23:59:37 Started by upstream project "Trigger" build number 91
23:59:37 originally caused by:
23:59:37 Started by timer
23:59:37 Running as SYSTEM
23:59:37 Building remotely on omero (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/OMERO-server
23:59:37 [OMERO-server] $ /bin/bash -xe /tmp/jenkins9954775935059920430.sh
23:59:37 + source /home/settings.env
23:59:37 ++ OMERO_DB_HOST=pg
23:59:37 ++ OMERO_DB_USER=postgres
23:59:37 ++ OMERO_DB_PASS=
23:59:37 ++ OMERO_ROOT_PASS=omero
23:59:37 ++ OMERO_DATA_DIR=/OMERO
23:59:37 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
23:59:37 + OMERO_DB_NAME=OMERO-server
23:59:37 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
23:59:37 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
23:59:37 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
23:59:37 + OMERO_DATA_DIR=/home/omero/omero-server-data
23:59:37 + '[' -e /home/omero/workspace/OMERO-server/OMERO.server ']'
23:59:37 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
23:59:37 ++ deactivate nondestructive
23:59:37 ++ '[' -n '' ']'
23:59:37 ++ '[' -n '' ']'
23:59:37 ++ hash -r
23:59:37 ++ '[' -n '' ']'
23:59:37 ++ unset VIRTUAL_ENV
23:59:37 ++ unset VIRTUAL_ENV_PROMPT
23:59:37 ++ '[' '!' nondestructive = nondestructive ']'
23:59:37 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
23:59:37 ++ export VIRTUAL_ENV
23:59:37 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
23:59:37 ++ 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
23:59:37 ++ export PATH
23:59:37 ++ '[' -n '' ']'
23:59:37 ++ '[' -z '' ']'
23:59:37 ++ _OLD_VIRTUAL_PS1=
23:59:37 ++ PS1='(.venv3) '
23:59:37 ++ export PS1
23:59:37 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
23:59:37 ++ export VIRTUAL_ENV_PROMPT
23:59:37 ++ hash -r
23:59:37 + omero admin stop
00:00:16 Waiting on shutdown. Use CTRL-C to exit
00:00:16 .+ sleep 5
00:00:32 + deactivate
00:00:32 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:00:32 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:00:32 + export PATH
00:00:32 + unset _OLD_VIRTUAL_PATH
00:00:32 + '[' -n '' ']'
00:00:32 + hash -r
00:00:32 + '[' -n '' ']'
00:00:32 + unset VIRTUAL_ENV
00:00:32 + unset VIRTUAL_ENV_PROMPT
00:00:32 + '[' '!' '' = nondestructive ']'
00:00:32 + unset -f deactivate
00:00:32 + rm -rf /home/omero/workspace/OMERO-server/.venv3
00:03:48 + python3.11 -m venv /home/omero/workspace/OMERO-server/.venv3
00:04:11 + '[' false = true ']'
00:04:11 + echo 'Skipping PURGE_DATA:CleanDbAndRepo'
00:04:11 Skipping PURGE_DATA:CleanDbAndRepo
00:04:11 + rm -rf /home/omero/workspace/OMERO-server/omero-blitz-5.8.6-SNAPSHOT-python.zip /home/omero/workspace/OMERO-server/omero_dropbox-5.7.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_marshal-0.9.2.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_py-5.23.1.dev0.tar.gz /home/omero/workspace/OMERO-server/omero_scripts-5.10.1.dev0.tar.gz /home/omero/workspace/OMERO-server/OMERO.server /home/omero/workspace/OMERO-server/omero_web-5.33.1.dev0.tar.gz /home/omero/workspace/OMERO-server/version.properties
00:04:18 Copied 1 artifact from "OMERO-build" build number 74
00:04:18 Copied 5 artifacts from "OMERO-python-superbuild-build" build number 65
00:04:19 Copied 2 artifacts from "OMERO-build-build" build number 76
00:04:19 [OMERO-server] $ /bin/bash -xe /tmp/jenkins8246759160542937789.sh
00:04:19 + source /home/settings.env
00:04:19 ++ OMERO_DB_HOST=pg
00:04:19 ++ OMERO_DB_USER=postgres
00:04:19 ++ OMERO_DB_PASS=
00:04:19 ++ OMERO_ROOT_PASS=omero
00:04:19 ++ OMERO_DATA_DIR=/OMERO
00:04:19 ++ export OMERO_DB_USER OMERO_DB_PASS OMERO_ROOT_PASS OMERO_DATA_DIR
00:04:19 + OMERO_DB_NAME=OMERO-server
00:04:19 + OMERO_DATA_DIR=/home/omero/omero-server-data
00:04:19 + mkdir -p /home/omero/omero-server-data
00:04:19 + OMERO_DIST=/home/omero/workspace/OMERO-server/OMERO.server
00:04:19 + export OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:04:19 + OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:04:19 + export ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:04:19 + ZIP_FILE=/home/omero/workspace/OMERO-server/omero-blitz-VERSION-python.zip
00:04:19 + export VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:04:19 + VERSION_PROPERTIES=/home/omero/workspace/OMERO-server/version.properties
00:04:19 ++ ls OMERO.server-5.6.3-677-18978195ab-ice36-b74.zip
00:04:19 + ZIP=OMERO.server-5.6.3-677-18978195ab-ice36-b74.zip
00:04:19 + '[' '!' -z '' ']'
00:04:19 + DIST=OMERO.server-5.6.3-677-18978195ab-ice36-b74
00:04:19 + unzip OMERO.server-5.6.3-677-18978195ab-ice36-b74.zip
00:04:19 Archive: OMERO.server-5.6.3-677-18978195ab-ice36-b74.zip
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/blitz/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/grid/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/profiles/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/templates/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/templates/error/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/templates/grid/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/client/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/luts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/luts/janelia/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/luts/matplotlib/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/luts/ncsa_paledit/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/luts/seaborn/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/luts/wcif/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/analysis_scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/annotation_scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/export_scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/figure_scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/import_scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/scripts/omero/util_scripts/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/lib/server/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/misc/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__1/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__10/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__11/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__2/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__3/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__4/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__5/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__6/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__7/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__8/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__9/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__4/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__5/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__6/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__7/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.1__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.2__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.2__0/t/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.3__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.4__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.0__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.1__1/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.2__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4DEV__1/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4DEV__2/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4DEV__3/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/var/
00:04:19 creating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/var/tmp/
00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/LICENSE.txt
00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/backup.cfg
00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/blitz/mail-senders.example
00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/blitz/mail-server.example
00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/build.properties
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00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/env.sh
00:04:19 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/etc/hibernate.properties
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00:04:39 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/crystalclear.txt
00:04:39 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/django.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/dom4j.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/epl-v1.0.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/fbsd.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/freemarker.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/gpl-v2.0.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/gpl.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/gtest.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/iconsweets_license.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/jamon.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/jmock.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/jquery.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/jtidy.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/lgpl-3.0.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/lgpl-v2.0.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/lgpl-v2.1.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/lgpl-v3.0.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/lgpl.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/matplotlib.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/mit.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/mpl-v1_0.htm
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/npl-1_1.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/path.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/pil.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/postgresql.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/psf-v2.0.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/psf-v2.5.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/scons.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/slf4j.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/tablelayout.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/which.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/zlib-libpng.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/share/licenses/zpl-v2.1.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/README.txt
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/misc/Makefile
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/misc/current.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/misc/enums.py
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__1/OMERO3__7.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__10/OMERO3A__9.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__11/OMERO3A__10.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__11/OMERO3A__5.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__2/OMERO3A__1.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__3/OMERO3A__2.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__3/OMERO3__5.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__4/OMERO3A__3.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__4/OMERO3__5.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__5/OMERO3A__4.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__6/OMERO3A__5.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__7/OMERO3A__6.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__8/OMERO3A__6.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3A__9/OMERO3A__8.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__4/OMERO3__1.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__5/OMERO3__4.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__6/OMERO3__5.sql
00:04:40 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO3__7/OMERO3__6.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.1__0/OMERO4__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.2__0/OMERO4.1__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.2__0/t/OMERO4.1__0.py
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.2__0/t/OMERO4.1__0.test
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.3__0/OMERO4.2__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.3__0/omero-4.2-data-fix.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.4__0/OMERO4.1__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4.4__0/OMERO4.3__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO4__0/OMERO3A__11.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-fix.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.0__0/2014-SV2-empty-passwords-list.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.0__0/OMERO4.4__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.1__1/OMERO5.0__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.1__1/OMERO5.1-delete-and-disable-shares.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.1__1/OMERO5.1-enable-shares.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.1__1/OMERO5.1__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.2__0/OMERO5.1__1.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.2__0/OMERO5.2-delete-and-disable-shares.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.2__0/OMERO5.2-enable-shares.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/OMERO5.2__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/OMERO5.3-index-files.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/delete-ns-orphans.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/reverse_shape_color_argb_to_rgba.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.3__0/shape_color_argb_to_rgba.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4DEV__1/OMERO5.4DEV__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4DEV__2/OMERO5.4DEV__1.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4DEV__3/OMERO5.4DEV__2.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/OMERO5.3__0.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/OMERO5.3__1.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/OMERO5.4DEV__3.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/psql-footer.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/psql-header.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/schema.sql
00:04:41 inflating: OMERO.server-5.6.3-677-18978195ab-ice36-b74/sql/psql/OMERO5.4__0/views.sql
00:04:41 + rm -f OMERO.server-5.6.3-677-18978195ab-ice36-b74.zip
00:04:41 + mv /home/omero/workspace/OMERO-server/OMERO.server-5.6.3-677-18978195ab-ice36-b74 /home/omero/workspace/OMERO-server/OMERO.server
00:04:41 + source /home/omero/workspace/OMERO-server/.venv3/bin/activate
00:04:41 ++ deactivate nondestructive
00:04:41 ++ '[' -n '' ']'
00:04:41 ++ '[' -n '' ']'
00:04:41 ++ hash -r
00:04:41 ++ '[' -n '' ']'
00:04:41 ++ unset VIRTUAL_ENV
00:04:41 ++ unset VIRTUAL_ENV_PROMPT
00:04:41 ++ '[' '!' nondestructive = nondestructive ']'
00:04:41 ++ VIRTUAL_ENV=/home/omero/workspace/OMERO-server/.venv3
00:04:41 ++ export VIRTUAL_ENV
00:04:41 ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:04:41 ++ 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
00:04:41 ++ export PATH
00:04:41 ++ '[' -n '' ']'
00:04:41 ++ '[' -z '' ']'
00:04:41 ++ _OLD_VIRTUAL_PS1=
00:04:41 ++ PS1='(.venv3) '
00:04:41 ++ export PS1
00:04:41 ++ VIRTUAL_ENV_PROMPT='(.venv3) '
00:04:41 ++ export VIRTUAL_ENV_PROMPT
00:04:41 ++ hash -r
00:04:41 + pip install -U pip
00:04:43 Requirement already satisfied: pip in ./.venv3/lib64/python3.11/site-packages (22.3.1)
00:04:43 Collecting pip
00:04:43 Using cached pip-26.2.1-py3-none-any.whl (1.8 MB)
00:04:44 Installing collected packages: pip
00:04:44 Attempting uninstall: pip
00:04:44 Found existing installation: pip 22.3.1
00:04:45 Uninstalling pip-22.3.1:
00:04:45 Successfully uninstalled pip-22.3.1
00:05:03 Successfully installed pip-26.2.1
00:05:03 + pip install https://github.com/glencoesoftware/zeroc-ice-py-linux-x86_64/releases/download/20240202/zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl
00:05:04 Collecting zeroc-ice==3.6.5
00:05:05 Downloading zeroc_ice-3.6.5-cp311-cp311-manylinux_2_28_x86_64.whl (37.3 MB)
00:05:07 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 37.3/37.3 MB 15.5 MB/s 0:00:02
00:05:07 Installing collected packages: zeroc-ice
00:05:11 Successfully installed zeroc-ice-3.6.5
00:05:11 + pip install markdown
00:05:12 Collecting markdown
00:05:12 Using cached markdown-3.10.3-py3-none-any.whl.metadata (5.1 kB)
00:05:12 Using cached markdown-3.10.3-py3-none-any.whl (110 kB)
00:05:12 Installing collected packages: markdown
00:05:14 Successfully installed markdown-3.10.3
00:05:14 + pip install reportlab
00:05:15 Collecting reportlab
00:05:15 Using cached reportlab-5.0.1-py3-none-any.whl.metadata (1.6 kB)
00:05:15 Collecting pillow>=9.0.0 (from reportlab)
00:05:15 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.1 kB)
00:05:15 Collecting charset-normalizer (from reportlab)
00:05:15 Using cached charset_normalizer-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (45 kB)
00:05:16 Using cached reportlab-5.0.1-py3-none-any.whl (2.0 MB)
00:05:16 Using cached pillow-12.3.0-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.9 MB)
00:05:16 Using cached charset_normalizer-3.5.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (262 kB)
00:05:16 Installing collected packages: pillow, charset-normalizer, reportlab
00:05:27
00:05:27 Successfully installed charset-normalizer-3.5.1 pillow-12.3.0 reportlab-5.0.1
00:05:27 + pip install pyarrow
00:05:28 Collecting pyarrow
00:05:28 Using cached pyarrow-25.0.1-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (3.0 kB)
00:05:28 Using cached pyarrow-25.0.1-cp311-cp311-manylinux_2_28_x86_64.whl (50.1 MB)
00:05:29 Installing collected packages: pyarrow
00:05:42 Successfully installed pyarrow-25.0.1
00:05:42 + pip install omego
00:05:43 Collecting omego
00:05:43 Using cached omego-0.8.0-py3-none-any.whl.metadata (1.9 kB)
00:05:43 Collecting future (from omego)
00:05:43 Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
00:05:43 Collecting yaclifw>=0.1.1 (from omego)
00:05:43 Using cached yaclifw-0.2.0-py3-none-any.whl
00:05:44 Collecting six (from yaclifw>=0.1.1->omego)
00:05:44 Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB)
00:05:44 Using cached omego-0.8.0-py3-none-any.whl (41 kB)
00:05:44 Using cached future-1.0.0-py3-none-any.whl (491 kB)
00:05:44 Using cached six-1.17.0-py2.py3-none-any.whl (11 kB)
00:05:44 Installing collected packages: six, future, yaclifw, omego
00:05:51
00:05:51 Successfully installed future-1.0.0 omego-0.8.0 six-1.17.0 yaclifw-0.2.0
00:05:51 + pip install tables
00:05:53 Collecting tables
00:05:53 Using cached tables-3.11.1-cp311-abi3-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.1 kB)
00:05:53 Collecting numpy>=1.20.0 (from tables)
00:05:53 Using cached numpy-2.4.6-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (6.6 kB)
00:05:53 Collecting numexpr>=2.6.2 (from tables)
00:05:53 Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB)
00:05:53 Collecting packaging (from tables)
00:05:53 Using cached packaging-26.3-py3-none-any.whl.metadata (3.5 kB)
00:05:54 Collecting py-cpuinfo (from tables)
00:05:54 Using cached py_cpuinfo-9.0.0-py3-none-any.whl.metadata (794 bytes)
00:05:54 Collecting blosc2>=2.3.0 (from tables)
00:05:54 Using cached blosc2-4.12.0-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (7.8 kB)
00:05:54 Collecting ndindex (from blosc2>=2.3.0->tables)
00:05:54 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (3.6 kB)
00:05:54 Collecting msgpack (from blosc2>=2.3.0->tables)
00:05:54 Using cached msgpack-1.2.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
00:05:55 Collecting pydantic (from blosc2>=2.3.0->tables)
00:05:55 Using cached pydantic-2.13.5-py3-none-any.whl.metadata (110 kB)
00:05:55 Collecting httpx[http2] (from blosc2>=2.3.0->tables)
00:05:55 Using cached httpx-0.28.1-py3-none-any.whl.metadata (7.1 kB)
00:05:55 Collecting rich (from blosc2>=2.3.0->tables)
00:05:55 Using cached rich-15.0.0-py3-none-any.whl.metadata (18 kB)
00:05:55 Collecting threadpoolctl (from blosc2>=2.3.0->tables)
00:05:55 Using cached threadpoolctl-3.6.0-py3-none-any.whl.metadata (13 kB)
00:05:55 Collecting anyio (from httpx[http2]->blosc2>=2.3.0->tables)
00:05:55 Using cached anyio-4.15.1-py3-none-any.whl.metadata (4.7 kB)
00:05:55 Collecting certifi (from httpx[http2]->blosc2>=2.3.0->tables)
00:05:56 Using cached certifi-2026.7.22-py3-none-any.whl.metadata (2.5 kB)
00:05:56 Collecting httpcore==1.* (from httpx[http2]->blosc2>=2.3.0->tables)
00:05:56 Using cached httpcore-1.0.9-py3-none-any.whl.metadata (21 kB)
00:05:56 Collecting idna (from httpx[http2]->blosc2>=2.3.0->tables)
00:05:56 Using cached idna-3.19-py3-none-any.whl.metadata (9.2 kB)
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00:05:56 Collecting hyperframe<7,>=6.1 (from h2<5,>=3->httpx[http2]->blosc2>=2.3.0->tables)
00:05:56 Using cached hyperframe-6.1.0-py3-none-any.whl.metadata (4.3 kB)
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00:05:56 Using cached hpack-4.2.0-py3-none-any.whl.metadata (3.3 kB)
00:05:56 Collecting h11>=0.16 (from httpcore==1.*->httpx[http2]->blosc2>=2.3.0->tables)
00:05:56 Using cached h11-0.16.0-py3-none-any.whl.metadata (8.3 kB)
00:05:57 Collecting typing_extensions>=4.16.0 (from anyio->httpx[http2]->blosc2>=2.3.0->tables)
00:05:57 Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB)
00:05:57 Collecting annotated-types>=0.6.0 (from pydantic->blosc2>=2.3.0->tables)
00:05:57 Using cached annotated_types-0.8.0-py3-none-any.whl.metadata (15 kB)
00:05:58 Collecting pydantic-core==2.46.5 (from pydantic->blosc2>=2.3.0->tables)
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00:05:58 Collecting typing-inspection>=0.4.2 (from pydantic->blosc2>=2.3.0->tables)
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00:05:58 Collecting markdown-it-py>=2.2.0 (from rich->blosc2>=2.3.0->tables)
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00:05:58 Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich->blosc2>=2.3.0->tables)
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00:05:58 Using cached blosc2-4.12.0-cp311-abi3-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (6.6 MB)
00:05:59 Using cached numexpr-2.14.2-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (443 kB)
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00:05:59 Using cached msgpack-1.2.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (422 kB)
00:05:59 Using cached ndindex-1.10.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (516 kB)
00:06:00 Using cached packaging-26.3-py3-none-any.whl (129 kB)
00:06:00 Using cached py_cpuinfo-9.0.0-py3-none-any.whl (22 kB)
00:06:00 Using cached pydantic-2.13.5-py3-none-any.whl (472 kB)
00:06:00 Using cached pydantic_core-2.46.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.1 MB)
00:06:00 Using cached annotated_types-0.8.0-py3-none-any.whl (13 kB)
00:06:00 Using cached typing_inspection-0.4.4-py3-none-any.whl (14 kB)
00:06:00 Using cached rich-15.0.0-py3-none-any.whl (310 kB)
00:06:00 Using cached pygments-2.21.0-py3-none-any.whl (1.3 MB)
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00:06:00 Using cached threadpoolctl-3.6.0-py3-none-any.whl (18 kB)
00:06:00 Installing collected packages: py-cpuinfo, typing_extensions, threadpoolctl, pygments, packaging, numpy, ndindex, msgpack, mdurl, idna, hyperframe, hpack, h11, certifi, annotated-types, typing-inspection, pydantic-core, numexpr, markdown-it-py, httpcore, h2, anyio, rich, pydantic, httpx, blosc2, tables
00:06:59
00:06:59 Successfully installed annotated-types-0.8.0 anyio-4.15.1 blosc2-4.12.0 certifi-2026.7.22 h11-0.16.0 h2-4.4.1 hpack-4.2.0 httpcore-1.0.9 httpx-0.28.1 hyperframe-6.1.0 idna-3.19 markdown-it-py-4.2.0 mdurl-0.1.2 msgpack-1.2.2 ndindex-1.10.1 numexpr-2.14.2 numpy-2.4.6 packaging-26.3 py-cpuinfo-9.0.0 pydantic-2.13.5 pydantic-core-2.46.5 pygments-2.21.0 rich-15.0.0 tables-3.11.1 threadpoolctl-3.6.0 typing-inspection-0.4.4 typing_extensions-4.16.0
00:06:59 + pip install jinja2
00:07:00 Collecting jinja2
00:07:00 Using cached jinja2-3.1.6-py3-none-any.whl.metadata (2.9 kB)
00:07:00 Collecting MarkupSafe>=2.0 (from jinja2)
00:07:01 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.7 kB)
00:07:01 Using cached jinja2-3.1.6-py3-none-any.whl (134 kB)
00:07:01 Using cached markupsafe-3.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (22 kB)
00:07:01 Installing collected packages: MarkupSafe, jinja2
00:07:02
00:07:02 Successfully installed MarkupSafe-3.0.3 jinja2-3.1.6
00:07:02 + pip install omero-py
00:07:03 Collecting omero-py
00:07:03 Using cached omero_py-5.23.0-py3-none-any.whl.metadata (6.5 kB)
00:07:03 Collecting appdirs (from omero-py)
00:07:03 Using cached appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
00:07:03 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py) (1.0.0)
00:07:03 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (2.4.6)
00:07:03 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (12.3.0)
00:07:04 Collecting PyYAML (from omero-py)
00:07:04 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB)
00:07:04 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py) (3.6.5)
00:07:04 Collecting requests (from omero-py)
00:07:04 Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB)
00:07:04 Collecting portalocker (from omero-py)
00:07:04 Using cached portalocker-4.3.0-py3-none-any.whl.metadata (11 kB)
00:07:04 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.5.1)
00:07:04 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (3.19)
00:07:04 Collecting urllib3<3,>=1.26 (from requests->omero-py)
00:07:04 Using cached urllib3-2.7.0-py3-none-any.whl.metadata (6.9 kB)
00:07:04 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py) (2026.7.22)
00:07:04 Using cached omero_py-5.23.0-py3-none-any.whl (2.8 MB)
00:07:04 Using cached appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
00:07:04 Using cached portalocker-4.3.0-py3-none-any.whl (129 kB)
00:07:04 Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB)
00:07:05 Using cached requests-2.34.2-py3-none-any.whl (73 kB)
00:07:05 Using cached urllib3-2.7.0-py3-none-any.whl (131 kB)
00:07:05 Installing collected packages: appdirs, urllib3, PyYAML, portalocker, requests, omero-py
00:07:26
00:07:26 Successfully installed PyYAML-6.0.3 appdirs-1.4.4 omero-py-5.23.0 portalocker-4.3.0 requests-2.34.2 urllib3-2.7.0
00:07:26 + pip install git+https://github.com/snoopycrimecop/omero-metadata.git@merge_ci#egg=omero-metadata
00:07:27 Collecting omero-metadata
00:07:27 Cloning https://github.com/snoopycrimecop/omero-metadata.git (to revision merge_ci) to /tmp/pip-install-3vv__t6a/omero-metadata_91c718f5bd4848dba04b27183f456fc1
00:07:27 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-metadata.git /tmp/pip-install-3vv__t6a/omero-metadata_91c718f5bd4848dba04b27183f456fc1
00:07:29 Resolved https://github.com/snoopycrimecop/omero-metadata.git to commit 7f9848cadecc726120aa20f6c79bf022f2b526a0
00:07:29 Installing build dependencies: started
00:07:30 Installing build dependencies: finished with status 'done'
00:07:30 Getting requirements to build wheel: started
00:07:31 Getting requirements to build wheel: finished with status 'done'
00:07:31 Preparing metadata (pyproject.toml): started
00:07:31 Preparing metadata (pyproject.toml): finished with status 'done'
00:07:31 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-metadata) (5.23.0)
00:07:31 Collecting pandas<3,>=2 (from omero-metadata)
00:07:31 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (91 kB)
00:07:31 Requirement already satisfied: numpy>=1.23.2 in ./.venv3/lib64/python3.11/site-packages (from pandas<3,>=2->omero-metadata) (2.4.6)
00:07:31 Collecting python-dateutil>=2.8.2 (from pandas<3,>=2->omero-metadata)
00:07:31 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)
00:07:32 Collecting pytz>=2020.1 (from pandas<3,>=2->omero-metadata)
00:07:32 Using cached pytz-2026.3.post1-py2.py3-none-any.whl.metadata (22 kB)
00:07:32 Collecting tzdata>=2022.7 (from pandas<3,>=2->omero-metadata)
00:07:32 Using cached tzdata-2026.3-py2.py3-none-any.whl.metadata (1.4 kB)
00:07:32 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.4.4)
00:07:32 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (1.0.0)
00:07:32 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (12.3.0)
00:07:32 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (6.0.3)
00:07:32 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (3.6.5)
00:07:32 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (2.34.2)
00:07:32 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-metadata) (4.3.0)
00:07:32 Requirement already satisfied: six>=1.5 in ./.venv3/lib64/python3.11/site-packages (from python-dateutil>=2.8.2->pandas<3,>=2->omero-metadata) (1.17.0)
00:07:32 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.5.1)
00:07:32 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (3.19)
00:07:32 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2.7.0)
00:07:32 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-metadata) (2026.7.22)
00:07:32 Using cached pandas-2.3.3-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (12.8 MB)
00:07:32 Using cached python_dateutil-2.9.0.post0-py2.py3-none-any.whl (229 kB)
00:07:32 Using cached pytz-2026.3.post1-py2.py3-none-any.whl (508 kB)
00:07:32 Using cached tzdata-2026.3-py2.py3-none-any.whl (348 kB)
00:07:32 Building wheels for collected packages: omero-metadata
00:07:32 Building wheel for omero-metadata (pyproject.toml): started
00:07:33 Building wheel for omero-metadata (pyproject.toml): finished with status 'done'
00:07:33 Created wheel for omero-metadata: filename=omero_metadata-0.14.1.dev0-py3-none-any.whl size=39360 sha256=28934ec96db4f3b9789464248578faa3605c67c8ed885f51c1196294c7f49fc0
00:07:33 Stored in directory: /tmp/pip-ephem-wheel-cache-o3_9ala_/wheels/6b/49/26/d56ff0fc3b918823c05ff86cc0686c3a577289ddc39151269b
00:07:33 Successfully built omero-metadata
00:07:33 Installing collected packages: pytz, tzdata, python-dateutil, pandas, omero-metadata
00:08:32
00:08:33 Successfully installed omero-metadata-0.14.1.dev0 pandas-2.3.3 python-dateutil-2.9.0.post0 pytz-2026.3.post1 tzdata-2026.3
00:08:33 + pip install git+https://github.com/snoopycrimecop/omero-cli-render.git@merge_ci#egg=omero-cli-render
00:08:34 Collecting omero-cli-render
00:08:34 Cloning https://github.com/snoopycrimecop/omero-cli-render.git (to revision merge_ci) to /tmp/pip-install-lweamo5w/omero-cli-render_22e6953de5f747fdaebab253322c30c0
00:08:34 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-render.git /tmp/pip-install-lweamo5w/omero-cli-render_22e6953de5f747fdaebab253322c30c0
00:08:35 Running command git checkout -b merge_ci --track origin/merge_ci
00:08:36 Switched to a new branch 'merge_ci'
00:08:36 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:08:36 Resolved https://github.com/snoopycrimecop/omero-cli-render.git to commit 438e3b43e894ce6181cc2d3602623a7d89ea49d2
00:08:36 Installing build dependencies: started
00:08:37 Installing build dependencies: finished with status 'done'
00:08:37 Getting requirements to build wheel: started
00:08:37 Getting requirements to build wheel: finished with status 'done'
00:08:37 Preparing metadata (pyproject.toml): started
00:08:37 Preparing metadata (pyproject.toml): finished with status 'done'
00:08:37 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (6.0.3)
00:08:37 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-render) (5.23.0)
00:08:37 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.4.4)
00:08:37 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (1.0.0)
00:08:37 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.4.6)
00:08:37 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (12.3.0)
00:08:37 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (3.6.5)
00:08:37 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (2.34.2)
00:08:37 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-render) (4.3.0)
00:08:37 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.5.1)
00:08:37 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (3.19)
00:08:37 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2.7.0)
00:08:37 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-cli-render) (2026.7.22)
00:08:37 Building wheels for collected packages: omero-cli-render
00:08:37 Building wheel for omero-cli-render (pyproject.toml): started
00:08:38 Building wheel for omero-cli-render (pyproject.toml): finished with status 'done'
00:08:38 Created wheel for omero-cli-render: filename=omero_cli_render-0.8.2.dev0-py3-none-any.whl size=19841 sha256=b2cf5e15efd7b555d625493e8a4529539783f609b7ed26e510386ca0cb29c728
00:08:38 Stored in directory: /tmp/pip-ephem-wheel-cache-3kiw1vnk/wheels/cc/67/86/ff54ee10a8ea8ae7a21cceb878741010ef1de4a7d93df129ee
00:08:38 Successfully built omero-cli-render
00:08:38 Installing collected packages: omero-cli-render
00:08:38 Successfully installed omero-cli-render-0.8.2.dev0
00:08:38 + pip install git+https://github.com/snoopycrimecop/omero-cli-duplicate.git@merge_ci#egg=omero-cli-duplicate
00:08:39 Collecting omero-cli-duplicate
00:08:39 Cloning https://github.com/snoopycrimecop/omero-cli-duplicate.git (to revision merge_ci) to /tmp/pip-install-_ehtsrw9/omero-cli-duplicate_ce6632731ad34d528b174111a8e4900a
00:08:39 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-duplicate.git /tmp/pip-install-_ehtsrw9/omero-cli-duplicate_ce6632731ad34d528b174111a8e4900a
00:08:40 Running command git checkout -b merge_ci --track origin/merge_ci
00:08:40 Switched to a new branch 'merge_ci'
00:08:40 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:08:40 Resolved https://github.com/snoopycrimecop/omero-cli-duplicate.git to commit 5abd1307f07bee8e19d71d3e9dac911612268bbc
00:08:40 Installing build dependencies: started
00:08:42 Installing build dependencies: finished with status 'done'
00:08:42 Getting requirements to build wheel: started
00:08:42 Getting requirements to build wheel: finished with status 'done'
00:08:42 Preparing metadata (pyproject.toml): started
00:08:42 Preparing metadata (pyproject.toml): finished with status 'done'
00:08:42 Requirement already satisfied: omero-py>=5.8 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-duplicate) (5.23.0)
00:08:42 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.4.4)
00:08:42 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (1.0.0)
00:08:42 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (2.4.6)
00:08:42 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (12.3.0)
00:08:42 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.8->omero-cli-duplicate) (6.0.3)
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00:08:42 Building wheels for collected packages: omero-cli-duplicate
00:08:42 Building wheel for omero-cli-duplicate (pyproject.toml): started
00:08:43 Building wheel for omero-cli-duplicate (pyproject.toml): finished with status 'done'
00:08:43 Created wheel for omero-cli-duplicate: filename=omero_cli_duplicate-0.4.1.dev0-py3-none-any.whl size=11540 sha256=39a45a4b46c7ed6e055b12a4848a7c44370bb268c6255c9e72fae1b214d31e41
00:08:43 Stored in directory: /tmp/pip-ephem-wheel-cache-418ctuiq/wheels/28/e4/77/20667ec1be487a1994d60f59ce11eeba2ac0c8c34aea209b46
00:08:43 Successfully built omero-cli-duplicate
00:08:43 Installing collected packages: omero-cli-duplicate
00:08:43 Successfully installed omero-cli-duplicate-0.4.1.dev0
00:08:43 + pip install git+https://github.com/snoopycrimecop/omero-cli-zarr.git@merge_ci#egg=omero-cli-zarr
00:08:44 Collecting omero-cli-zarr
00:08:44 Cloning https://github.com/snoopycrimecop/omero-cli-zarr.git (to revision merge_ci) to /tmp/pip-install-eq9i4eeu/omero-cli-zarr_4572dfdb36e34c2db964902ba4ad167c
00:08:44 Running command git clone --filter=blob:none --quiet https://github.com/snoopycrimecop/omero-cli-zarr.git /tmp/pip-install-eq9i4eeu/omero-cli-zarr_4572dfdb36e34c2db964902ba4ad167c
00:08:45 Running command git checkout -b merge_ci --track origin/merge_ci
00:08:46 Switched to a new branch 'merge_ci'
00:08:46 branch 'merge_ci' set up to track 'origin/merge_ci'.
00:08:46 Resolved https://github.com/snoopycrimecop/omero-cli-zarr.git to commit 48c019d30cf2e05cb5416322efb501389bec9cfe
00:08:46 Installing build dependencies: started
00:08:47 Installing build dependencies: finished with status 'done'
00:08:47 Getting requirements to build wheel: started
00:08:47 Getting requirements to build wheel: finished with status 'done'
00:08:47 Installing backend dependencies: started
00:08:49 Installing backend dependencies: finished with status 'done'
00:08:49 Preparing metadata (pyproject.toml): started
00:08:50 Preparing metadata (pyproject.toml): finished with status 'done'
00:08:50 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-cli-zarr) (5.23.0)
00:08:50 Collecting ome-zarr>=0.13.0 (from omero-cli-zarr)
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00:08:50 Requirement already satisfied: numpy in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.4.6)
00:08:50 Collecting dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
00:08:50 Using cached dask-2026.8.0-py3-none-any.whl.metadata (3.8 kB)
00:08:50 Collecting zarr>=3.0.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
00:08:50 Using cached zarr-3.1.6-py3-none-any.whl.metadata (8.6 kB)
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00:08:51 Using cached fsspec-2026.7.0-py3-none-any.whl.metadata (10 kB)
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00:08:51 Using cached aiohttp-3.14.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (8.3 kB)
00:08:51 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from ome-zarr>=0.13.0->omero-cli-zarr) (2.34.2)
00:08:51 Collecting scikit-image>=0.19.0 (from ome-zarr>=0.13.0->omero-cli-zarr)
00:08:52 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl.metadata (15 kB)
00:08:52 Collecting toolz (from ome-zarr>=0.13.0->omero-cli-zarr)
00:08:52 Using cached toolz-1.1.0-py3-none-any.whl.metadata (5.1 kB)
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00:08:52 Using cached ome_zarr_models-1.7-py3-none-any.whl.metadata (3.0 kB)
00:08:52 Collecting Deprecated (from ome-zarr>=0.13.0->omero-cli-zarr)
00:08:52 Using cached deprecated-1.3.1-py2.py3-none-any.whl.metadata (5.9 kB)
00:08:52 Collecting click>=8.1 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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00:08:52 Using cached cloudpickle-3.1.2-py3-none-any.whl.metadata (7.1 kB)
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00:08:53 Collecting partd>=1.4.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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00:08:53 Collecting importlib_metadata>=4.13.0 (from dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
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00:08:54 Collecting pydantic-core==2.41.5 (from pydantic<2.13,>=2.11.5->ome-zarr-models>=1.6->ome-zarr>=0.13.0->omero-cli-zarr)
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00:08:54 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-cli-zarr) (1.4.4)
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00:08:54 Collecting locket (from partd>=1.4.0->dask!=2025.12.*,!=2026.1.*,!=2026.2.*,>=2025.2.0->ome-zarr>=0.13.0->omero-cli-zarr)
00:08:54 Using cached locket-1.0.0-py2.py3-none-any.whl.metadata (2.8 kB)
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00:09:00 Using cached attrs-26.1.0-py3-none-any.whl (67 kB)
00:09:00 Using cached frozenlist-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux_2_28_x86_64.manylinux_2_5_x86_64.whl (231 kB)
00:09:00 Using cached propcache-0.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (58 kB)
00:09:00 Using cached scikit_image-0.26.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl (13.7 MB)
00:09:00 Using cached imageio-2.37.4-py3-none-any.whl (318 kB)
00:09:00 Using cached lazy_loader-0.5-py3-none-any.whl (8.0 kB)
00:09:00 Using cached networkx-3.6.1-py3-none-any.whl (2.1 MB)
00:09:00 Using cached scipy-1.17.1-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl (35.3 MB)
00:09:00 Using cached tifffile-2026.3.3-py3-none-any.whl (243 kB)
00:09:00 Using cached toolz-1.1.0-py3-none-any.whl (58 kB)
00:09:01 Using cached zarr-3.1.6-py3-none-any.whl (295 kB)
00:09:01 Using cached donfig-0.8.1.post1-py3-none-any.whl (21 kB)
00:09:01 Using cached google_crc32c-1.8.0-cp311-cp311-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (33 kB)
00:09:01 Using cached numcodecs-0.16.5-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (9.1 MB)
00:09:01 Using cached zipp-4.1.0-py3-none-any.whl (10 kB)
00:09:01 Using cached deprecated-1.3.1-py2.py3-none-any.whl (11 kB)
00:09:01 Using cached locket-1.0.0-py2.py3-none-any.whl (4.4 kB)
00:09:01 Using cached rangehttpserver-1.4.0-py2.py3-none-any.whl (7.8 kB)
00:09:01 Building wheels for collected packages: omero-cli-zarr
00:09:01 Building wheel for omero-cli-zarr (pyproject.toml): started
00:09:02 Building wheel for omero-cli-zarr (pyproject.toml): finished with status 'done'
00:09:02 Created wheel for omero-cli-zarr: filename=omero_cli_zarr-0.5.5.dev186+g48c019d-py3-none-any.whl size=39537 sha256=1779d778b0c4dd8bec2a4038c25a93b0521af79f69557671c1952b902516d6b3
00:09:02 Stored in directory: /tmp/pip-ephem-wheel-cache-fk72cg7d/wheels/23/9b/a6/58188c5a16d0876457bd9f2c6a2fb9759c671db67032a0e529
00:09:02 Successfully built omero-cli-zarr
00:09:02 Installing collected packages: rangehttpserver, zipp, wrapt, toolz, tifffile, scipy, pydantic-core, propcache, numcodecs, networkx, multidict, locket, lazy-loader, jmespath, imageio, google-crc32c, fsspec, frozenlist, donfig, cloudpickle, click, attrs, aioitertools, aiohappyeyeballs, zarr, yarl, scikit-image, pydantic, partd, importlib_metadata, Deprecated, botocore, aiosignal, pydantic-zarr, dask, aiohttp, ome-zarr-models, aiobotocore, s3fs, ome-zarr, omero-cli-zarr
00:09:39 Attempting uninstall: pydantic-core
00:09:39 Found existing installation: pydantic_core 2.46.5
00:09:39 Uninstalling pydantic_core-2.46.5:
00:09:39 Successfully uninstalled pydantic_core-2.46.5
00:10:14 Attempting uninstall: pydantic
00:10:14 Found existing installation: pydantic 2.13.5
00:10:14 Uninstalling pydantic-2.13.5:
00:10:14 Successfully uninstalled pydantic-2.13.5
00:10:54
00:10:54 Successfully installed Deprecated-1.3.1 aiobotocore-3.9.1 aiohappyeyeballs-2.7.1 aiohttp-3.14.3 aioitertools-0.13.0 aiosignal-1.4.0 attrs-26.1.0 botocore-1.43.75 click-8.5.0 cloudpickle-3.1.2 dask-2026.8.0 donfig-0.8.1.post1 frozenlist-1.8.0 fsspec-2026.7.0 google-crc32c-1.8.0 imageio-2.37.4 importlib_metadata-9.0.1 jmespath-1.1.0 lazy-loader-0.5 locket-1.0.0 multidict-6.8.0 networkx-3.6.1 numcodecs-0.16.5 ome-zarr-0.18.0 ome-zarr-models-1.7 omero-cli-zarr-0.5.5.dev186+g48c019d partd-1.4.2 propcache-0.5.2 pydantic-2.12.5 pydantic-core-2.41.5 pydantic-zarr-0.9.2 rangehttpserver-1.4.0 s3fs-2026.7.0 scikit-image-0.26.0 scipy-1.17.1 tifffile-2026.3.3 toolz-1.1.0 wrapt-2.4.0 yarl-1.24.5 zarr-3.1.6 zipp-4.1.0
00:10:54 + pip install omero-certificates
00:10:55 Collecting omero-certificates
00:10:55 Using cached omero_certificates-0.4.0-py3-none-any.whl.metadata (3.3 kB)
00:10:55 Requirement already satisfied: omero-py>=5.6.0 in ./.venv3/lib64/python3.11/site-packages (from omero-certificates) (5.23.0)
00:10:55 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.4.4)
00:10:55 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (1.0.0)
00:10:55 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.4.6)
00:10:55 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (12.3.0)
00:10:55 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (6.0.3)
00:10:55 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (3.6.5)
00:10:55 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (2.34.2)
00:10:55 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.6.0->omero-certificates) (4.3.0)
00:10:55 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.5.1)
00:10:55 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (3.19)
00:10:55 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2.7.0)
00:10:55 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.6.0->omero-certificates) (2026.7.22)
00:10:55 Using cached omero_certificates-0.4.0-py3-none-any.whl (11 kB)
00:10:56 Installing collected packages: omero-certificates
00:10:56 Successfully installed omero-certificates-0.4.0
00:10:56 + for x in *.tar.gz
00:10:56 + pip install -U omero_dropbox-5.7.1.dev0.tar.gz
00:10:57 Processing ./omero_dropbox-5.7.1.dev0.tar.gz
00:10:57 Installing build dependencies: started
00:10:58 Installing build dependencies: finished with status 'done'
00:10:58 Getting requirements to build wheel: started
00:10:58 Getting requirements to build wheel: finished with status 'done'
00:10:58 Preparing metadata (pyproject.toml): started
00:10:59 Preparing metadata (pyproject.toml): finished with status 'done'
00:10:59 Requirement already satisfied: omero-py in ./.venv3/lib64/python3.11/site-packages (from omero-dropbox==5.7.1.dev0) (5.23.0)
00:10:59 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.4.4)
00:10:59 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (1.0.0)
00:10:59 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.4.6)
00:10:59 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (12.3.0)
00:10:59 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (6.0.3)
00:10:59 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (3.6.5)
00:10:59 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (2.34.2)
00:10:59 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py->omero-dropbox==5.7.1.dev0) (4.3.0)
00:10:59 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.5.1)
00:10:59 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (3.19)
00:10:59 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2.7.0)
00:10:59 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py->omero-dropbox==5.7.1.dev0) (2026.7.22)
00:10:59 Building wheels for collected packages: omero-dropbox
00:10:59 Building wheel for omero-dropbox (pyproject.toml): started
00:10:59 Building wheel for omero-dropbox (pyproject.toml): finished with status 'done'
00:10:59 Created wheel for omero-dropbox: filename=omero_dropbox-5.7.1.dev0-py3-none-any.whl size=49155 sha256=e1049cb46396de0642f97dd88a5b6d11ac2490818186de6a8b479e695105b2cb
00:10:59 Stored in directory: /home/omero/.cache/pip/wheels/97/54/5f/8dccf5c24b891c9bef25978dac72ee622eda35946855e06c92
00:10:59 Successfully built omero-dropbox
00:10:59 Installing collected packages: omero-dropbox
00:11:00 Successfully installed omero-dropbox-5.7.1.dev0
00:11:00 + for x in *.tar.gz
00:11:00 + pip install -U omero_marshal-0.9.2.dev0.tar.gz
00:11:01 Processing ./omero_marshal-0.9.2.dev0.tar.gz
00:11:01 Installing build dependencies: started
00:11:02 Installing build dependencies: finished with status 'done'
00:11:02 Getting requirements to build wheel: started
00:11:02 Getting requirements to build wheel: finished with status 'done'
00:11:02 Preparing metadata (pyproject.toml): started
00:11:03 Preparing metadata (pyproject.toml): finished with status 'done'
00:11:03 Building wheels for collected packages: omero_marshal
00:11:03 Building wheel for omero_marshal (pyproject.toml): started
00:11:03 Building wheel for omero_marshal (pyproject.toml): finished with status 'done'
00:11:03 Created wheel for omero_marshal: filename=omero_marshal-0.9.2.dev0-py3-none-any.whl size=88121 sha256=fe52a9f014872b14fb4024934d6b5ac9b547f19e0219b68d716570de8955c352
00:11:03 Stored in directory: /home/omero/.cache/pip/wheels/38/19/f8/b7cbc5aa44dc10bd3c24777f40a22cf6ed1baeac622bbf8230
00:11:03 Successfully built omero_marshal
00:11:03 Installing collected packages: omero_marshal
00:11:06 Successfully installed omero_marshal-0.9.2.dev0
00:11:06 + for x in *.tar.gz
00:11:06 + pip install -U omero_py-5.23.1.dev0.tar.gz
00:11:06 Processing ./omero_py-5.23.1.dev0.tar.gz
00:11:07 Installing build dependencies: started
00:11:08 Installing build dependencies: finished with status 'done'
00:11:08 Getting requirements to build wheel: started
00:11:08 Getting requirements to build wheel: finished with status 'done'
00:11:08 Preparing metadata (pyproject.toml): started
00:11:08 Preparing metadata (pyproject.toml): finished with status 'done'
00:11:09 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (1.4.4)
00:11:09 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (1.0.0)
00:11:09 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (2.4.6)
00:11:09 Requirement already satisfied: Pillow>=10.0.0 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (12.3.0)
00:11:09 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (6.0.3)
00:11:09 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (3.6.5)
00:11:09 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (2.34.2)
00:11:09 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-py==5.23.1.dev0) (4.3.0)
00:11:09 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (3.5.1)
00:11:09 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (3.19)
00:11:09 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (2.7.0)
00:11:09 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py==5.23.1.dev0) (2026.7.22)
00:11:09 Building wheels for collected packages: omero-py
00:11:09 Building wheel for omero-py (pyproject.toml): started
00:11:10 Building wheel for omero-py (pyproject.toml): finished with status 'done'
00:11:10 Created wheel for omero-py: filename=omero_py-5.23.1.dev0-py3-none-any.whl size=2787190 sha256=16f75650ee8f47b4b5813f4d1e36a56822ffeb4b934236f800ec8a105ff3bd2b
00:11:10 Stored in directory: /home/omero/.cache/pip/wheels/99/0a/38/75d301c3c2feff37b61c572a590c9d07ab2e52df205857b74d
00:11:10 Successfully built omero-py
00:11:10 Installing collected packages: omero-py
00:11:10 Attempting uninstall: omero-py
00:11:10 Found existing installation: omero-py 5.23.0
00:11:11 Uninstalling omero-py-5.23.0:
00:11:21 Successfully uninstalled omero-py-5.23.0
00:11:37 Successfully installed omero-py-5.23.1.dev0
00:11:37 + for x in *.tar.gz
00:11:37 + pip install -U omero_scripts-5.10.1.dev0.tar.gz
00:11:38 Processing ./omero_scripts-5.10.1.dev0.tar.gz
00:11:38 Installing build dependencies: started
00:11:39 Installing build dependencies: finished with status 'done'
00:11:39 Getting requirements to build wheel: started
00:11:39 Getting requirements to build wheel: finished with status 'done'
00:11:39 Preparing metadata (pyproject.toml): started
00:11:40 Preparing metadata (pyproject.toml): finished with status 'done'
00:11:40 Building wheels for collected packages: omero-scripts
00:11:40 Building wheel for omero-scripts (pyproject.toml): started
00:11:40 Building wheel for omero-scripts (pyproject.toml): finished with status 'done'
00:11:40 Created wheel for omero-scripts: filename=omero_scripts-5.10.1.dev0-py3-none-any.whl size=137217 sha256=d6e5b75fdd9f5e569ecee1a75af5a6ad7b7e174754c7b6165aa260b560b0ff65
00:11:40 Stored in directory: /home/omero/.cache/pip/wheels/42/27/9e/76575465f2b255db596bcfcfc1a50c113f5603b7dc93ec491e
00:11:40 Successfully built omero-scripts
00:11:40 Installing collected packages: omero-scripts
00:11:41 Successfully installed omero-scripts-5.10.1.dev0
00:11:41 + for x in *.tar.gz
00:11:41 + pip install -U omero_web-5.33.2.dev0.tar.gz
00:11:42 Processing ./omero_web-5.33.2.dev0.tar.gz
00:11:42 Installing build dependencies: started
00:11:43 Installing build dependencies: finished with status 'done'
00:11:43 Getting requirements to build wheel: started
00:11:44 Getting requirements to build wheel: finished with status 'done'
00:11:44 Preparing metadata (pyproject.toml): started
00:11:44 Preparing metadata (pyproject.toml): finished with status 'done'
00:11:44 Requirement already satisfied: omero-py>=5.19.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.2.dev0) (5.23.1.dev0)
00:11:44 Collecting concurrent-log-handler>=0.9.20 (from omero-web==5.33.2.dev0)
00:11:44 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl.metadata (27 kB)
00:11:44 Collecting Django<5.3,>=5.2.9 (from omero-web==5.33.2.dev0)
00:11:44 Using cached django-5.2.17-py3-none-any.whl.metadata (4.1 kB)
00:11:45 Collecting django-pipeline>=4.1.0 (from omero-web==5.33.2.dev0)
00:11:45 Using cached django_pipeline-4.1.0-py3-none-any.whl.metadata (5.9 kB)
00:11:45 Collecting django-cors-headers==3.7.0 (from omero-web==5.33.2.dev0)
00:11:45 Using cached django_cors_headers-3.7.0-py3-none-any.whl.metadata (15 kB)
00:11:45 Collecting whitenoise>=5.3.0 (from omero-web==5.33.2.dev0)
00:11:45 Using cached whitenoise-6.12.0-py3-none-any.whl.metadata (3.7 kB)
00:11:45 Collecting gunicorn>=19.3 (from omero-web==5.33.2.dev0)
00:11:45 Using cached gunicorn-26.2.0-py3-none-any.whl.metadata (5.5 kB)
00:11:45 Requirement already satisfied: omero-marshal>=0.7.0 in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.2.dev0) (0.9.2.dev0)
00:11:45 Requirement already satisfied: Pillow in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.2.dev0) (12.3.0)
00:11:45 Requirement already satisfied: pytz in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.2.dev0) (2026.3.post1)
00:11:45 Requirement already satisfied: portalocker in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.2.dev0) (4.3.0)
00:11:45 Requirement already satisfied: packaging in ./.venv3/lib64/python3.11/site-packages (from omero-web==5.33.2.dev0) (26.3)
00:11:45 Collecting importlib-resources (from omero-web==5.33.2.dev0)
00:11:45 Using cached importlib_resources-7.1.0-py3-none-any.whl.metadata (4.0 kB)
00:11:46 Collecting asgiref>=3.8.1 (from Django<5.3,>=5.2.9->omero-web==5.33.2.dev0)
00:11:46 Using cached asgiref-3.12.1-py3-none-any.whl.metadata (9.4 kB)
00:11:46 Collecting sqlparse>=0.3.1 (from Django<5.3,>=5.2.9->omero-web==5.33.2.dev0)
00:11:46 Using cached sqlparse-0.6.0-py3-none-any.whl.metadata (6.0 kB)
00:11:46 Requirement already satisfied: setuptools in ./.venv3/lib64/python3.11/site-packages (from django-pipeline>=4.1.0->omero-web==5.33.2.dev0) (65.5.1)
00:11:46 Collecting wheel (from django-pipeline>=4.1.0->omero-web==5.33.2.dev0)
00:11:46 Using cached wheel-0.48.0-py3-none-any.whl.metadata (2.3 kB)
00:11:46 Requirement already satisfied: appdirs in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.2.dev0) (1.4.4)
00:11:46 Requirement already satisfied: future in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.2.dev0) (1.0.0)
00:11:46 Requirement already satisfied: numpy<3,>=2 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.2.dev0) (2.4.6)
00:11:46 Requirement already satisfied: PyYAML in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.2.dev0) (6.0.3)
00:11:46 Requirement already satisfied: zeroc-ice<3.7,>=3.6.5 in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.2.dev0) (3.6.5)
00:11:46 Requirement already satisfied: requests in ./.venv3/lib64/python3.11/site-packages (from omero-py>=5.19.0->omero-web==5.33.2.dev0) (2.34.2)
00:11:46 Requirement already satisfied: charset_normalizer<4,>=2 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.2.dev0) (3.5.1)
00:11:46 Requirement already satisfied: idna<4,>=2.5 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.2.dev0) (3.19)
00:11:46 Requirement already satisfied: urllib3<3,>=1.26 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.2.dev0) (2.7.0)
00:11:46 Requirement already satisfied: certifi>=2023.5.7 in ./.venv3/lib64/python3.11/site-packages (from requests->omero-py>=5.19.0->omero-web==5.33.2.dev0) (2026.7.22)
00:11:46 Using cached django_cors_headers-3.7.0-py3-none-any.whl (12 kB)
00:11:46 Using cached django-5.2.17-py3-none-any.whl (8.3 MB)
00:11:46 Using cached asgiref-3.12.1-py3-none-any.whl (25 kB)
00:11:46 Using cached concurrent_log_handler-0.9.29-py3-none-any.whl (32 kB)
00:11:46 Using cached django_pipeline-4.1.0-py3-none-any.whl (75 kB)
00:11:46 Using cached gunicorn-26.2.0-py3-none-any.whl (228 kB)
00:11:46 Using cached sqlparse-0.6.0-py3-none-any.whl (50 kB)
00:11:46 Using cached whitenoise-6.12.0-py3-none-any.whl (20 kB)
00:11:46 Using cached importlib_resources-7.1.0-py3-none-any.whl (37 kB)
00:11:46 Using cached wheel-0.48.0-py3-none-any.whl (33 kB)
00:11:46 Building wheels for collected packages: omero-web
00:11:47 Building wheel for omero-web (pyproject.toml): started
00:11:48 Building wheel for omero-web (pyproject.toml): finished with status 'done'
00:11:48 Created wheel for omero-web: filename=omero_web-5.33.2.dev0-py3-none-any.whl size=2821672 sha256=58eb1865042149ab2825cfde83cd219d7d16726c5ee9232a03046d3013a4505f
00:11:48 Stored in directory: /home/omero/.cache/pip/wheels/fa/8a/56/2d65bd15d81cf391163d964dfe77b84f76dd1b0ce6f0ee9292
00:11:48 Successfully built omero-web
00:11:48 Installing collected packages: whitenoise, wheel, sqlparse, importlib-resources, gunicorn, concurrent-log-handler, asgiref, django-pipeline, Django, django-cors-headers, omero-web
00:12:57
00:12:57 Successfully installed Django-5.2.17 asgiref-3.12.1 concurrent-log-handler-0.9.29 django-cors-headers-3.7.0 django-pipeline-4.1.0 gunicorn-26.2.0 importlib-resources-7.1.0 omero-web-5.33.2.dev0 sqlparse-0.6.0 wheel-0.48.0 whitenoise-6.12.0
00:12:57 + wget https://raw.githubusercontent.com/ome/figure/refs/heads/master/ome_figure/Figure_To_Pdf.py
00:12:57 Will not apply HSTS. The HSTS database must be a regular and non-world-writable file.
00:12:57 ERROR: could not open HSTS store at '/home/omero/.wget-hsts'. HSTS will be disabled.
00:12:57 --2026-09-10 00:12:57-- https://raw.githubusercontent.com/ome/figure/refs/heads/master/ome_figure/Figure_To_Pdf.py
00:12:57 Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...
00:12:57 Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.
00:12:57 HTTP request sent, awaiting response... 200 OK
00:12:58 Length: 133662 (131K) [text/plain]
00:12:58 Saving to: ‘Figure_To_Pdf.py’
00:12:58
00:12:58 0K .......... .......... .......... .......... .......... 38% 2.89M 0s
00:12:58 50K .......... .......... .......... .......... .......... 76% 4.99M 0s
00:12:58 100K .......... .......... .......... 100% 6.30M=0.03s
00:12:58
00:12:58 2026-09-10 00:12:58 (4.06 MB/s) - ‘Figure_To_Pdf.py’ saved [133662/133662]
00:12:58
00:12:58 + chmod 755 Figure_To_Pdf.py
00:12:58 + mv Figure_To_Pdf.py /home/omero/workspace/OMERO-server/OMERO.server/lib/scripts/omero/figure_scripts
00:12:58 + omero config set omero.db.name OMERO-server
00:13:08 + omero config set omero.db.host pg
00:13:13 + omero config set omero.db.user postgres
00:13:18 + omero config set omero.data.dir /home/omero/omero-server-data
00:13:23 + omero config set omero.fs.repo.path %user%_%userId%/%thread%//%year%-%month%/%day%/%time%
00:13:27 + omero config set omero.db.poolsize 25
00:13:33 + omero config set omero.security.trustStore /etc/pki/ca-trust/extracted/java/cacerts
00:13:38 + omero config set omero.security.trustStorePassword changeit
00:13:43 + omero config set omero.mail.config true
00:13:48 + omero config set omero.server.nodedescriptors master:Blitz-0,Indexer-0,Processor-0,Storm,Tables-0
00:13:53 + omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED'
00:13:57 + omero certificates
00:14:02 OpenSSL 3.5.5 27 Jan 2026 (Library: OpenSSL 3.5.5 27 Jan 2026)
00:14:02 certificates created: /home/omero/omero-server-data/certs/server.pem /home/omero/omero-server-data/certs/server.p12
00:14:02 + '[' false = true ']'
00:14:02 + echo 'Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade'
00:14:02 Skipping PURGE_DATA:CleanDbAndRepo. Check for DB upgrade
00:14:02 + omego db -vvv upgrade --serverdir /home/omero/workspace/OMERO-server/OMERO.server --dbname OMERO-server
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG dbcommand => upgrade
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG dbhost => localhost
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG dbname => OMERO-server
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG dbpass => omero
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG dbuser => omero
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG rootpass => omero
00:14:03 2026-09-10 00:14:03,050 [ omego.db] DEBUG serverdir => /home/omero/workspace/OMERO-server/OMERO.server
00:14:03 2026-09-10 00:14:03,051 [omego.extern] INFO Executing : omero version
00:14:07 OMERO.py version:
00:14:07 OMERO.server version:
00:14:07 5.6.3-677-18978195ab-ice36-b74
00:14:07 5.23.1.dev0
00:14:07 2026-09-10 00:14:07,892 [omego.extern] INFO Completed [4.841 s]
00:14:07 2026-09-10 00:14:07,893 [omego.extern] DEBUG Using omero CLI from omero
00:14:07 2026-09-10 00:14:07,893 [ omego.db] INFO DbAdmin: DbAdmin /home/omero/workspace/OMERO-server/OMERO.server ...
00:14:07 2026-09-10 00:14:07,893 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:14:07 2026-09-10 00:14:07,893 [omego.extern] INFO Executing : omero config get --show-password
00:14:12 2026-09-10 00:14:12,896 [omego.extern] INFO Completed [5.003 s]
00:14:12 2026-09-10 00:14:12,897 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:14:12 2026-09-10 00:14:12,897 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t --version
00:14:13 2026-09-10 00:14:13,021 [omego.extern] INFO Completed [0.124 s]
00:14:13 2026-09-10 00:14:13,021 [ omego.db] DEBUG stdout: b'psql (PostgreSQL) 16.14\n'
00:14:13 2026-09-10 00:14:13,021 [ omego.db] INFO psql version: psql (PostgreSQL) 16.14
00:14:13
00:14:13 2026-09-10 00:14:13,021 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:14:13 2026-09-10 00:14:13,021 [omego.extern] INFO Executing : omero config get --show-password
00:14:18 2026-09-10 00:14:18,184 [omego.extern] INFO Completed [5.163 s]
00:14:18 2026-09-10 00:14:18,184 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:14:18 2026-09-10 00:14:18,184 [omego.extern] INFO Executing [custom environment]: psql -v ON_ERROR_STOP=on -d OMERO-server -h pg -U postgres -w -A -t -c \conninfo
00:14:18 2026-09-10 00:14:18,203 [omego.extern] INFO Completed [0.019 s]
00:14:18 2026-09-10 00:14:18,203 [ omego.db] DEBUG stdout: b'You are connected to database "OMERO-server" as user "postgres" on host "pg" (address "172.18.0.6") at port "5432".\n'
00:14:18 2026-09-10 00:14:18,203 [ omego.db] DEBUG Executing query: SELECT currentversion, currentpatch FROM dbpatch ORDER BY id DESC LIMIT 1
00:14:18 2026-09-10 00:14:18,203 [omego.extern] INFO Running [current environment]: omero config get --show-password
00:14:18 2026-09-10 00:14:18,203 [omego.extern] INFO Executing : omero config get --show-password
00:14:23 2026-09-10 00:14:23,185 [omego.extern] INFO Completed [4.982 s]
00:14:23 2026-09-10 00:14:23,185 [ omego.db] INFO Failed to lookup parameter omero.db.pass, using omero
00:14:23 2026-09-10 00:14:23,185 [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
00:14:23 2026-09-10 00:14:23,266 [omego.extern] INFO Completed [0.081 s]
00:14:23 2026-09-10 00:14:23,266 [ omego.db] DEBUG stdout: b'OMERO5.4|0\n'
00:14:23 2026-09-10 00:14:23,266 [ omego.db] INFO Current omero db version: ('OMERO5.4', '0')
00:14:23 2026-09-10 00:14:23,312 [ omego.db] INFO Database is already at OMERO5.4__0
00:14:23 + export LANG=en_US.UTF-8
00:14:23 + LANG=en_US.UTF-8
00:14:23 + export LANGUAGE=en_US:en
00:14:23 + LANGUAGE=en_US:en
00:14:23 + export LC_ALL=en_US.UTF-8
00:14:23 + LC_ALL=en_US.UTF-8
00:14:23 + BUILD_ID=DONT_KILL_ME
00:14:23 + omero admin start
00:14:35 No descriptor given. Using etc/grid/default.xml
00:14:46 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/master
00:14:46 Initializing /home/omero/workspace/OMERO-server/OMERO.server/var/log
00:14:46 Creating /home/omero/workspace/OMERO-server/OMERO.server/var/registry
00:14:46 Waiting on startup. Use CTRL-C to exit
00:14:46 + omero admin waitup
00:14:54 Waiting on startup. Use CTRL-C to exit
00:14:54 + omero admin diagnostics
00:14:59
00:14:59 ================================================================================
00:14:59 OMERO Diagnostics (admin)
00:14:59 ================================================================================
00:14:59
00:14:59 Commands: java -version 21.0.12 (/usr/bin/java)
00:14:59 Commands: python -V 3.11.13 (/home/omero/workspace/OMERO-server/.venv3/bin/python)
00:14:59 Commands: icegridnode --version 3.6.5 (/opt/ice-3.6.5/bin/icegridnode)
00:14:59 Commands: icegridadmin --version 3.6.5 (/opt/ice-3.6.5/bin/icegridadmin)
00:14:59 Commands: psql --version 16.14 (/usr/bin/psql)
00:14:59 Commands: openssl version 3.5.527 (/usr/bin/openssl)
00:14:59
00:14:59 Component: OMERO.py 5.23.1.dev0
00:14:59 Component: OMERO.server 5.6.3-677-18978195ab-ice36-b74
00:14:59
00:14:59 Server: icegridnode running
00:14:59 Server: Blitz-0 active (pid = 3738, enabled)
00:14:59 Server: Indexer-0 active (pid = 3757, enabled)
00:14:59 Server: OMERO.Glacier2 active (pid = 3762, enabled)
00:14:59 Server: OMERO.IceStorm active (pid = 3794, enabled)
00:14:59 Server: Processor-0 active (pid = 3787, enabled)
00:14:59 Server: Tables-0 active (pid = 3778, enabled)
00:14:59
00:14:59 Log dir: /home/omero/workspace/OMERO-server/OMERO.server/var/log exists
00:14:59 Log files: Blitz-0.log 32.3 KB errors=0 warnings=1
00:14:59 Log files: DropBox.log n/a
00:14:59 Log files: FileServer.log n/a
00:14:59 Log files: Indexer-0.log 2.6 KB
00:14:59 Log files: MonitorServer.log n/a
00:14:59 Log files: Processor-0.log 735 B
00:14:59 Log files: Tables-0.log 961 B
00:14:59 Log files: TestDropBox.log n/a
00:14:59 Log files: master.err empty
00:14:59 Log files: master.out 30.7 KB
00:14:59 Log files: Total size 0.07 MB
00:14:59
00:14:59
00:14:59 Environment:OMERO_HOME=(unset)
00:14:59 Environment:OMERODIR=/home/omero/workspace/OMERO-server/OMERO.server
00:14:59 Environment:OMERO_NODE=(unset)
00:14:59 Environment:OMERO_MASTER=(unset)
00:14:59 Environment:OMERO_USERDIR=(unset)
00:14:59 Environment:OMERO_TMPDIR=(unset)
00:14:59 Environment:PATH=/home/omero/workspace/OMERO-server/.venv3/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:14:59 Environment:PYTHONPATH=(unset)
00:14:59 Environment:ICE_HOME=/opt/ice-3.6.5
00:14:59 Environment:LD_LIBRARY_PATH=(unset)
00:14:59 Environment:DYLD_LIBRARY_PATH=(unset)
00:14:59
00:14:59 OMERO SSL port:4064
00:14:59 OMERO TCP port:4063
00:14:59 OMERO data dir:'/home/omero/omero-server-data' Exists? True Is writable? True
00:14:59 OMERO temp dir:'/home/omero/omero/tmp' Exists? True Is writable? True (Size: 0)
00:14:59
00:14:59 JVM settings: Blitz-${index} -Xmx5007m
00:14:59 JVM settings: Indexer-${index} -Xmx3338m
00:14:59 JVM settings: PixelData-${index} -Xmx5007m
00:14:59 JVM settings: Repository-${index} -Xmx3338m
00:14:59
00:14:59 Jar: lib/server/formats-api.jar Bio-Formats API 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
00:14:59 Jar: lib/server/formats-bsd.jar BSD Bio-Formats readers and writers 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
00:14:59 Jar: lib/server/formats-gpl.jar Bio-Formats library 8.5.0 18 March 2026 877c317e4e396381dc76e56c1539b24947f71dce
00:14:59 Jar: lib/server/ome-codecs.jar OME Codecs 1.1.3 26 February 2026 70fd9b72a9834f1af4852c1e5b5676c57a2c360e
00:14:59 Jar: lib/server/ome-common.jar OME Common Java 6.2.1 27 February 2026 a24fbcbf04a3a3acba14e9575d7fb1d36a484dff
00:14:59 Jar: lib/server/ome-jai.jar OME JAI 0.1.5 30 June 2025 257a1c1410c0103485248d05752a5174262a38b6
00:14:59 Jar: lib/server/ome-mdbtools.jar MDB Tools (Java port) 5.3.4 25 June 2025 57553b46e5f0cf9aefe5d97d2b1c8dd2073a4d37
00:14:59 Jar: lib/server/ome-poi.jar OME POI 5.3.11 11 November 2025 a2f3944ac71db9e7e51a6f64ec46beeb60613afb
00:14:59 Jar: lib/server/ome-xml.jar OME XML library 6.5.3 22 January 2026 21d1362abd9ce26e13888d2b2d028753d21ac96e
00:14:59 Jar: lib/server/omero-blitz.jar jar 5.8.6-SNAPSHOT
00:14:59 Jar: lib/server/omero-common.jar jar 5.7.6-SNAPSHOT
00:14:59 Jar: lib/server/omero-gateway.jar jar 5.11.1-SNAPSHOT
00:14:59 Jar: lib/server/omero-model.jar jar 5.7.6-SNAPSHOT
00:14:59 Jar: lib/server/omero-renderer.jar jar 5.6.6-SNAPSHOT
00:14:59 Jar: lib/server/omero-romio.jar jar 5.8.6-SNAPSHOT
00:14:59 Jar: lib/server/omero-server.jar jar 5.7.6-SNAPSHOT
00:14:59 Jar: lib/server/omero-zarr-pixel-buffer.jar OMERO Zarr Pixel Buffer 0.7.0-rc3 4c6a6c7d8fb12449c8080808fd12bf95e996e398
00:14:59 + deactivate
00:14:59 + '[' -n /opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ']'
00:14:59 + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
00:14:59 + export PATH
00:14:59 + unset _OLD_VIRTUAL_PATH
00:14:59 + '[' -n '' ']'
00:14:59 + hash -r
00:14:59 + '[' -n '' ']'
00:14:59 + unset VIRTUAL_ENV
00:14:59 + unset VIRTUAL_ENV_PROMPT
00:14:59 + '[' '!' '' = nondestructive ']'
00:14:59 + unset -f deactivate
00:15:00 Finished: SUCCESS
