832719d38b0da9ae42172559f
07:06:59 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 18 October 2024 1bf7027180f3fef832719d38b0da9ae42172559f
07:06:59 Jar: lib/server/ome-xml.jar OME XML library 6.3.7-SNAPSHOT 18 October 2024 1bf7027180f3fef832719d38b0da9ae42172559f
07:06:59 Jar: lib/server/omero-blitz.jar jar 5.7.5-SNAPSHOT
07:06:59 Jar: lib/server/omero-common.jar jar 5.6.8-SNAPSHOT
07:06:59 Jar: lib/server/omero-gateway.jar jar 5.9.4-SNAPSHOT
07:06:59 Jar: lib/server/omero-model.jar jar 5.6.16-SNAPSHOT
07:06:59 Jar: lib/server/omero-renderer.jar jar 5.5.18-SNAPSHOT
07:06:59 Jar: lib/server/omero-romio.jar jar 5.7.8-SNAPSHOT
07:06:59 Jar: lib/server/omero-server.jar jar 5.6.13-SNAPSHOT
07:06:59 + deactivate
07:06:59 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
07:06:59 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
07:06:59 + export PATH
07:06:59 + unset _OLD_VIRTUAL_PATH
07:06:59 + '[' -n '' ']'
07:06:59 + '[' -n /bin/bash -o -n '' ']'
07:06:59 + hash -r
07:06:59 + '[' -n '' ']'
07:06:59 + unset VIRTUAL_ENV
07:06:59 + '[' '!' '' = nondestructive ']'
07:06:59 + unset -f deactivate
07:07:00 Finished: SUCCESS
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