00:48:16 Started by upstream project "Trigger" build number 257 00:48:16 originally caused by: 00:48:16 Started by timer 00:48:16 Running as SYSTEM 00:48:17 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server 00:48:17 [OMERO-server] $ /bin/bash -xe /tmp/jenkins14367922846249850795.sh 00:48:17 + source /home/settings.env 00:48:17 ++ OMERO_DB_HOST=pg 00:48:17 ++ OMERO_DB_USER=postgres 00:48:17 ++ OMERO_DB_PASS= 00:48:17 ++ OMERO_ROOT_PASS=omero 00:48:17 ++ OMERO_DATA_DIR=/OMERO 00:48:17 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR 00:48:17 + OMERO_DB_NAME=OMERO-server 00:48:17 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server 00:48:17 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:48:17 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:48:17 + OMERO_DATA_DIR=/home/omero/omero-server-data 00:48:17 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']' 00:48:17 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate 00:48:17 ++ deactivate nondestructive 00:48:17 ++ '[' -n '' ']' 00:48:17 ++ '[' -n '' ']' 00:48:17 ++ '[' -n /bin/bash -o -n '' ']' 00:48:17 ++ hash -r 00:48:17 ++ '[' -n '' ']' 00:48:17 ++ unset VIRTUAL_ENV 00:48:17 ++ '[' '!' nondestructive = nondestructive ']' 00:48:17 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3 00:48:17 ++ export VIRTUAL_ENV 00:48:17 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:48:17 ++ PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:48:17 ++ export PATH 00:48:17 ++ '[' -n '' ']' 00:48:17 ++ '[' -z '' ']' 00:48:17 ++ _OLD_VIRTUAL_PS1= 00:48:17 ++ PS1='(.venv3) ' 00:48:17 ++ export PS1 00:48:17 ++ '[' -n /bin/bash -o -n '' ']' 00:48:17 ++ hash -r 00:48:17 + omero admin stop 00:48:57 Server not running 00:48:57 + echo not running 00:48:57 not running 00:48:57 + sleep 5 00:49:02 + deactivate 00:49:02 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' 00:49:02 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:49:02 + export PATH 00:49:02 + unset _OLD_VIRTUAL_PATH 00:49:02 + '[' -n '' ']' 00:49:02 + '[' -n /bin/bash -o -n '' ']' 00:49:02 + hash -r 00:49:02 + '[' -n '' ']' 00:49:02 + unset VIRTUAL_ENV 00:49:02 + '[' '!' '' = nondestructive ']' 00:49:02 + unset -f deactivate 00:49:02 + rm -rf /home/omero/workspace/OMERO-server/.venv3 00:49:03 + python3 -m venv /home/omero/workspace/OMERO-server/.venv3 00:49:08 + '[' false = true ']' 00:49:08 + echo 'Skipping PURGE_DATA:CleanDbAndRepo' 00:49:08 Skipping PURGE_DATA:CleanDbAndRepo 00:49:08 + 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 00:49:11 Copied 1 artifact from "OMERO-build" build number 213 00:49:11 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 210 00:49:11 Copied 2 artifacts from "OMERO-build-build" build number 221 00:49:11 [OMERO-server] $ /bin/bash -xe /tmp/jenkins13514857487630317653.sh 00:49:11 + source /home/settings.env 00:49:11 ++ OMERO_DB_HOST=pg 00:49:11 ++ OMERO_DB_USER=postgres 00:49:11 ++ OMERO_DB_PASS= 00:49:11 ++ OMERO_ROOT_PASS=omero 00:49:11 ++ OMERO_DATA_DIR=/OMERO 00:49:11 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR 00:49:11 + OMERO_DB_NAME=OMERO-server 00:49:11 + OMERO_DATA_DIR=/home/omero/omero-server-data 00:49:11 + mkdir -p /home/omero/omero-server-data 00:49:11 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server 00:49:11 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:49:11 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:49:11 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip 00:49:11 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip 00:49:11 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties 00:49:11 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties 00:49:11 ++ ls OMERO.server-5.6.3-513-2661accdbd-ice36.zip 00:49:11 + ZIP=OMERO.server-5.6.3-513-2661accdbd-ice36.zip 00:49:11 + '[' '!' -z '' ']' 00:49:11 + DIST=OMERO.server-5.6.3-513-2661accdbd-ice36 00:49:11 + unzip OMERO.server-5.6.3-513-2661accdbd-ice36.zip 00:49:11 Archive: OMERO.server-5.6.3-513-2661accdbd-ice36.zip 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/blitz/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/grid/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/profiles/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/error/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/grid/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/luts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/luts/janelia/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/luts/ncsa_paledit/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/luts/wcif/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/analysis_scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/annotation_scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/export_scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/figure_scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/import_scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/scripts/omero/util_scripts/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/server/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/share/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/share/licenses/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/misc/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__1/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__10/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__11/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__2/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__3/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__4/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__5/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__6/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__7/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__8/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3A__9/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3__4/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3__5/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3__6/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO3__7/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO4.1__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO4.2__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO4.2__0/t/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO4.3__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO4.4__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO4__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.0__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.1__1/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.2__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.3__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4DEV__1/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4DEV__2/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4DEV__3/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/ 00:49:11 creating: OMERO.server-5.6.3-513-2661accdbd-ice36/var/ 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/LICENSE.txt 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/backup.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/blitz/mail-senders.example 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/blitz/mail-server.example 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/build.properties 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/env.bat 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/env.sh 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/hibernate.properties 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/ice.config 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/logback-cli.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/logback-indexing-cli.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/logback-indexing.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/logback.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/mime.types 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/node1.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/node2.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/omero.properties 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/profiles/psql 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/rollover.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/Windows.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/error/maintainance.html 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/grid/README 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/grid/default.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/grid/templates.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/grid/windefault.xml 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/ice.config 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/internal.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/master.cfg 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/templates/robot.template 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/etc/testdropbox.config 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/history.rst 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/OMEZarrReader.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/activation.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/aggdesigner-algorithm.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/aircompressor.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/annotations.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/antlr.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/aopalliance.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/avatica-core.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/avatica-metrics.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/aws-java-sdk-core.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/aws-java-sdk-kms.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/aws-java-sdk-s3.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/base.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-all.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-anim.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-awt-util.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-bridge.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-codec.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-constants.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-css.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-dom.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-ext.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-extension.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-gui-util.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-gvt.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-i18n.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-parser.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-rasterizer-ext.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-rasterizer.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-script.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-slideshow.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-squiggle-ext.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-squiggle.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-svg-dom.jar 00:49:11 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/lib/client/batik-svgbrowser.jar 00:49:11 inflating: 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OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/OMERO5.3__0.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/OMERO5.3__1.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/psql-footer.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/psql-header.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/schema.sql 00:49:13 inflating: OMERO.server-5.6.3-513-2661accdbd-ice36/sql/psql/OMERO5.4__0/views.sql 00:49:13 + rm -f OMERO.server-5.6.3-513-2661accdbd-ice36.zip 00:49:15 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-513-2661accdbd-ice36 /home/omero/workspace/OMERO-server/OMERO.server 00:49:15 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate 00:49:15 ++ deactivate nondestructive 00:49:15 ++ '[' -n '' ']' 00:49:15 ++ '[' -n '' ']' 00:49:15 ++ '[' -n /bin/bash -o -n '' ']' 00:49:15 ++ hash -r 00:49:15 ++ '[' -n '' ']' 00:49:15 ++ unset VIRTUAL_ENV 00:49:15 ++ '[' '!' nondestructive = nondestructive ']' 00:49:15 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3 00:49:15 ++ export VIRTUAL_ENV 00:49:15 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:49:15 ++ 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 00:49:15 ++ export PATH 00:49:15 ++ '[' -n '' ']' 00:49:15 ++ '[' -z '' ']' 00:49:15 ++ _OLD_VIRTUAL_PS1= 00:49:15 ++ PS1='(.venv3) ' 00:49:15 ++ export PS1 00:49:15 ++ '[' -n /bin/bash -o -n '' ']' 00:49:15 ++ hash -r 00:49:15 + 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 00:49:16 Collecting zeroc-ice==3.6.5 00:49:17 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) 00:49:18 Installing collected packages: zeroc-ice 00:49:19 Successfully installed zeroc-ice-3.6.5 00:49:19 + pip install -U pip future 00:49:19 Requirement already satisfied: pip in ./.venv3/lib/python3.9/site-packages (21.2.3) 00:49:20 Collecting pip 00:49:20 Using cached pip-24.2-py3-none-any.whl (1.8 MB) 00:49:20 Collecting future 00:49:20 Using cached future-1.0.0-py3-none-any.whl (491 kB) 00:49:20 Installing collected packages: pip, future 00:49:20 Attempting uninstall: pip 00:49:20 Found existing installation: pip 21.2.3 00:49:20 Uninstalling pip-21.2.3: 00:49:20 Successfully uninstalled pip-21.2.3 00:49:22 Successfully installed future-1.0.0 pip-24.2 00:49:22 + pip install markdown 00:49:22 Collecting markdown 00:49:22 Using cached Markdown-3.7-py3-none-any.whl.metadata (7.0 kB) 00:49:22 Collecting importlib-metadata>=4.4 (from markdown) 00:49:22 Using cached importlib_metadata-8.5.0-py3-none-any.whl.metadata (4.8 kB) 00:49:22 Collecting zipp>=3.20 (from importlib-metadata>=4.4->markdown) 00:49:23 Using cached zipp-3.20.2-py3-none-any.whl.metadata (3.7 kB) 00:49:23 Using cached Markdown-3.7-py3-none-any.whl (106 kB) 00:49:23 Using cached importlib_metadata-8.5.0-py3-none-any.whl (26 kB) 00:49:23 Using cached zipp-3.20.2-py3-none-any.whl (9.2 kB) 00:49:23 Installing collected packages: zipp, importlib-metadata, markdown 00:49:23 Successfully installed importlib-metadata-8.5.0 markdown-3.7 zipp-3.20.2 00:49:23 + pip install reportlab 00:49:24 Collecting reportlab 00:49:24 Using cached reportlab-4.2.5-py3-none-any.whl.metadata (1.5 kB) 00:49:24 Collecting pillow>=9.0.0 (from reportlab) 00:49:24 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl.metadata (9.1 kB) 00:49:24 Collecting chardet (from reportlab) 00:49:25 Using cached chardet-5.2.0-py3-none-any.whl.metadata (3.4 kB) 00:49:25 Using cached reportlab-4.2.5-py3-none-any.whl (1.9 MB) 00:49:25 Using cached pillow-11.0.0-cp39-cp39-manylinux_2_28_x86_64.whl (4.4 MB) 00:49:25 Using cached chardet-5.2.0-py3-none-any.whl (199 kB) 00:49:25 Installing collected packages: pillow, chardet, reportlab 00:49:26 Successfully installed chardet-5.2.0 pillow-11.0.0 reportlab-4.2.5 00:49:26 + pip install omego 00:49:27 Collecting omego 00:49:27 Using cached omego-0.7.0-py3-none-any.whl 00:49:27 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omego) (1.0.0) 00:49:27 Collecting yaclifw>=0.1.1 (from omego) 00:49:27 Using cached yaclifw-0.2.0-py3-none-any.whl 00:49:27 Collecting six (from yaclifw>=0.1.1->omego) 00:49:27 Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB) 00:49:27 Using cached six-1.16.0-py2.py3-none-any.whl (11 kB) 00:49:27 Installing collected packages: six, yaclifw, omego 00:49:27 Successfully installed omego-0.7.0 six-1.16.0 yaclifw-0.2.0 00:49:27 + pip install tables 00:49:28 Collecting tables 00:49:28 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.3 kB) 00:49:29 Collecting numpy>=1.19.0 (from tables) 00:49:29 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB) 00:49:29 Collecting numexpr>=2.6.2 (from tables) 00:49:29 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (1.2 kB) 00:49:29 Collecting packaging (from tables) 00:49:29 Using cached packaging-24.1-py3-none-any.whl.metadata (3.2 kB) 00:49:29 Collecting py-cpuinfo (from tables) 00:49:29 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes) 00:49:29 Collecting blosc2>=2.3.0 (from tables) 00:49:29 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.2 kB) 00:49:30 Collecting ndindex>=1.4 (from blosc2>=2.3.0->tables) 00:49:30 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.4 kB) 00:49:30 Collecting msgpack (from blosc2>=2.3.0->tables) 00:49:30 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (8.4 kB) 00:49:30 Using cached tables-3.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (7.5 MB) 00:49:30 Using cached blosc2-2.5.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.4 MB) 00:49:30 Using cached numexpr-2.10.1-cp39-cp39-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (404 kB) 00:49:31 Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (19.5 MB) 00:49:31 Using cached packaging-24.1-py3-none-any.whl (53 kB) 00:49:31 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB) 00:49:31 Using cached ndindex-1.9.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (478 kB) 00:49:31 Using cached msgpack-1.1.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (377 kB) 00:49:31 Installing collected packages: py-cpuinfo, packaging, numpy, ndindex, msgpack, numexpr, blosc2, tables 00:49:35 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 00:49:36 + pip install jinja2 00:49:36 Collecting jinja2 00:49:36 Using cached jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB) 00:49:36 Collecting MarkupSafe>=2.0 (from jinja2) 00:49:36 Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB) 00:49:37 Using cached jinja2-3.1.4-py3-none-any.whl (133 kB) 00:49:37 Using cached MarkupSafe-3.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (20 kB) 00:49:37 Installing collected packages: MarkupSafe, jinja2 00:49:37 Successfully installed MarkupSafe-3.0.2 jinja2-3.1.4 00:49:37 + pip install omero-py 00:49:38 Collecting omero-py 00:49:38 Using cached omero_py-5.19.5-py3-none-any.whl.metadata (6.3 kB) 00:49:38 Collecting urllib3<2 (from omero-py) 00:49:38 Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) 00:49:38 Collecting appdirs (from omero-py) 00:49:38 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB) 00:49:38 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py) (1.0.0) 00:49:38 Collecting numpy<2 (from omero-py) 00:49:38 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB) 00:49:38 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py) (11.0.0) 00:49:38 Collecting PyYAML (from omero-py) 00:49:38 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) 00:49:38 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib/python3.9/site-packages (from omero-py) (3.6.5) 00:49:38 Collecting requests (from omero-py) 00:49:38 Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB) 00:49:38 Collecting portalocker (from omero-py) 00:49:38 Using cached portalocker-2.10.1-py3-none-any.whl.metadata (8.5 kB) 00:49:39 Collecting charset-normalizer<4,>=2 (from requests->omero-py) 00:49:39 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (34 kB) 00:49:39 Collecting idna<4,>=2.5 (from requests->omero-py) 00:49:39 Using cached idna-3.10-py3-none-any.whl.metadata (10 kB) 00:49:39 Collecting certifi>=2017.4.17 (from requests->omero-py) 00:49:39 Using cached certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB) 00:49:39 Using cached omero_py-5.19.5-py3-none-any.whl (2.8 MB) 00:49:39 Using cached numpy-1.26.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB) 00:49:39 Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) 00:49:39 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB) 00:49:39 Using cached portalocker-2.10.1-py3-none-any.whl (18 kB) 00:49:40 Using cached PyYAML-6.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (737 kB) 00:49:40 Using cached requests-2.32.3-py3-none-any.whl (64 kB) 00:49:40 Using cached certifi-2024.8.30-py3-none-any.whl (167 kB) 00:49:40 Using cached charset_normalizer-3.4.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (144 kB) 00:49:40 Using cached idna-3.10-py3-none-any.whl (70 kB) 00:49:40 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, numpy, idna, charset-normalizer, certifi, requests, omero-py 00:49:41 Attempting uninstall: numpy 00:49:41 Found existing installation: numpy 2.0.2 00:49:41 Uninstalling numpy-2.0.2: 00:49:41 Successfully uninstalled numpy-2.0.2 00:49:46 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 00:49:46 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata 00:49:46 Collecting omero-metadata 00:49:46 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-19l8d3w4/omero-metadata_9b85043f628644c5a43da2732a58ad8f 00:49:47 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-19l8d3w4/omero-metadata_9b85043f628644c5a43da2732a58ad8f 00:49:48 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit e1b89c7c3f5f08bf0a1ca0dec0ee175fafb6c21c 00:49:48 Installing build dependencies: started 00:49:50 Installing build dependencies: finished with status 'done' 00:49:50 Getting requirements to build wheel: started 00:49:50 Getting requirements to build wheel: finished with status 'done' 00:49:50 Preparing metadata (pyproject.toml): started 00:49:50 Preparing metadata (pyproject.toml): finished with status 'done' 00:49:50 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (5.19.5) 00:49:50 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (6.0.2) 00:49:50 Requirement already satisfied: jinja2 in ./.venv3/lib/python3.9/site-packages (from omero-metadata) (3.1.4) 00:49:51 Collecting pandas (from omero-metadata) 00:49:51 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (89 kB) 00:49:51 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.20) 00:49:51 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4) 00:49:51 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0) 00:49:51 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (1.26.4) 00:49:51 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) 00:49:51 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) 00:49:51 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.32.3) 00:49:51 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-metadata) (2.10.1) 00:49:51 Requirement already satisfied: MarkupSafe>=2.0 in ./.venv3/lib/python3.9/site-packages (from jinja2->omero-metadata) (3.0.2) 00:49:51 Collecting python-dateutil>=2.8.2 (from pandas->omero-metadata) 00:49:51 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) 00:49:51 Collecting pytz>=2020.1 (from pandas->omero-metadata) 00:49:51 Using cached pytz-2024.2-py2.py3-none-any.whl.metadata (22 kB) 00:49:51 Collecting tzdata>=2022.7 (from pandas->omero-metadata) 00:49:51 Using cached tzdata-2024.2-py2.py3-none-any.whl.metadata (1.4 kB) 00:49:51 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) 00:49:51 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) 00:49:51 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) 00:49:51 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) 00:49:51 Using cached pandas-2.2.3-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (13.1 MB) 00:49:51 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB) 00:49:52 Using cached pytz-2024.2-py2.py3-none-any.whl (508 kB) 00:49:52 Using cached tzdata-2024.2-py2.py3-none-any.whl (346 kB) 00:49:52 Building wheels for collected packages: omero-metadata 00:49:52 Building wheel for omero-metadata (pyproject.toml): started 00:49:52 Building wheel for omero-metadata (pyproject.toml): finished with status 'done' 00:49:52 Created wheel for omero-metadata: filename=omero_metadata-0.12.1.dev0-py3-none-any.whl size=39187 sha256=e86c028315e34c1f31902e1b39624b2a8239c54f09c86da0b0e1a987b8841128 00:49:52 Stored in directory: /tmp/pip-ephem-wheel-cache-hgo15rkf/wheels/64/09/47/3b86b706f8f6f4bec1b7fd6641d2e4a09814e754fa4c85c82d 00:49:52 Successfully built omero-metadata 00:49:52 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata 00:49:57 Successfully installed omero-metadata-0.12.1.dev0 pandas-2.2.3 python-dateutil-2.9.0.post0 pytz-2024.2 tzdata-2024.2 00:49:57 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render 00:49:58 Collecting omero-cli-render 00:49:58 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-86ncibu9/omero-cli-render_06c2164bd57245f99164db677d7b193a 00:49:58 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-86ncibu9/omero-cli-render_06c2164bd57245f99164db677d7b193a 00:49:59 Running command git checkout -b merge_ci --track origin/merge_ci 00:49:59 Switched to a new branch 'merge_ci' 00:49:59 branch 'merge_ci' set up to track 'origin/merge_ci'. 00:49:59 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit dae8b5a34a98c05a6ff00ad9a5d5dd24853c7099 00:49:59 Installing build dependencies: started 00:50:01 Installing build dependencies: finished with status 'done' 00:50:01 Getting requirements to build wheel: started 00:50:01 Getting requirements to build wheel: finished with status 'done' 00:50:01 Preparing metadata (pyproject.toml): started 00:50:01 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:01 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (6.0.2) 00:50:01 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-cli-render) (5.19.5) 00:50:01 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.20) 00:50:01 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4) 00:50:01 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0) 00:50:01 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.26.4) 00:50:01 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) 00:50:01 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) 00:50:01 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.32.3) 00:50:01 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.10.1) 00:50:01 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) 00:50:01 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) 00:50:01 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) 00:50:01 Building wheels for collected packages: omero-cli-render 00:50:01 Building wheel for omero-cli-render (pyproject.toml): started 00:50:01 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done' 00:50:01 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=18030 sha256=5b449ec3bde824149e69595884d69c69d1273f9b1f4f92302b6fa2f8b09057df 00:50:01 Stored in directory: /tmp/pip-ephem-wheel-cache-vwx9ha7o/wheels/58/32/1b/746489b3c7c17a98c6cd7195bdd3b426dd4137caeb1045a994 00:50:01 Successfully built omero-cli-render 00:50:02 Installing collected packages: omero-cli-render 00:50:02 Successfully installed omero-cli-render-0.8.2.dev0 00:50:02 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate 00:50:02 Collecting omero-cli-duplicate 00:50:02 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-s7py9jfk/omero-cli-duplicate_9c7540e31370498d92ee715d9e22ac7b 00:50:02 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-s7py9jfk/omero-cli-duplicate_9c7540e31370498d92ee715d9e22ac7b 00:50:03 Running command git checkout -b merge_ci --track origin/merge_ci 00:50:03 Switched to a new branch 'merge_ci' 00:50:03 branch 'merge_ci' set up to track 'origin/merge_ci'. 00:50:03 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 80eb5eda6b17144980b43df90736d55dc52caa28 00:50:03 Installing build dependencies: started 00:50:05 Installing build dependencies: finished with status 'done' 00:50:05 Getting requirements to build wheel: started 00:50:06 Getting requirements to build wheel: finished with status 'done' 00:50:06 Preparing metadata (pyproject.toml): started 00:50:06 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:06 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib/python3.9/site-packages (from omero-cli-duplicate) (5.19.5) 00:50:06 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.20) 00:50:06 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4) 00:50:06 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0) 00:50:06 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.26.4) 00:50:06 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) 00:50:06 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.2) 00:50:06 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) 00:50:06 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.32.3) 00:50:06 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.10.1) 00:50:06 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) 00:50:06 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) 00:50:06 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) 00:50:06 Building wheels for collected packages: omero-cli-duplicate 00:50:06 Building wheel for omero-cli-duplicate (pyproject.toml): started 00:50:06 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done' 00:50:06 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11442 sha256=680c0110ec03a1e60e29c3a7e0e1c1e1fde866ad688da7e969602a27b4c335cb 00:50:06 Stored in directory: /tmp/pip-ephem-wheel-cache-ypmnl83e/wheels/f1/55/ac/0cb8b093a4c417e5157143839711e7613efa64eaa21c29ef84 00:50:06 Successfully built omero-cli-duplicate 00:50:06 Installing collected packages: omero-cli-duplicate 00:50:06 Successfully installed omero-cli-duplicate-0.4.1.dev0 00:50:06 + pip install omero-certificates 00:50:07 Collecting omero-certificates 00:50:07 Using cached omero_certificates-0.3.2-py3-none-any.whl.metadata (3.7 kB) 00:50:07 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib/python3.9/site-packages (from omero-certificates) (5.19.5) 00:50:07 Collecting distro==1.8.0 (from omero-certificates) 00:50:07 Using cached distro-1.8.0-py3-none-any.whl.metadata (6.9 kB) 00:50:07 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.20) 00:50:07 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4) 00:50:07 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0) 00:50:07 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (1.26.4) 00:50:07 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) 00:50:07 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.2) 00:50:07 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) 00:50:07 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.32.3) 00:50:07 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py>=5.6.0->omero-certificates) (2.10.1) 00:50:07 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) 00:50:07 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) 00:50:07 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) 00:50:07 Using cached omero_certificates-0.3.2-py3-none-any.whl (13 kB) 00:50:07 Using cached distro-1.8.0-py3-none-any.whl (20 kB) 00:50:07 Installing collected packages: distro, omero-certificates 00:50:07 Successfully installed distro-1.8.0 omero-certificates-0.3.2 00:50:07 + for x in *.tar.gz 00:50:07 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz 00:50:08 Processing ./omero_dropbox-5.7.1.dev0.tar.gz 00:50:08 Installing build dependencies: started 00:50:10 Installing build dependencies: finished with status 'done' 00:50:10 Getting requirements to build wheel: started 00:50:10 Getting requirements to build wheel: finished with status 'done' 00:50:10 Preparing metadata (pyproject.toml): started 00:50:10 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:10 Requirement already satisfied: omero-py in ./.venv3/lib/python3.9/site-packages (from omero-dropbox==5.7.1.dev0) (5.19.5) 00:50:10 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.20) 00:50:10 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4) 00:50:10 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0) 00:50:10 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.26.4) 00:50:10 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) 00:50:10 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.2) 00:50:10 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) 00:50:10 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.32.3) 00:50:10 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.10.1) 00:50:10 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) 00:50:10 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) 00:50:10 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) 00:50:10 Building wheels for collected packages: omero-dropbox 00:50:10 Building wheel for omero-dropbox (pyproject.toml): started 00:50:11 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done' 00:50:11 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49058 sha256=c5a7eec8443ead6a2ec41f36e23ff750760399826095521536ed1554c9b68a3c 00:50:11 Stored in directory: /home/omero/.cache/pip/wheels/eb/76/85/58476368b176f793423899407c96293c22f9c9edc28cf54079 00:50:11 Successfully built omero-dropbox 00:50:11 Installing collected packages: omero-dropbox 00:50:11 Successfully installed omero-dropbox-5.7.1.dev0 00:50:11 + for x in *.tar.gz 00:50:11 + pip install -U omero_marshal-0.9.1.dev0.tar.gz 00:50:11 Processing ./omero_marshal-0.9.1.dev0.tar.gz 00:50:11 Installing build dependencies: started 00:50:13 Installing build dependencies: finished with status 'done' 00:50:13 Getting requirements to build wheel: started 00:50:13 Getting requirements to build wheel: finished with status 'done' 00:50:13 Preparing metadata (pyproject.toml): started 00:50:14 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:14 Building wheels for collected packages: omero_marshal 00:50:14 Building wheel for omero_marshal (pyproject.toml): started 00:50:14 Building wheel for omero_marshal (pyproject.toml): finished with status 'done' 00:50:14 Created wheel for omero_marshal: filename=omero_marshal-0.9.1.dev0-py3-none-any.whl size=88031 sha256=2f5cc4bc07a6230a6e479f4d888f8255849005c29eb219c28e1fdc3519316607 00:50:14 Stored in directory: /home/omero/.cache/pip/wheels/8b/40/f1/dbed071eff57c96e0824ead2a420a7a1a080f7fbdfe0431d7f 00:50:14 Successfully built omero_marshal 00:50:14 Installing collected packages: omero_marshal 00:50:14 Successfully installed omero_marshal-0.9.1.dev0 00:50:14 + for x in *.tar.gz 00:50:14 + pip install -U omero_py-5.19.6.dev0.tar.gz 00:50:15 Processing ./omero_py-5.19.6.dev0.tar.gz 00:50:15 Installing build dependencies: started 00:50:17 Installing build dependencies: finished with status 'done' 00:50:17 Getting requirements to build wheel: started 00:50:17 Getting requirements to build wheel: finished with status 'done' 00:50:17 Preparing metadata (pyproject.toml): started 00:50:17 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:17 Requirement already satisfied: urllib3<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.20) 00:50:17 Requirement already satisfied: appdirs in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.4.4) 00:50:17 Requirement already satisfied: future in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.0.0) 00:50:17 Requirement already satisfied: numpy<2 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (1.26.4) 00:50:17 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (11.0.0) 00:50:17 Requirement already satisfied: PyYAML in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (6.0.2) 00:50:17 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) 00:50:17 Requirement already satisfied: requests in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.32.3) 00:50:17 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-py==5.19.6.dev0) (2.10.1) 00:50:17 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) 00:50:17 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib/python3.9/site-packages (from requests->omero-py==5.19.6.dev0) (3.10) 00:50:17 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) 00:50:17 Building wheels for collected packages: omero-py 00:50:17 Building wheel for omero-py (pyproject.toml): started 00:50:18 Building wheel for omero-py (pyproject.toml): finished with status 'done' 00:50:18 Created wheel for omero-py: filename=omero_py-5.19.6.dev0-py3-none-any.whl size=2783246 sha256=a6dfb73a5d3da0deeba015711afd40cec2d178b2caff0bac15ac30b8cd6e3c54 00:50:18 Stored in directory: /home/omero/.cache/pip/wheels/80/e5/37/a3ff2b54d2fa16a058bb39e8eb6b77b050109520fb9f16931d 00:50:18 Successfully built omero-py 00:50:19 Installing collected packages: omero-py 00:50:19 Attempting uninstall: omero-py 00:50:19 Found existing installation: omero-py 5.19.5 00:50:19 Uninstalling omero-py-5.19.5: 00:50:19 Successfully uninstalled omero-py-5.19.5 00:50:21 Successfully installed omero-py-5.19.6.dev0 00:50:21 + for x in *.tar.gz 00:50:21 + pip install -U omero_scripts-5.8.4.dev0.tar.gz 00:50:22 Processing ./omero_scripts-5.8.4.dev0.tar.gz 00:50:22 Installing build dependencies: started 00:50:23 Installing build dependencies: finished with status 'done' 00:50:23 Getting requirements to build wheel: started 00:50:24 Getting requirements to build wheel: finished with status 'done' 00:50:24 Preparing metadata (pyproject.toml): started 00:50:24 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:24 Building wheels for collected packages: omero-scripts 00:50:24 Building wheel for omero-scripts (pyproject.toml): started 00:50:24 Building wheel for omero-scripts (pyproject.toml): finished with status 'done' 00:50:24 Created wheel for omero-scripts: filename=omero_scripts-5.8.4.dev0-py3-none-any.whl size=116645 sha256=d7c45f0de9b3d3780ac3bb4803554f463d28d700e4212effeabdb2c47d191b63 00:50:24 Stored in directory: /home/omero/.cache/pip/wheels/50/80/aa/1e175e4f2a5b0a5343d01937a727d990d08c8e12000390ad9c 00:50:24 Successfully built omero-scripts 00:50:24 Installing collected packages: omero-scripts 00:50:24 Successfully installed omero-scripts-5.8.4.dev0 00:50:25 + for x in *.tar.gz 00:50:25 + pip install -U omero_web-5.27.3.dev0.tar.gz 00:50:25 Processing ./omero_web-5.27.3.dev0.tar.gz 00:50:25 Installing build dependencies: started 00:50:27 Installing build dependencies: finished with status 'done' 00:50:27 Getting requirements to build wheel: started 00:50:28 Getting requirements to build wheel: finished with status 'done' 00:50:28 Preparing metadata (pyproject.toml): started 00:50:28 Preparing metadata (pyproject.toml): finished with status 'done' 00:50:28 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) 00:50:28 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.27.3.dev0) 00:50:28 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl.metadata (17 kB) 00:50:28 Collecting Django<4.3,>=4.2.3 (from omero-web==5.27.3.dev0) 00:50:28 Using cached Django-4.2.16-py3-none-any.whl.metadata (4.1 kB) 00:50:28 Collecting django-pipeline==2.1.0 (from omero-web==5.27.3.dev0) 00:50:28 Using cached django_pipeline-2.1.0-py3-none-any.whl.metadata (12 kB) 00:50:28 Collecting django-cors-headers==3.7.0 (from omero-web==5.27.3.dev0) 00:50:29 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB) 00:50:29 Collecting django-csp (from omero-web==5.27.3.dev0) 00:50:29 Using cached django_csp-3.8-py3-none-any.whl.metadata (2.7 kB) 00:50:29 Collecting whitenoise>=5.3.0 (from omero-web==5.27.3.dev0) 00:50:29 Using cached whitenoise-6.7.0-py3-none-any.whl.metadata (3.7 kB) 00:50:29 Collecting gunicorn>=19.3 (from omero-web==5.27.3.dev0) 00:50:29 Using cached gunicorn-23.0.0-py3-none-any.whl.metadata (4.4 kB) 00:50:29 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) 00:50:29 Requirement already satisfied: Pillow in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (11.0.0) 00:50:29 Requirement already satisfied: pytz in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2024.2) 00:50:29 Requirement already satisfied: portalocker in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (2.10.1) 00:50:29 Requirement already satisfied: packaging in ./.venv3/lib/python3.9/site-packages (from omero-web==5.27.3.dev0) (24.1) 00:50:29 Collecting asgiref<4,>=3.6.0 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0) 00:50:29 Using cached asgiref-3.8.1-py3-none-any.whl.metadata (9.3 kB) 00:50:29 Collecting sqlparse>=0.3.1 (from Django<4.3,>=4.2.3->omero-web==5.27.3.dev0) 00:50:29 Using cached sqlparse-0.5.1-py3-none-any.whl.metadata (3.9 kB) 00:50:29 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) 00:50:29 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) 00:50:29 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) 00:50:29 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) 00:50:29 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) 00:50:29 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) 00:50:29 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) 00:50:29 Collecting typing-extensions>=4 (from asgiref<4,>=3.6.0->Django<4.3,>=4.2.3->omero-web==5.27.3.dev0) 00:50:29 Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB) 00:50:29 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) 00:50:29 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) 00:50:29 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) 00:50:29 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB) 00:50:29 Using cached django_pipeline-2.1.0-py3-none-any.whl (38 kB) 00:50:29 Using cached concurrent_log_handler-0.9.25-py3-none-any.whl (25 kB) 00:50:29 Using cached Django-4.2.16-py3-none-any.whl (8.0 MB) 00:50:29 Using cached gunicorn-23.0.0-py3-none-any.whl (85 kB) 00:50:29 Using cached whitenoise-6.7.0-py3-none-any.whl (19 kB) 00:50:29 Using cached django_csp-3.8-py3-none-any.whl (17 kB) 00:50:29 Using cached asgiref-3.8.1-py3-none-any.whl (23 kB) 00:50:29 Using cached sqlparse-0.5.1-py3-none-any.whl (44 kB) 00:50:29 Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB) 00:50:30 Building wheels for collected packages: omero-web 00:50:30 Building wheel for omero-web (pyproject.toml): started 00:50:31 Building wheel for omero-web (pyproject.toml): finished with status 'done' 00:50:31 Created wheel for omero-web: filename=omero_web-5.27.3.dev0-py3-none-any.whl size=2766670 sha256=ed83cf0290a5730c88754f5605418bd8ca5149f2fb016f1d0de1dc976d48154a 00:50:31 Stored in directory: /home/omero/.cache/pip/wheels/ae/1e/5f/7127f5403b089e5e8280a504b3d30303e78d1102aa8854c22b 00:50:31 Successfully built omero-web 00:50:31 Installing collected packages: django-pipeline, whitenoise, typing-extensions, sqlparse, gunicorn, concurrent-log-handler, asgiref, Django, django-csp, django-cors-headers, omero-web 00:50:34 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 00:50:34 + wget https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py 00:50:35 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file. 00:50:35 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled. 00:50:35 --2024-10-23 00:50:35-- https://raw.githubusercontent.com/snoopycrimecop/omero-figure/merge_ci/omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py 00:50:35 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ... 00:50:35 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected. 00:50:35 HTTP request sent, awaiting response... 200 OK 00:50:36 Length: 99504 (97K) [text/plain] 00:50:36 Saving to: ‘Figure_To_Pdf.py’ 00:50:36 00:50:36 0K .......... .......... .......... .......... .......... 51% 3.26M 0s 00:50:36 50K .......... .......... .......... .......... ....... 100% 5.18M=0.02s 00:50:36 00:50:36 2024-10-23 00:50:36 (3.98 MB/s) - ‘Figure_To_Pdf.py’ saved [99504/99504] 00:50:36 00:50:36 + chmod 755 Figure_To_Pdf.py 00:50:36 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts 00:50:36 + omero config set omero.db.name OMERO-server 00:50:37 + omero config set omero.db.host pg 00:50:39 + omero config set omero.db.user postgres 00:50:40 + omero config set omero.data.dir /home/omero/omero-server-data 00:50:41 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time% 00:50:43 + omero config set omero.db.poolsize 25 00:50:44 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts 00:50:46 + omero config set omero.security.trustStorePassword changeit 00:50:47 + omero config set omero.mail.config true 00:50:49 + omero config set omero.mail.from qa@openmicroscopy.org.uk 00:50:50 + omero config set omero.mail.host smtp.dundee.ac.uk 00:50:52 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0 00:50:53 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED' 00:50:55 + omero certificates 00:50:56 OpenSSL 3.0.7 1 Nov 2022 (Library: OpenSSL 3.0.7 1 Nov 2022) 00:50:57 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12 00:50:57 + '[' false = true ']' 00:50:57 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade' 00:50:57 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade 00:50:57 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG dbcommand => upgrade 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG dbhost => localhost 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG dbname => OMERO-server 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG dbpass => omero 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG dbuser => omero 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG rootpass => omero 00:50:57 2024-10-23 00:50:57,522 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server 00:50:57 2024-10-23 00:50:57,522 [omego.extern] INFO Executing : omero version 00:50:58 OMERO.py version: 00:50:58 OMERO.server version: 00:50:58 5.6.3-513-2661accdbd-ice36 00:50:58 5.19.6.dev0 00:50:59 2024-10-23 00:50:59,053 [omego.extern] INFO Completed [1.531 s] 00:50:59 2024-10-23 00:50:59,054 [omego.extern] DEBUG Using omero CLI from omero 00:50:59 2024-10-23 00:50:59,054 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ... 00:50:59 2024-10-23 00:50:59,054 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:50:59 2024-10-23 00:50:59,054 [omego.extern] INFO Executing : omero config get --show-password 00:51:00 2024-10-23 00:51:00,500 [omego.extern] INFO Completed [1.446 s] 00:51:00 2024-10-23 00:51:00,501 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:51:00 2024-10-23 00:51:00,501 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version 00:51:01 2024-10-23 00:51:01,107 [omego.extern] INFO Completed [0.606 s] 00:51:01 2024-10-23 00:51:01,108 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.4\n' 00:51:01 2024-10-23 00:51:01,108 [ omego.db] INFO psql version: psql (PostgreSQL) 16.4 00:51:01 00:51:01 2024-10-23 00:51:01,108 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:51:01 2024-10-23 00:51:01,108 [omego.extern] INFO Executing : omero config get --show-password 00:51:02 2024-10-23 00:51:02,646 [omego.extern] INFO Completed [1.538 s] 00:51:02 2024-10-23 00:51:02,646 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:51:02 2024-10-23 00:51:02,647 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo 00:51:02 2024-10-23 00:51:02,974 [omego.extern] INFO Completed [0.327 s] 00:51:02 2024-10-23 00:51:02,974 [ 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' 00:51:02 2024-10-23 00:51:02,974 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1 00:51:02 2024-10-23 00:51:02,974 [omego.extern] INFO Running [current environment]: omero config get --show-password 00:51:02 2024-10-23 00:51:02,974 [omego.extern] INFO Executing : omero config get --show-password 00:51:04 2024-10-23 00:51:04,355 [omego.extern] INFO Completed [1.380 s] 00:51:04 2024-10-23 00:51:04,355 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero 00:51:04 2024-10-23 00:51:04,355 [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 00:51:05 2024-10-23 00:51:05,617 [omego.extern] INFO Completed [1.261 s] 00:51:05 2024-10-23 00:51:05,617 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n' 00:51:05 2024-10-23 00:51:05,617 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0') 00:51:05 2024-10-23 00:51:05,619 [ omego.db] INFO Database is already at OMERO5.4__0 00:51:05 + export LANG=en_US.UTF-8 00:51:05 + LANG=en_US.UTF-8 00:51:05 + export LANGUAGE=en_US:en 00:51:05 + LANGUAGE=en_US:en 00:51:05 + export LC_ALL=en_US.UTF-8 00:51:05 + LC_ALL=en_US.UTF-8 00:51:05 + BUILD_ID=DONT_KILL_ME 00:51:05 + omero admin start 00:51:17 No descriptor given. Using etc/grid/default.xml 00:51:42 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master 00:51:42 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log 00:51:42 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry 00:51:42 Waiting on startup. Use CTRL-C to exit 00:51:42 + omero admin waitup 00:51:43 Waiting on startup. Use CTRL-C to exit 00:51:44 + omero admin diagnostics 00:51:51 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 0x7fef7a775070>, 'Connection to upgrade.openmicroscopy.org.uk timed out. (connect timeout=6.0)')) 00:51:51 00:51:51 ================================================================================ 00:51:51 OMERO Diagnostics (admin) 00:51:51 ================================================================================ 00:51:51 00:51:51 Commands: java -version 11.0.24 (/usr/bin/java) 00:51:51 Commands: python -V 3.9.18 (/home/omero/workspace/OMERO-server/.venv3/bin/python) 00:51:51 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode) 00:51:51 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin) 00:51:51 Commands: psql --version 16.4 (/usr/bin/psql) 00:51:51 Commands: openssl version 3.0.71 (/usr/bin/openssl) 00:51:51 00:51:51 Component: OMERO.py 5.19.6.dev0 00:51:51 Component: OMERO.server 5.6.3-513-2661accdbd-ice36 00:51:51 00:51:51 Server: icegridnode running 00:51:51 Server: Blitz-0 active (pid = 2625, enabled) 00:51:51 Server: Indexer-0 active (pid = 2646, enabled) 00:51:51 Server: OMERO.Glacier2 active (pid = 2674, enabled) 00:51:51 Server: OMERO.IceStorm active (pid = 2670, enabled) 00:51:51 Server: Processor-0 activating (enabled) 00:51:51 Server: Tables-0 activating (enabled) 00:51:51 00:51:51 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists 00:51:51 Log files: Blitz-0.log 21.8 KB errors=1 warnings=0 00:51:51 Log files: DropBox.log n/a 00:51:51 Log files: FileServer.log n/a 00:51:51 Log files: Indexer-0.log 2.6 KB 00:51:51 Log files: MonitorServer.log n/a 00:51:51 Log files: Processor-0.log 592 B 00:51:51 Log files: Tables-0.log 841 B 00:51:51 Log files: TestDropBox.log n/a 00:51:51 Log files: master.err 180 B 00:51:51 Log files: master.out 30.1 KB 00:51:51 Log files: Total size 0.06 MB 00:51:51 00:51:51 00:51:51 Environment:OMERO_HOME=(unset) 00:51:51 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server 00:51:51 Environment:OMERO_NODE=(unset) 00:51:51 Environment:OMERO_MASTER=(unset) 00:51:51 Environment:OMERO_USERDIR=(unset) 00:51:51 Environment:OMERO_TMPDIR=(unset) 00:51:51 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 00:51:51 Environment:PYTHONPATH=(unset) 00:51:51 Environment:ICE_HOME=/opt/ice-3.6.5 00:51:51 Environment:LD_LIBRARY_PATH=(unset) 00:51:51 Environment:DYLD_LIBRARY_PATH=(unset) 00:51:51 00:51:51 OMERO SSL port:4064 00:51:51 OMERO TCP port:4063 00:51:51 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True 00:51:51 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0) 00:51:51 00:51:51 JVM settings: Blitz-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions 00:51:51 JVM settings: Indexer-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions 00:51:51 JVM settings: PixelData-${index} -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions 00:51:51 JVM settings: Repository-${index} -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions 00:51:52 00:51:52 Jar: lib/server/formats-api.jar Bio-Formats API 8.0.0-SNAPSHOT 23 October 2024 2a0fda426e76f17a0940f4d7f943e57083ad7986 00:51:52 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.0.0-SNAPSHOT 23 October 2024 2a0fda426e76f17a0940f4d7f943e57083ad7986 00:51:52 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.0.0-SNAPSHOT 23 October 2024 2a0fda426e76f17a0940f4d7f943e57083ad7986 00:51:52 Jar: lib/server/ome-codecs.jar OME Codecs 1.0.4-SNAPSHOT 23 October 2024 6017c42343df1266447cba310db537bbd5ddd57c 00:51:52 Jar: lib/server/ome-common.jar OME Common Java 6.0.25-SNAPSHOT 23 October 2024 6017c42343df1266447cba310db537bbd5ddd57c 00:51:52 Jar: lib/server/ome-jai.jar OME JAI 0.1.5-SNAPSHOT 23 October 2024 6017c42343df1266447cba310db537bbd5ddd57c 00:51:52 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4-SNAPSHOT 23 October 2024 6017c42343df1266447cba310db537bbd5ddd57c 00:51:52 Jar: lib/server/ome-poi.jar OME POI 5.3.10-SNAPSHOT 23 October 2024 6017c42343df1266447cba310db537bbd5ddd57c 00:51:52 Jar: lib/server/ome-xml.jar OME XML library 6.3.7-SNAPSHOT 23 October 2024 6017c42343df1266447cba310db537bbd5ddd57c 00:51:52 Jar: lib/server/omero-blitz.jar jar 5.7.5-SNAPSHOT 00:51:52 Jar: lib/server/omero-common.jar jar 5.6.8-SNAPSHOT 00:51:52 Jar: lib/server/omero-gateway.jar jar 5.9.4-SNAPSHOT 00:51:52 Jar: lib/server/omero-model.jar jar 5.6.16-SNAPSHOT 00:51:52 Jar: lib/server/omero-renderer.jar jar 5.5.18-SNAPSHOT 00:51:52 Jar: lib/server/omero-romio.jar jar 5.7.8-SNAPSHOT 00:51:52 Jar: lib/server/omero-server.jar jar 5.6.13-SNAPSHOT 00:51:52 + deactivate 00:51:52 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']' 00:51:52 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin 00:51:52 + export PATH 00:51:52 + unset _OLD_VIRTUAL_PATH 00:51:52 + '[' -n '' ']' 00:51:52 + '[' -n /bin/bash -o -n '' ']' 00:51:52 + hash -r 00:51:52 + '[' -n '' ']' 00:51:52 + unset VIRTUAL_ENV 00:51:52 + '[' '!' '' = nondestructive ']' 00:51:52 + unset -f deactivate 00:51:52 Finished: SUCCESS