00:47:27 Started by upstream project "Trigger" build number 259
00:47:27 originally caused by:
00:47:27 Started by timer
00:47:27 Running as SYSTEM
00:47:27 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
00:47:27 [OMERO-server] $ /bin/bash -xe /tmp/jenkins16514303281551853800.sh
00:47:27 + source /home/settings.env
00:47:27 ++ OMERO_DB_HOST=pg
00:47:27 ++ OMERO_DB_USER=postgres
00:47:27 ++ OMERO_DB_PASS=
00:47:27 ++ OMERO_ROOT_PASS=omero
00:47:27 ++ OMERO_DATA_DIR=/OMERO
00:47:27 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:47:27 + OMERO_DB_NAME=OMERO-server
00:47:27 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:47:27 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:27 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:47:27 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:47:27 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
00:47:27 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:47:28 ++ deactivate nondestructive
00:47:28 ++ '[' -n '' ']'
00:47:28 ++ '[' -n '' ']'
00:47:28 ++ '[' -n /bin/bash -o -n '' ']'
00:47:28 ++ hash -r
00:47:28 ++ '[' -n '' ']'
00:47:28 ++ unset VIRTUAL_ENV
00:47:28 ++ '[' '!' nondestructive = nondestructive ']'
00:47:28 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:47:28 ++ export VIRTUAL_ENV
00:47:28 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:47:28 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:47:28 ++ export PATH
00:47:28 ++ '[' -n '' ']'
00:47:28 ++ '[' -z '' ']'
00:47:28 ++ _OLD_VIRTUAL_PS1=
00:47:28 ++ PS1='(.venv3) '
00:47:28 ++ export PS1
00:47:28 ++ '[' -n /bin/bash -o -n '' ']'
00:47:28 ++ hash -r
00:47:28 + omero admin stop
00:47:35 Waiting on shutdown. Use CTRL-C to exit
00:47:35 .+ sleep 5
00:47:50 + deactivate
00:47:50 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:47:50 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:47:50 + export PATH
00:47:50 + unset _OLD_VIRTUAL_PATH
00:47:50 + '[' -n '' ']'
00:47:50 + '[' -n /bin/bash -o -n '' ']'
00:47:50 + hash -r
00:47:50 + '[' -n '' ']'
00:47:50 + unset VIRTUAL_ENV
00:47:50 + '[' '!' '' = nondestructive ']'
00:47:50 + unset -f deactivate
00:47:50 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:47:51 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3
00:47:55 + '[' false = true ']'
00:47:55 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:47:55 Skipping PURGE_DATA:CleanDbAndRepo
00:47:55 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.7.5-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.19.6.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.8.4.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.27.3.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:48:04 Copied 1 artifact from "OMERO-build" build number 215
00:48:07 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 212
00:48:07 Copied 2 artifacts from "OMERO-build-build" build number 223
00:48:07 [OMERO-server] $ /bin/bash -xe /tmp/jenkins3678074831693771591.sh
00:48:07 + source /home/settings.env
00:48:07 ++ OMERO_DB_HOST=pg
00:48:07 ++ OMERO_DB_USER=postgres
00:48:07 ++ OMERO_DB_PASS=
00:48:07 ++ OMERO_ROOT_PASS=omero
00:48:07 ++ OMERO_DATA_DIR=/OMERO
00:48:07 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:48:07 + OMERO_DB_NAME=OMERO-server
00:48:07 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:48:07 + mkdir -p /home/omero/omero-server-data
00:48:07 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:48:07 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:07 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:48:07 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:07 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:48:07 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:07 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:48:07 ++ ls OMERO.server-5.6.3-513-edc8e2180c-ice36.zip
00:48:07 + ZIP=OMERO.server-5.6.3-513-edc8e2180c-ice36.zip
00:48:07 + '[' '!' -z '' ']'
00:48:07 + DIST=OMERO.server-5.6.3-513-edc8e2180c-ice36
00:48:07 + unzip OMERO.server-5.6.3-513-edc8e2180c-ice36.zip
00:48:07 Archive: OMERO.server-5.6.3-513-edc8e2180c-ice36.zip
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/blitz/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/grid/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/profiles/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/error/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/grid/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/luts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/luts/janelia/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/luts/ncsa_paledit/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/luts/wcif/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/analysis_scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/annotation_scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/export_scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/figure_scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/import_scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/scripts/omero/util_scripts/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/server/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/share/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/share/licenses/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/misc/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__1/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__10/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__11/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__2/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__3/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__4/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__5/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__6/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__7/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__8/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3A__9/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3__4/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3__5/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3__6/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO3__7/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO4.1__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO4.2__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO4.2__0/t/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO4.3__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO4.4__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO4__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.0__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.1__1/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.2__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.3__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.4DEV__1/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.4DEV__2/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.4DEV__3/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.4__0/
00:48:07 creating: OMERO.server-5.6.3-513-edc8e2180c-ice36/var/
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/LICENSE.txt
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/backup.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/blitz/mail-senders.example
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/blitz/mail-server.example
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/build.properties
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/env.bat
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/env.sh
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/hibernate.properties
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/ice.config
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/logback-cli.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/logback-indexing-cli.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/logback-indexing.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/logback.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/mime.types
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/node1.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/node2.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/omero.properties
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/profiles/psql
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/rollover.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/Windows.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/error/maintainance.html
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/grid/README
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/grid/default.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/grid/templates.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/grid/windefault.xml
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/ice.config
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/internal.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/master.cfg
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/templates/robot.template
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/etc/testdropbox.config
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/history.rst
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/OMEZarrReader.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/activation.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/aggdesigner-algorithm.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/aircompressor.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/annotations.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/antlr.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/aopalliance.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/avatica-core.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/avatica-metrics.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/aws-java-sdk-core.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/aws-java-sdk-kms.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/aws-java-sdk-s3.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/base.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-all.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-anim.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-awt-util.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-bridge.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-codec.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-constants.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-css.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-dom.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-ext.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-extension.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-gui-util.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-gvt.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-i18n.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-parser.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-rasterizer-ext.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-rasterizer.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-script.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-slideshow.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-squiggle-ext.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-squiggle.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-svg-dom.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-svgbrowser.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-svggen.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-svgpp.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-svgrasterizer.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-swing.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-transcoder.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-ttf2svg.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-util.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/batik-xml.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/btm.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/bufr.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/c3p0.jar
00:48:07 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/lib/client/calcite-core.jar
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00:48:10 inflating: OMERO.server-5.6.3-513-edc8e2180c-ice36/sql/psql/OMERO5.4__0/views.sql
00:48:10 + rm -f OMERO.server-5.6.3-513-edc8e2180c-ice36.zip
00:48:10 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-513-edc8e2180c-ice36 /home/omero/workspace/OMERO-server/OMERO.server
00:48:10 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:48:10 ++ deactivate nondestructive
00:48:10 ++ '[' -n '' ']'
00:48:10 ++ '[' -n '' ']'
00:48:10 ++ '[' -n /bin/bash -o -n '' ']'
00:48:10 ++ hash -r
00:48:10 ++ '[' -n '' ']'
00:48:10 ++ unset VIRTUAL_ENV
00:48:10 ++ '[' '!' nondestructive = nondestructive ']'
00:48:10 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:48:10 ++ export VIRTUAL_ENV
00:48:10 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:10 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:48:10 ++ export PATH
00:48:10 ++ '[' -n '' ']'
00:48:10 ++ '[' -z '' ']'
00:48:10 ++ _OLD_VIRTUAL_PS1=
00:48:10 ++ PS1='(.venv3) '
00:48:10 ++ export PS1
00:48:10 ++ '[' -n /bin/bash -o -n '' ']'
00:48:10 ++ hash -r
00:48:10 + pip install https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl
00:48:10 Collecting zeroc-ice==3.6.5
00:48:11 Downloading https://github.com/glencoesoftware/zeroc-ice-py-rhel9-x86_64/releases/download/20230830/zeroc_ice-3.6.5-cp39-cp39-linux_x86_64.whl (31.3 MB)
00:48:12 Installing collected packages: zeroc-ice
00:48:13 Successfully installed zeroc-ice-3.6.5
00:48:13 + pip install -U pip future
00:48:13 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3)
00:48:14 Collecting pip
00:48:14 Using cached pip-24.2-py3-none-any.whl (1.8 MB)
00:48:14 Collecting future
00:48:14 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:48:14 Installing collected packages: pip, future
00:48:14 Attempting uninstall: pip
00:48:14 Found existing installation: pip 21.2.3
00:48:14 Uninstalling pip-21.2.3:
00:48:14 Successfully uninstalled pip-21.2.3
00:48:15 Successfully installed future-1.0.0 pip-24.2
00:48:15 + pip install markdown
00:48:16 Collecting markdown
00:48:16 Using cached Markdown-3.7-py3-none-any.whl.metadata (7.0 kB)
00:48:16 Collecting importlib-metadata>=4.4 (from markdown)
00:48:16 Using cached importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB)
00:48:16 Collecting zipp>=3.20 (from importlib-metadata>=4.4->markdown)
00:48:16 Using cached zipp-3.20.2-py3-none-any.whl.metadata (3.7 kB)
00:48:16 Using cached Markdown-3.7-py3-none-any.whl (106 kB)
00:48:16 Using cached importlib_metadata-8.5.0-py3-none-any.whl (26 kB)
00:48:16 Using cached zipp-3.20.2-py3-none-any.whl (9.2 kB)
00:48:16 Installing collected packages: zipp, importlib-metadata, markdown
00:48:16 Successfully installed importlib-metadata-8.5.0 markdown-3.7 zipp-3.20.2
00:48:16 + pip install reportlab
00:48:17 Collecting reportlab
00:48:17 Using cached reportlab-4.2.5-py3-none-any.whl.metadata (1.5 kB)
00:48:17 Collecting pillow>=9.0.0 (from reportlab)
00:48:17 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.1 kB)
00:48:17 Collecting chardet (from reportlab)
00:48:18 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB)
00:48:18 Using cached reportlab-4.2.5-py3-none-any.whl (1.9 MB)
00:48:18 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.4 MB)
00:48:18 Using cached chardet-5.2.0-py3-none-any.whl (199 kB)
00:48:18 Installing collected packages: pillow, chardet, reportlab
00:48:20 Successfully installed chardet-5.2.0 pillow-11.0.0 reportlab-4.2.5
00:48:20 + pip install omego
00:48:20 Collecting omego
00:48:20 Using cached omego-0.7.0-py3-none-any.whl
00:48:20 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0)
00:48:20 Collecting yaclifw>=0.1.1 (from omego)
00:48:20 Using cached yaclifw-0.2.0-py3-none-any.whl
00:48:20 Collecting six (from yaclifw>=0.1.1->omego)
00:48:20 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
00:48:20 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
00:48:20 Installing collected packages: six, yaclifw, omego
00:48:20 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0
00:48:21 + pip install tables
00:48:21 Collecting tables
00:48:21 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB)
00:48:21 Collecting numpy>=1.19.0 (from tables)
00:48:21 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
00:48:21 Collecting numexpr>=2.6.2 (from tables)
00:48:21 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.2 kB)
00:48:21 Collecting packaging (from tables)
00:48:21 Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB)
00:48:21 Collecting py-cpuinfo (from tables)
00:48:21 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:48:22 Collecting blosc2>=2.3.0 (from tables)
00:48:22 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB)
00:48:22 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables)
00:48:22 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB)
00:48:22 Collecting msgpack (from blosc2>=2.3.0->tables)
00:48:22 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB)
00:48:22 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB)
00:48:22 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB)
00:48:22 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (404 kB)
00:48:22 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB)
00:48:23 Using cached packaging-24.1-py3-none-any.whl (53 kB)
00:48:23 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:48:23 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (478 kB)
00:48:23 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB)
00:48:23 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables
00:48:26 Successfully installed blosc2-2.5.1 msgpack-1.1.0 ndindex-1.9.2 numexpr-2.10.1 numpy-2.0.2 packaging-24.1 py-cpuinfo-9.0.0 tables-3.9.2
00:48:26 + pip install jinja2
00:48:27 Collecting jinja2
00:48:27 Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)
00:48:27 Collecting MarkupSafe>=2.0 (from jinja2)
00:48:27 Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
00:48:27 Using cached jinja2-3.1.4-py3-none-any.whl (133 kB)
00:48:27 Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB)
00:48:27 Installing collected packages: MarkupSafe, jinja2
00:48:27 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.4
00:48:27 + pip install omero-py
00:48:28 Collecting omero-py
00:48:28 Using cached omero_py-5.19.5-py3-none-any.whl.metadata (6.3 kB)
00:48:28 Collecting urllib3<2 (from omero-py)
00:48:28 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB)
00:48:28 Collecting appdirs (from omero-py)
00:48:28 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:48:28 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0)
00:48:28 Collecting numpy<2 (from omero-py)
00:48:28 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
00:48:28 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (11.0.0)
00:48:28 Collecting PyYAML (from omero-py)
00:48:28 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
00:48:28 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5)
00:48:29 Collecting requests (from omero-py)
00:48:29 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
00:48:29 Collecting portalocker (from omero-py)
00:48:29 Using cached portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB)
00:48:29 Collecting charset-normalizer<4,>=2 (from requests->omero-py)
00:48:29 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB)
00:48:29 Collecting idna<4,>=2.5 (from requests->omero-py)
00:48:29 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
00:48:29 Collecting certifi>=2017.4.17 (from requests->omero-py)
00:48:29 Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)
00:48:29 Using cached omero_py-5.19.5-py3-none-any.whl (2.8 MB)
00:48:29 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
00:48:29 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB)
00:48:29 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:48:29 Using cached portalocker-2.10.1-py3-none-any.whl (18 kB)
00:48:29 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB)
00:48:29 Using cached requests-2.32.3-py3-none-any.whl (64 kB)
00:48:29 Using cached certifi-2024.8.30-py3-none-any.whl (167 kB)
00:48:29 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (144 kB)
00:48:29 Using cached idna-3.10-py3-none-any.whl (70 kB)
00:48:29 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, numpy, idna, charset-normalizer, certifi, requests, omero-py
00:48:29 Attempting uninstall: numpy
00:48:29 Found existing installation: numpy 2.0.2
00:48:29 Uninstalling numpy-2.0.2:
00:48:29 Successfully uninstalled numpy-2.0.2
00:48:34 Successfully installed PyYAML-6.0.2 appdirs-1.4.4 certifi-2024.8.30 charset-normalizer-3.4.0 idna-3.10 numpy-1.26.4 omero-py-5.19.5 portalocker-2.10.1 requests-2.32.3 urllib3-1.26.20
00:48:34 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:48:34 Collecting omero-metadata
00:48:34 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-cifictpt/omero-metadata_4d7f454be1634b8e92c7fdbc2659a48e
00:48:34 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-cifictpt/omero-metadata_4d7f454be1634b8e92c7fdbc2659a48e
00:48:37 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit a9b779afcdfc90cec93c276f769af552ee12fe81
00:48:37 Installing build dependencies: started
00:48:39 Installing build dependencies: finished with status 'done'
00:48:39 Getting requirements to build wheel: started
00:48:39 Getting requirements to build wheel: finished with status 'done'
00:48:39 Preparing metadata (pyproject.toml): started
00:48:40 Preparing metadata (pyproject.toml): finished with status 'done'
00:48:40 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.5)
00:48:40 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.2)
00:48:40 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.4)
00:48:40 Collecting pandas (from omero-metadata)
00:48:40 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB)
00:48:40 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20)
00:48:40 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:48:40 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:48:40 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4)
00:48:40 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (11.0.0)
00:48:40 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
00:48:40 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3)
00:48:40 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.10.1)
00:48:40 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (3.0.2)
00:48:40 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata)
00:48:40 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:48:40 Collecting pytz>=2020.1 (from pandas->omero-metadata)
00:48:40 Using cached pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB)
00:48:42 Collecting tzdata>=2022.7 (from pandas->omero-metadata)
00:48:42 Using cached tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB)
00:48:42 Requirement already satisfied: six>=1.5 in ./.venv3/lib/python3.9/site-packages (from python-dateutil>=2.8.2->pandas->omero-metadata) (1.16.0)
00:48:42 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.4.0)
00:48:42 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.10)
00:48:42 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2024.8.30)
00:48:42 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB)
00:48:42 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:48:42 Using cached pytz-2024.2-py2.py3-none-any.whl (508 kB)
00:48:42 Using cached tzdata-2024.2-py2.py3-none-any.whl (346 kB)
00:48:43 Building wheels for collected packages: omero-metadata
00:48:43 Building wheel for omero-metadata (pyproject.toml): started
00:48:43 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:48:43 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39187 sha256=d4cf8770011feeeee1477499be39201dc16ecb2fec7144ca040ba705ef6c8d0f
00:48:43 Stored in directory: /tmp/pip-ephem-wheel-cache-lgm2rrxr/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d
00:48:43 Successfully built omero-metadata
00:48:43 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
00:48:48 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2024.2 tzdata-2024.2
00:48:48 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:48:49 Collecting omero-cli-render
00:48:49 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-_teqi5e5/omero-cli-render_b3b063c928a64f638b84a90c551f5afe
00:48:49 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-_teqi5e5/omero-cli-render_b3b063c928a64f638b84a90c551f5afe
00:48:50 Running command git checkout -b merge_ci --track origin/merge_ci
00:48:50 Switched to a new branch 'merge_ci'
00:48:50 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:48:50 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit b2377b7aff1240d68e57399ebe177c8c2298fa46
00:48:50 Installing build dependencies: started
00:48:52 Installing build dependencies: finished with status 'done'
00:48:52 Getting requirements to build wheel: started
00:48:52 Getting requirements to build wheel: finished with status 'done'
00:48:52 Preparing metadata (pyproject.toml): started
00:48:52 Preparing metadata (pyproject.toml): finished with status 'done'
00:48:52 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.2)
00:48:52 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.5)
00:48:52 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20)
00:48:52 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:48:52 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:48:52 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4)
00:48:52 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (11.0.0)
00:48:52 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
00:48:52 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3)
00:48:52 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.10.1)
00:48:52 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.4.0)
00:48:52 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.10)
00:48:52 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2024.8.30)
00:48:52 Building wheels for collected packages: omero-cli-render
00:48:52 Building wheel for omero-cli-render (pyproject.toml): started
00:48:52 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:48:52 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=18030 sha256=15570c86eade08fc0af7f68c946c8aff897cc919a1c895eb5097c7488c1bf0d8
00:48:52 Stored in directory: /tmp/pip-ephem-wheel-cache-dc387xdb/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994
00:48:52 Successfully built omero-cli-render
00:48:52 Installing collected packages: omero-cli-render
00:48:53 Successfully installed omero-cli-render-0.8.2.dev0
00:48:53 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:48:53 Collecting omero-cli-duplicate
00:48:53 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-lt1svzjm/omero-cli-duplicate_318a642f48934bc3adb162bf6a8230b3
00:48:53 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-lt1svzjm/omero-cli-duplicate_318a642f48934bc3adb162bf6a8230b3
00:48:54 Running command git checkout -b merge_ci --track origin/merge_ci
00:48:54 Switched to a new branch 'merge_ci'
00:48:54 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:48:54 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 603f441ce6063845fc04d4bd1d2a05a117e8c1f9
00:48:54 Installing build dependencies: started
00:48:57 Installing build dependencies: finished with status 'done'
00:48:57 Getting requirements to build wheel: started
00:48:57 Getting requirements to build wheel: finished with status 'done'
00:48:57 Preparing metadata (pyproject.toml): started
00:48:57 Preparing metadata (pyproject.toml): finished with status 'done'
00:48:57 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.5)
00:48:57 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20)
00:48:57 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:48:57 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:48:57 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4)
00:48:57 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (11.0.0)
00:48:57 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2)
00:48:57 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (3.6.5)
00:48:57 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3)
00:48:57 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.10.1)
00:48:57 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.4.0)
00:48:57 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (3.10)
00:48:57 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.8->omero-cli-duplicate) (2024.8.30)
00:48:57 Building wheels for collected packages: omero-cli-duplicate
00:48:57 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:48:57 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:48:57 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11442 sha256=de99dc506659d663e3abc4a2821df49b1306f688d8209cd4da6add254ec1082c
00:48:57 Stored in directory: /tmp/pip-ephem-wheel-cache-kgn2e61v/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84
00:48:57 Successfully built omero-cli-duplicate
00:48:58 Installing collected packages: omero-cli-duplicate
00:48:58 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:48:58 + pip install omero-certificates
00:48:58 Collecting omero-certificates
00:48:58 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB)
00:48:58 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.5)
00:48:58 Collecting distro==1.8.0 (from omero-certificates)
00:48:58 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB)
00:48:59 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20)
00:48:59 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:48:59 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:48:59 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4)
00:48:59 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (11.0.0)
00:48:59 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2)
00:48:59 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
00:48:59 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3)
00:48:59 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.10.1)
00:48:59 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.4.0)
00:48:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.10)
00:48:59 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2024.8.30)
00:48:59 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB)
00:48:59 Using cached distro-1.8.0-py3-none-any.whl (20 kB)
00:48:59 Installing collected packages: distro, omero-certificates
00:48:59 Successfully installed distro-1.8.0 omero-certificates-0.3.2
00:48:59 + for x in *.tar.gz
00:48:59 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:48:59 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:48:59 Installing build dependencies: started
00:49:01 Installing build dependencies: finished with status 'done'
00:49:01 Getting requirements to build wheel: started
00:49:01 Getting requirements to build wheel: finished with status 'done'
00:49:01 Preparing metadata (pyproject.toml): started
00:49:02 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:02 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.7.1.dev0) (5.19.5)
00:49:02 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20)
00:49:02 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:49:02 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:49:02 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.4)
00:49:02 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (11.0.0)
00:49:02 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2)
00:49:02 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5)
00:49:02 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3)
00:49:02 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.10.1)
00:49:02 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.4.0)
00:49:02 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.10)
00:49:02 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2024.8.30)
00:49:02 Building wheels for collected packages: omero-dropbox
00:49:02 Building wheel for omero-dropbox (pyproject.toml): started
00:49:02 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:49:02 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49058 sha256=43f7c61d832de20f8d4fa240b0db4e1dc18f59fa16358a978c1eb349f660e391
00:49:02 Stored in directory: /home/omero/.cache/pip/wheels/eb/76/85/58476368b176f793423899407c96293c22f9c9edc28cf54079
00:49:02 Successfully built omero-dropbox
00:49:02 Installing collected packages: omero-dropbox
00:49:02 Successfully installed omero-dropbox-5.7.1.dev0
00:49:02 + for x in *.tar.gz
00:49:02 + pip install -U omero_marshal-0.9.1.dev0.tar.gz
00:49:03 Processing ./omero_marshal-0.9.1.dev0.tar.gz
00:49:03 Installing build dependencies: started
00:49:07 Installing build dependencies: finished with status 'done'
00:49:07 Getting requirements to build wheel: started
00:49:08 Getting requirements to build wheel: finished with status 'done'
00:49:08 Preparing metadata (pyproject.toml): started
00:49:08 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:08 Building wheels for collected packages: omero_marshal
00:49:08 Building wheel for omero_marshal (pyproject.toml): started
00:49:08 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:49:08 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88031 sha256=3ab1b528b5dca80bc6c566811154dcab924fb7eddcc9ea47d5ec11a761429def
00:49:08 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f
00:49:08 Successfully built omero_marshal
00:49:08 Installing collected packages: omero_marshal
00:49:09 Successfully installed omero_marshal-0.9.1.dev0
00:49:09 + for x in *.tar.gz
00:49:09 + pip install -U omero_py-5.19.6.dev0.tar.gz
00:49:09 Processing ./omero_py-5.19.6.dev0.tar.gz
00:49:10 Installing build dependencies: started
00:49:11 Installing build dependencies: finished with status 'done'
00:49:11 Getting requirements to build wheel: started
00:49:12 Getting requirements to build wheel: finished with status 'done'
00:49:12 Preparing metadata (pyproject.toml): started
00:49:12 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:12 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.20)
00:49:12 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.4.4)
00:49:12 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.0.0)
00:49:12 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.4)
00:49:12 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (11.0.0)
00:49:12 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (6.0.2)
00:49:12 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (3.6.5)
00:49:12 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.32.3)
00:49:12 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.10.1)
00:49:12 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.4.0)
00:49:12 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.10)
00:49:12 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (2024.8.30)
00:49:12 Building wheels for collected packages: omero-py
00:49:12 Building wheel for omero-py (pyproject.toml): started
00:49:13 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:49:13 Created wheel for omero-py: filename=omero_py-5.19.6.dev0-py3-none-any.whl size=2783246 sha256=0054ea608db15d1d55cd010c6bd673d242919d636724456e18f0e2340cc93c80
00:49:13 Stored in directory: /home/omero/.cache/pip/wheels/80/e5/37/a3ff2b54d2fa16a058bb39e8eb6b77b050109520fb9f16931d
00:49:13 Successfully built omero-py
00:49:13 Installing collected packages: omero-py
00:49:13 Attempting uninstall: omero-py
00:49:13 Found existing installation: omero-py 5.19.5
00:49:13 Uninstalling omero-py-5.19.5:
00:49:14 Successfully uninstalled omero-py-5.19.5
00:49:16 Successfully installed omero-py-5.19.6.dev0
00:49:16 + for x in *.tar.gz
00:49:16 + pip install -U omero_scripts-5.8.4.dev0.tar.gz
00:49:16 Processing ./omero_scripts-5.8.4.dev0.tar.gz
00:49:16 Installing build dependencies: started
00:49:18 Installing build dependencies: finished with status 'done'
00:49:18 Getting requirements to build wheel: started
00:49:18 Getting requirements to build wheel: finished with status 'done'
00:49:18 Preparing metadata (pyproject.toml): started
00:49:19 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:19 Building wheels for collected packages: omero-scripts
00:49:19 Building wheel for omero-scripts (pyproject.toml): started
00:49:19 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:49:19 Created wheel for omero-scripts: filename=omero_scripts-5.8.4.dev0-py3-none-any.whl size=116645 sha256=2be81d4be198004da817561eec0a852cdd089fa23ff69baf78cb94ca96851f4d
00:49:19 Stored in directory: /home/omero/.cache/pip/wheels/50/80/aa/1e175e4f2a5b0a5343d01937a727d990d08c8e12000390ad9c
00:49:19 Successfully built omero-scripts
00:49:19 Installing collected packages: omero-scripts
00:49:19 Successfully installed omero-scripts-5.8.4.dev0
00:49:19 + for x in *.tar.gz
00:49:19 + pip install -U omero_web-5.27.3.dev0.tar.gz
00:49:20 Processing ./omero_web-5.27.3.dev0.tar.gz
00:49:20 Installing build dependencies: started
00:49:22 Installing build dependencies: finished with status 'done'
00:49:22 Getting requirements to build wheel: started
00:49:22 Getting requirements to build wheel: finished with status 'done'
00:49:22 Preparing metadata (pyproject.toml): started
00:49:23 Preparing metadata (pyproject.toml): finished with status 'done'
00:49:23 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (5.19.6.dev0)
00:49:23 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.27.3.dev0)
00:49:23 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB)
00:49:23 Collecting Django<4.3,>=4.2.3 (from omero-web==5.27.3.dev0)
00:49:23 Using cached Django-4.2.16-py3-none-any.whl.metadata (4.1 kB)
00:49:23 Collecting django-pipeline==2.1.0 (from omero-web==5.27.3.dev0)
00:49:23 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB)
00:49:23 Collecting django-cors-headers==3.7.0 (from omero-web==5.27.3.dev0)
00:49:23 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:49:23 Collecting django-csp (from omero-web==5.27.3.dev0)
00:49:23 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB)
00:49:23 Collecting whitenoise>=5.3.0 (from omero-web==5.27.3.dev0)
00:49:23 Using cached whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB)
00:49:23 Collecting gunicorn>=19.3 (from omero-web==5.27.3.dev0)
00:49:23 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB)
00:49:23 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (0.9.1.dev0)
00:49:23 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (11.0.0)
00:49:23 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2024.2)
00:49:23 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2.10.1)
00:49:23 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (24.1)
00:49:23 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
00:49:23 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB)
00:49:23 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
00:49:23 Using cached sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB)
00:49:23 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.26.20)
00:49:23 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.4.4)
00:49:23 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.0.0)
00:49:23 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (1.26.4)
00:49:23 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (6.0.2)
00:49:23 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.6.5)
00:49:23 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.19.0->omero-web==5.27.3.dev0) (2.32.3)
00:49:23 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.27.3.dev0)
00:49:23 Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
00:49:23 Requirement already satisfied: charset-normalizer<4,>=2 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.4.0)
00:49:23 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (3.10)
00:49:23 Requirement already satisfied: certifi>=2017.4.17 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py>=5.19.0->omero-web==5.27.3.dev0) (2024.8.30)
00:49:23 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:49:23 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB)
00:49:23 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB)
00:49:23 Using cached Django-4.2.16-py3-none-any.whl (8.0 MB)
00:49:23 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB)
00:49:23 Using cached whitenoise-6.7.0-py3-none-any.whl (19 kB)
00:49:23 Using cached django_csp-3.8-py3-none-any.whl (17 kB)
00:49:23 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB)
00:49:23 Using cached sqlparse-0.5.1-py3-none-any.whl (44 kB)
00:49:23 Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
00:49:23 Building wheels for collected packages: omero-web
00:49:23 Building wheel for omero-web (pyproject.toml): started
00:49:25 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:49:25 Created wheel for omero-web: filename=omero_web-5.27.3.dev0-py3-none-any.whl size=2766670 sha256=86eb3968d03dd7429640c0f4a25c5eddeed4d16b9b450a5c448da795731e5a51
00:49:25 Stored in directory: /home/omero/.cache/pip/wheels/ae/1e/5f/7127f5403b089e5e8280a504b3d30303e78d1102aa8854c22b
00:49:25 Successfully built omero-web
00:49:25 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web
00:49:28 Successfully installed Django-4.2.16 asgiref-3.8.1 concurrent-log-handler-0.9.25 django-cors-headers-3.7.0 django-csp-3.8 django-pipeline-2.1.0 gunicorn-23.0.0 omero-web-5.27.3.dev0 sqlparse-0.5.1 typing-extensions-4.12.2 whitenoise-6.7.0
00:49:28 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:49:29 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:49:29 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:49:29 --2024-10-25 00:49:29-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py
00:49:30 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.110.133, ...
00:49:30 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
00:49:30 HTTP request sent, awaiting response... 200 OK
00:49:30 Length: 101739 (99K) [text/plain]
00:49:30 Saving to: ‘Figure_To_Pdf.py’
00:49:30
00:49:30 0K .......... .......... .......... .......... .......... 50% 3.08M 0s
00:49:30 50K .......... .......... .......... .......... ......... 100% 6.03M=0.02s
00:49:30
00:49:30 2024-10-25 00:49:30 (4.06 MB/s) - ‘Figure_To_Pdf.py’ saved [101739/101739]
00:49:30
00:49:30 + chmod 755 Figure_To_Pdf.py
00:49:30 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:49:30 + omero config set omero.db.name OMERO-server
00:49:31 + omero config set omero.db.host pg
00:49:33 + omero config set omero.db.user postgres
00:49:35 + omero config set omero.data.dir /home/omero/omero-server-data
00:49:36 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:49:38 + omero config set omero.db.poolsize 25
00:49:39 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:49:41 + omero config set omero.security.trustStorePassword changeit
00:49:42 + omero config set omero.mail.config true
00:49:44 + omero config set omero.mail.from qa@openmicroscopy.org.uk
00:49:46 + omero config set omero.mail.host smtp.dundee.ac.uk
00:49:47 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:49:49 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
00:49:50 + omero certificates
00:49:52 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022)
00:49:52 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:49:52 + '[' false = true ']'
00:49:52 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:49:52 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:49:52 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:49:52 2024-10-25 00:49:52,577 [ omego.db] DEBUG dbcommand => upgrade
00:49:52 2024-10-25 00:49:52,577 [ omego.db] DEBUG dbhost => localhost
00:49:52 2024-10-25 00:49:52,577 [ omego.db] DEBUG dbname => OMERO-server
00:49:52 2024-10-25 00:49:52,577 [ omego.db] DEBUG dbpass => omero
00:49:52 2024-10-25 00:49:52,577 [ omego.db] DEBUG dbuser => omero
00:49:52 2024-10-25 00:49:52,578 [ omego.db] DEBUG rootpass => omero
00:49:52 2024-10-25 00:49:52,578 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:49:52 2024-10-25 00:49:52,578 [omego.extern] INFO Executing : omero version
00:49:53 OMERO.py version:
00:49:53 OMERO.server version:
00:49:53 5.6.3-513-edc8e2180c-ice36
00:49:53 5.19.6.dev0
00:49:54 2024-10-25 00:49:54,069 [omego.extern] INFO Completed [1.491 s]
00:49:54 2024-10-25 00:49:54,069 [omego.extern] DEBUG Using omero CLI from omero
00:49:54 2024-10-25 00:49:54,069 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:49:54 2024-10-25 00:49:54,069 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:54 2024-10-25 00:49:54,069 [omego.extern] INFO Executing : omero config get --show-password
00:49:55 2024-10-25 00:49:55,622 [omego.extern] INFO Completed [1.553 s]
00:49:55 2024-10-25 00:49:55,623 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:55 2024-10-25 00:49:55,623 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:49:55 2024-10-25 00:49:55,629 [omego.extern] INFO Completed [0.006 s]
00:49:55 2024-10-25 00:49:55,629 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.4\n'
00:49:55 2024-10-25 00:49:55,629 [ omego.db] INFO psql version: psql (PostgreSQL) 16.4
00:49:55
00:49:55 2024-10-25 00:49:55,630 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:55 2024-10-25 00:49:55,630 [omego.extern] INFO Executing : omero config get --show-password
00:49:57 2024-10-25 00:49:57,204 [omego.extern] INFO Completed [1.574 s]
00:49:57 2024-10-25 00:49:57,204 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:57 2024-10-25 00:49:57,204 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:49:57 2024-10-25 00:49:57,638 [omego.extern] INFO Completed [0.434 s]
00:49:57 2024-10-25 00:49:57,638 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.5") at port "5432".\n'
00:49:57 2024-10-25 00:49:57,638 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:49:57 2024-10-25 00:49:57,638 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:49:57 2024-10-25 00:49:57,638 [omego.extern] INFO Executing : omero config get --show-password
00:49:59 2024-10-25 00:49:59,126 [omego.extern] INFO Completed [1.487 s]
00:49:59 2024-10-25 00:49:59,126 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:49:59 2024-10-25 00:49:59,126 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:49:59 2024-10-25 00:49:59,138 [omego.extern] INFO Completed [0.011 s]
00:49:59 2024-10-25 00:49:59,138 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:49:59 2024-10-25 00:49:59,138 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:49:59 2024-10-25 00:49:59,141 [ omego.db] INFO Database is already at OMERO5.4__0
00:49:59 + export LANG=en_US.UTF-8
00:49:59 + LANG=en_US.UTF-8
00:49:59 + export LANGUAGE=en_US:en
00:49:59 + LANGUAGE=en_US:en
00:49:59 + export LC_ALL=en_US.UTF-8
00:49:59 + LC_ALL=en_US.UTF-8
00:49:59 + BUILD_ID=DONT_KILL_ME
00:49:59 + omero admin start
00:50:10 No descriptor given. Using etc/grid/default.xml
00:50:30 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:50:30 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:50:30 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:50:30 Waiting on startup. Use CTRL-C to exit
00:50:31 + omero admin waitup
00:50:32 Waiting on startup. Use CTRL-C to exit
00:50:32 + omero admin diagnostics
00:50:40 ERROR:omero.util.UpgradeCheck:HTTPConnectionPool(host='upgrade.openmicroscopy.org.uk', port=80): Max retries exceeded with url: /?version=5.19.6.dev0&os.name=Linux&os.arch=x86_64&os.version=Linux-5.14.0-427.40.1.el9_4.x86_64-x86_64-with-glibc2.34&python.version=3.9.18&python.compiler=GCC+11.4.1+20231218+%28Red+Hat+11.4.1-3%29&python.build=main&python.build=Aug+23+2024+00%3A00%3A00 (Caused by ConnectTimeoutError(<urllib3.connection.HTTPConnection object at 0x7f17448f0070>, 'Connection to upgrade.openmicroscopy.org.uk timed out. (connect timeout=6.0)'))
00:50:40
00:50:40 ================================================================================
00:50:40 OMERO Diagnostics (admin)
00:50:40 ================================================================================
00:50:40
00:50:40 Commands: java -version 11.0.24 (/usr/bin/java)
00:50:40 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:50:40 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:50:40 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:50:40 Commands: psql --version 16.4 (/usr/bin/psql)
00:50:40 Commands: openssl version 3.0.71 (/usr/bin/openssl)
00:50:40
00:50:40 Component: OMERO.py 5.19.6.dev0
00:50:40 Component: OMERO.server 5.6.3-513-edc8e2180c-ice36
00:50:40
00:50:40 Server: icegridnode running
00:50:40 Server: Blitz-0 active (pid = 23366, enabled)
00:50:40 Server: Indexer-0 active (pid = 23389, enabled)
00:50:40 Server: OMERO.Glacier2 active (pid = 23396, enabled)
00:50:40 Server: OMERO.IceStorm active (pid = 23424, enabled)
00:50:40 Server: Processor-0 activating (enabled)
00:50:40 Server: Tables-0 activating (enabled)
00:50:40
00:50:40 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:50:40 Log files: Blitz-0.log 21.8 KB errors=1 warnings=0
00:50:40 Log files: DropBox.log n/a
00:50:40 Log files: FileServer.log n/a
00:50:40 Log files: Indexer-0.log 2.6 KB
00:50:40 Log files: MonitorServer.log n/a
00:50:40 Log files: Processor-0.log 592 B
00:50:40 Log files: Tables-0.log 841 B
00:50:40 Log files: TestDropBox.log n/a
00:50:40 Log files: master.err 180 B
00:50:40 Log files: master.out 30.1 KB
00:50:40 Log files: Total size 0.06 MB
00:50:40
00:50:40
00:50:40 Environment:OMERO_HOME=(unset)
00:50:40 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:50:40 Environment:OMERO_NODE=(unset)
00:50:40 Environment:OMERO_MASTER=(unset)
00:50:40 Environment:OMERO_USERDIR=(unset)
00:50:40 Environment:OMERO_TMPDIR=(unset)
00:50:40 Environment:PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:40 Environment:PYTHONPATH=(unset)
00:50:40 Environment:ICE_HOME=/opt/ice-3.6.5
00:50:40 Environment:LD_LIBRARY_PATH=(unset)
00:50:40 Environment:DYLD_LIBRARY_PATH=(unset)
00:50:40
00:50:40 OMERO SSL port:4064
00:50:40 OMERO TCP port:4063
00:50:40 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:50:40 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:50:40
00:50:40 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:50:40 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:50:40 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:50:40 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
00:50:40
00:50:40 Jar: lib/server/formats-api.jar Bio-Formats API 8.1.0-SNAPSHOT 25 October 2024 acd014fd1e7336432e42783dc32370dc8f70166c
00:50:40 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.1.0-SNAPSHOT 25 October 2024 acd014fd1e7336432e42783dc32370dc8f70166c
00:50:40 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.1.0-SNAPSHOT 25 October 2024 acd014fd1e7336432e42783dc32370dc8f70166c
00:50:40 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.4-SNAPSHOT 25 October 2024 4d30c2f7ddbd77feb366152447dc37e7ab91d7a7
00:50:40 Jar: lib/server/ome-common.jar OME Common Java 6.0.25-SNAPSHOT 25 October 2024 4d30c2f7ddbd77feb366152447dc37e7ab91d7a7
00:50:40 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 25 October 2024 4d30c2f7ddbd77feb366152447dc37e7ab91d7a7
00:50:40 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4-SNAPSHOT 25 October 2024 4d30c2f7ddbd77feb366152447dc37e7ab91d7a7
00:50:40 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 25 October 2024 4d30c2f7ddbd77feb366152447dc37e7ab91d7a7
00:50:40 Jar: lib/server/ome-xml.jar OME XML library 6.3.7-SNAPSHOT 25 October 2024 4d30c2f7ddbd77feb366152447dc37e7ab91d7a7
00:50:40 Jar: lib/server/omero-blitz.jar jar 5.7.5-SNAPSHOT
00:50:40 Jar: lib/server/omero-common.jar jar 5.6.8-SNAPSHOT
00:50:40 Jar: lib/server/omero-gateway.jar jar 5.9.4-SNAPSHOT
00:50:40 Jar: lib/server/omero-model.jar jar 5.6.16-SNAPSHOT
00:50:40 Jar: lib/server/omero-renderer.jar jar 5.5.18-SNAPSHOT
00:50:40 Jar: lib/server/omero-romio.jar jar 5.7.8-SNAPSHOT
00:50:40 Jar: lib/server/omero-server.jar jar 5.6.13-SNAPSHOT
00:50:41 + deactivate
00:50:41 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:50:41 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:50:41 + export PATH
00:50:41 + unset _OLD_VIRTUAL_PATH
00:50:41 + '[' -n '' ']'
00:50:41 + '[' -n /bin/bash -o -n '' ']'
00:50:41 + hash -r
00:50:41 + '[' -n '' ']'
00:50:41 + unset VIRTUAL_ENV
00:50:41 + '[' '!' '' = nondestructive ']'
00:50:41 + unset -f deactivate
00:50:41 Finished: SUCCESS
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