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Started by upstream project "Trigger" build number 583 originally caused by: Started by timer Running as SYSTEM Building remotely on testintegration (swarm rocky9 ice36 java11) in workspace /home/omero/workspace/BIOFORMATS-push The recommended git tool is: NONE No credentials specified > git rev-parse --resolve-git-dir /home/omero/workspace/BIOFORMATS-push/bio-formats-build/.git # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/ome/bio-formats-build # timeout=10 Cleaning workspace > git rev-parse --verify HEAD # timeout=10 Resetting working tree > git reset --hard # timeout=10 > git clean -ffdx # timeout=10 > git submodule foreach --recursive git reset --hard # timeout=10 > git submodule foreach --recursive git clean -fdx # timeout=10 Fetching upstream changes from https://github.com/ome/bio-formats-build > git --version # timeout=10 > git --version # 'git version 2.43.5' > git fetch --tags --force --progress -- https://github.com/ome/bio-formats-build +refs/heads/*:refs/remotes/origin/* # timeout=10 > git rev-parse origin/master^{commit} # timeout=10 Checking out Revision 909e999ce879325a2ed6211dfa6e509de53f2d4e (origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 909e999ce879325a2ed6211dfa6e509de53f2d4e # timeout=10 Commit message: "Merge pull request #730 from ome/dependabot/submodules/bioformats-3f70394" > git rev-list --no-walk 909e999ce879325a2ed6211dfa6e509de53f2d4e # timeout=10 > git remote # timeout=10 > git submodule init # timeout=10 > git submodule sync # timeout=10 > git config --get remote.origin.url # timeout=10 > git submodule init # timeout=10 > git config -f .gitmodules --get-regexp ^submodule\.(.+)\.url # timeout=10 > git config --get submodule.ome-common-java.url # timeout=10 > git config -f .gitmodules --get submodule.ome-common-java.path # timeout=10 > git config --get submodule.ome-model.url # timeout=10 > git config -f .gitmodules --get submodule.ome-model.path # timeout=10 > git config --get submodule.ome-poi.url # timeout=10 > git config -f .gitmodules --get submodule.ome-poi.path # timeout=10 > git config --get submodule.ome-mdbtools.url # timeout=10 > git config -f .gitmodules --get submodule.ome-mdbtools.path # timeout=10 > git config --get submodule.ome-jai.url # timeout=10 > git config -f .gitmodules --get submodule.ome-jai.path # timeout=10 > git config --get submodule.ome-codecs.url # timeout=10 > git config -f .gitmodules --get submodule.ome-codecs.path # timeout=10 > git config --get submodule.ome-metakit.url # timeout=10 > git config -f .gitmodules --get submodule.ome-metakit.path # timeout=10 > git config --get submodule.ome-stubs.url # timeout=10 > git config -f .gitmodules --get submodule.ome-stubs.path # timeout=10 > git config --get submodule.bioformats.url # timeout=10 > git config -f .gitmodules --get submodule.bioformats.path # timeout=10 > git config --get submodule.bio-formats-documentation.url # timeout=10 > git config -f .gitmodules --get submodule.bio-formats-documentation.path # timeout=10 > git config --get submodule.bio-formats-examples.url # timeout=10 > git config -f .gitmodules --get submodule.bio-formats-examples.path # timeout=10 > git config --get submodule.ZarrReader.url # timeout=10 > git config -f .gitmodules --get submodule.ZarrReader.path # timeout=10 > git submodule update --init --recursive --remote ome-common-java # timeout=10 > git submodule update --init --recursive --remote ome-model # timeout=10 > git submodule update --init --recursive --remote ome-poi # timeout=10 > git submodule update --init --recursive --remote ome-mdbtools # timeout=10 > git submodule update --init --recursive --remote ome-jai # timeout=10 > git submodule update --init --recursive --remote ome-codecs # timeout=10 > git submodule update --init --recursive --remote ome-metakit # timeout=10 > git submodule update --init --recursive --remote ome-stubs # timeout=10 > git submodule update --init --recursive --remote bioformats # timeout=10 > git submodule update --init --recursive --remote bio-formats-documentation # timeout=10 > git submodule update --init --recursive --remote bio-formats-examples # timeout=10 > git submodule update --init --recursive --remote ZarrReader # timeout=10 [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins174287812615859959.sh + python3.11 -mvenv venv + source /home/omero/workspace/BIOFORMATS-push/venv/bin/activate ++ deactivate nondestructive ++ '[' -n '' ']' ++ '[' -n '' ']' ++ hash -r ++ '[' -n '' ']' ++ unset VIRTUAL_ENV ++ unset VIRTUAL_ENV_PROMPT ++ '[' '!' nondestructive = nondestructive ']' ++ VIRTUAL_ENV=/home/omero/workspace/BIOFORMATS-push/venv ++ export VIRTUAL_ENV ++ _OLD_VIRTUAL_PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ PATH=/home/omero/workspace/BIOFORMATS-push/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin ++ export PATH ++ '[' -n '' ']' ++ '[' -z '' ']' ++ _OLD_VIRTUAL_PS1= ++ PS1='(venv) ' ++ export PS1 ++ VIRTUAL_ENV_PROMPT='(venv) ' ++ export VIRTUAL_ENV_PROMPT ++ hash -r + pip install -U pip Requirement already satisfied: pip in ./venv/lib64/python3.11/site-packages (25.2) + pip install -U scc Requirement already satisfied: scc in ./venv/lib64/python3.11/site-packages (0.20.0) Requirement already satisfied: PyGithub>=1.54 in ./venv/lib64/python3.11/site-packages (from scc) (2.6.1) Requirement already satisfied: PyYAML>=5.1 in ./venv/lib64/python3.11/site-packages (from scc) (6.0.2) Requirement already satisfied: future in ./venv/lib64/python3.11/site-packages (from scc) (1.0.0) Requirement already satisfied: ruamel.yaml in ./venv/lib64/python3.11/site-packages (from scc) (0.18.10) Requirement already satisfied: ruamel.yaml.jinja2 in ./venv/lib64/python3.11/site-packages (from scc) (0.2.7) Requirement already satisfied: six in ./venv/lib64/python3.11/site-packages (from scc) (1.17.0) Requirement already satisfied: urllib3<2 in ./venv/lib64/python3.11/site-packages (from scc) (1.26.20) Requirement already satisfied: yaclifw<0.3,>=0.2.0 in ./venv/lib64/python3.11/site-packages (from scc) (0.2.0) Requirement already satisfied: pynacl>=1.4.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (1.5.0) Requirement already satisfied: requests>=2.14.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (2.32.3) Requirement already satisfied: pyjwt>=2.4.0 in ./venv/lib64/python3.11/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.10.1) Requirement already satisfied: typing-extensions>=4.0.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (4.13.0) Requirement already satisfied: Deprecated in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (1.2.18) Requirement already satisfied: cryptography>=3.4.0 in ./venv/lib64/python3.11/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (44.0.2) Requirement already satisfied: cffi>=1.12 in ./venv/lib64/python3.11/site-packages (from cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (1.17.1) Requirement already satisfied: pycparser in ./venv/lib64/python3.11/site-packages (from cffi>=1.12->cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.22) Requirement already satisfied: charset-normalizer<4,>=2 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.4.1) Requirement already satisfied: idna<4,>=2.5 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.10) Requirement already satisfied: certifi>=2017.4.17 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (2025.1.31) Requirement already satisfied: wrapt<2,>=1.10 in ./venv/lib64/python3.11/site-packages (from Deprecated->PyGithub>=1.54->scc) (1.17.2) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./venv/lib64/python3.11/site-packages (from ruamel.yaml->scc) (0.2.12) + PATH=/home/omero/workspace/BIOFORMATS-push/bio-formats-build/scripts:/home/omero/workspace/BIOFORMATS-push/venv/bin:/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin + MERGE_OPTIONS='--no-ask --reset --comment -S success-only' + cd bio-formats-build + echo 'Merge base repository (no submodule updates)' Merge base repository (no submodule updates) + scc merge --no-ask --reset --comment -S success-only --shallow master 2025-08-11 00:00:45,447 [ scc.merge] INFO Merging Pull Request(s) based on master 2025-08-11 00:00:45,447 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2025-08-11 00:00:45,447 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2025-08-11 00:00:45,448 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2025-08-11 00:00:45,448 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2025-08-11 00:00:45,448 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2025-08-11 00:00:45,858 [ scc.merge] INFO Repository: ome/bio-formats-build 2025-08-11 00:00:45,858 [ scc.merge] INFO Already up to date. 2025-08-11 00:00:45,858 [ scc.merge] INFO 2025-08-11 00:00:45,858 [ scc.merge] INFO + git submodule sync Synchronizing submodule url for 'ZarrReader' Synchronizing submodule url for 'bio-formats-documentation' Synchronizing submodule url for 'bio-formats-examples' Synchronizing submodule url for 'bioformats' Synchronizing submodule url for 'ome-codecs' Synchronizing submodule url for 'ome-common-java' Synchronizing submodule url for 'ome-jai' Synchronizing submodule url for 'ome-mdbtools' Synchronizing submodule url for 'ome-metakit' Synchronizing submodule url for 'ome-model' Synchronizing submodule url for 'ome-poi' Synchronizing submodule url for 'ome-stubs' + git submodule update --remote --recursive Submodule path 'bio-formats-documentation': checked out '3eb4a5a1d2cf029e8515a273ee14a1582d24328a' Submodule path 'bio-formats-examples': checked out 'b6449b11870d7d0c02c82c53dc3c9c52f1360344' Submodule path 'bioformats': checked out '382cfc5112ec32d3b2d2d18fe75e2c7d44417379' Submodule path 'ome-codecs': checked out 'a105f944171d0ce3be952d2e3558b1f417c3c30e' Submodule path 'ome-common-java': checked out '5fd163e5c069af5e2be725c4d9633b7f9e07fa3b' Submodule path 'ome-jai': checked out '9f1b4efff4c048da02bc6634ed3325cb38b41f0f' Submodule path 'ome-mdbtools': checked out '9c3c3e268e1e76dd602daa88788403073b532e24' Submodule path 'ome-metakit': checked out '8a3c6a1cd729108066c5b16df971632846fc3cac' Submodule path 'ome-model': checked out 'a3fb3465790b50398b69518a18c7f24bb5ebc829' Submodule path 'ome-poi': checked out '2df7a4ffd4736de8ad63161c3d816fae722a8b35' Submodule path 'ome-stubs': checked out '6a87342b85e0539247e64f53045ea776c90a269b' + echo 'Merge all submodules using repository configuration:' Merge all submodules using repository configuration: + cat scripts/repositories.yml base-branch: master submodules: ome-common-java: base-branch: master bioformats: base-branch: develop bio-formats-documentation: base-branch: master bio-formats-examples: base-branch: master ome-codecs: base-branch: master ome-common-java: base-branch: master ome-jai: base-branch: master ome-mdbtools: base-branch: master ome-metakit: base-branch: master ome-model: base-branch: master ome-poi: base-branch: master ome-stubs: base-branch: master ZarrReader: base-branch: main ++ pwd + scc merge --repository-config=/home/omero/workspace/BIOFORMATS-push/bio-formats-build/scripts/repositories.yml --no-ask --reset --comment -S success-only --update-gitmodules --push merge_ci master Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2025-08-11 00:01:02,317 [github.Reque] INFO Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2025-08-11 00:01:24,448 [ scc.merge] INFO Merging Pull Request(s) based on master 2025-08-11 00:01:24,448 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2025-08-11 00:01:24,448 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2025-08-11 00:01:24,448 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2025-08-11 00:01:24,448 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2025-08-11 00:01:24,448 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2025-08-11 00:01:24,717 [ scc.git] INFO Overriding base-branch from master to main 2025-08-11 00:01:41,102 [ scc.git] INFO Overriding base-branch from master to develop 2025-08-11 00:02:50,720 [ scc.merge] INFO Repository: ome/bio-formats-build 2025-08-11 00:02:50,721 [ scc.merge] INFO Already up to date. 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO Repository: ome/ZarrReader 2025-08-11 00:02:50,721 [ scc.merge] INFO Excluded PRs: 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 2025-08-11 00:02:50,721 [ scc.merge] INFO Already up to date. 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO Merged PRs: 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 110 dominikl 'Fix Issue 109' 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO Repository: ome/bio-formats-documentation 2025-08-11 00:02:50,721 [ scc.merge] INFO Updating db99c10d..3eb4a5a1 2025-08-11 00:02:50,721 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 434 sbesson 'Add format page for Zeiss XRM format' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 431 pwalczysko 'Fix limited javadoc syntax' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 430 pwalczysko 'Fix sourceforge' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 426 jburel 'Update EMAN2 URL' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 427 jburel 'Checking linkcheck config' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 422 melissalinkert 'Add page for JDCE' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 425 melissalinkert 'Release notes for 8.2.0' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 418 sbesson 'Update MATLAB documentation for colormap return value' 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 421 dominikl 'Exclude merckmillipore.com from link check' 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO Repository: ome/bio-formats-examples 2025-08-11 00:02:50,721 [ scc.merge] INFO Updating 3aa7013..b6449b1 2025-08-11 00:02:50,721 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 134 sbesson 'POM: cleanup outdated metadata' 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO 2025-08-11 00:02:50,721 [ scc.merge] INFO Repository: openmicroscopy/bioformats 2025-08-11 00:02:50,721 [ scc.merge] INFO Excluded PRs: 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) 2025-08-11 00:02:50,721 [ scc.merge] INFO - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) 2025-08-11 00:02:50,722 [ scc.merge] INFO Updating 3f70394503..382cfc5112 2025-08-11 00:02:50,722 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4307 jburel 'Build report' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4338 sbesson 'org.openmicroscopy component updates' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4327 melissalinkert 'Check modulo values in repository tests' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4284 ptahmose 'fix for garbled images with CZIs' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4303 melissalinkert 'Fix Unidata repository URLs' 2025-08-11 00:02:50,722 [ scc.merge] INFO 2025-08-11 00:02:50,722 [ scc.merge] INFO Merged PRs: 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4348 sbesson 'FakeReader: link instrument to all images' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' 2025-08-11 00:02:50,722 [ scc.merge] INFO - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' 2025-08-11 00:02:50,722 [ scc.merge] INFO 2025-08-11 00:02:50,722 [ scc.merge] INFO Repository: ome/ome-codecs 2025-08-11 00:02:50,722 [ scc.merge] INFO Updating fab1a01..a105f94 2025-08-11 00:02:50,722 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 42 sbesson 'Update publication build system to use Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-common-java 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating 2cb0b7b..5fd163e 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 99 melissalinkert 'Fix type of skipped bytes counter' 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-jai 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating e70c2ab..9f1b4ef 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 8 sbesson 'Update publication build system to use Central Portal ' 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-mdbtools 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating 9193930..9c3c3e2 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 14 sbesson 'Update publication system to use Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-metakit 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating 1ba6cf1..8a3c6a1 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 27 sbesson 'Update publication build system to use Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-model 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating 3d70a1f9..a3fb3465 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 222 sbesson 'Update publication build system to use Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-poi 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating da3a5f3..2df7a4f 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 19 sbesson 'Update publication system to use Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO Repository: ome/ome-stubs 2025-08-11 00:02:50,723 [ scc.merge] INFO Updating 1559997..6a87342 2025-08-11 00:02:50,723 [ scc.merge] INFO Previously merged: 2025-08-11 00:02:50,723 [ scc.merge] INFO - PR 12 sbesson 'Update publication build system to use Central Portal' 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:02:50,723 [ scc.merge] INFO 2025-08-11 00:03:13,010 [ scc.merge] INFO Merged branch pushed to https://github.com/snoopycrimecop/bio-formats-build/tree/merge_ci + echo 'Update maven component versions' Update maven component versions + update-versions OMEZarrReader=0.6.1-SNAPSHOT bio-formats-documentation=8.4.0-SNAPSHOT bio-formats-examples=8.4.0-SNAPSHOT bio-formats_plugins=8.4.0-SNAPSHOT bio-formats-tools=8.4.0-SNAPSHOT bioformats_package=8.4.0-SNAPSHOT turbojpeg=8.4.0-SNAPSHOT formats-api=8.4.0-SNAPSHOT formats-bsd=8.4.0-SNAPSHOT formats-gpl=8.4.0-SNAPSHOT test-suite=8.4.0-SNAPSHOT pom-bio-formats=8.4.0-SNAPSHOT bioformats=8.4.0-SNAPSHOT ome-codecs=1.1.2-SNAPSHOT ome-common=6.1.1-SNAPSHOT ome-jai=0.1.6-SNAPSHOT ome-mdbtools=5.3.5-SNAPSHOT metakit=5.3.10-SNAPSHOT ome-xml=6.5.1-SNAPSHOT specification=6.5.1-SNAPSHOT ome-model=6.5.1-SNAPSHOT ome-poi=5.3.11-SNAPSHOT mipav-stubs=6.0.4-SNAPSHOT ome-stubs=6.0.4-SNAPSHOT + echo 'Commit all component version changes' Commit all component version changes + git submodule foreach 'git add -u' Entering 'ZarrReader' Entering 'bio-formats-documentation' Entering 'bio-formats-examples' Entering 'bioformats' Entering 'ome-codecs' Entering 'ome-common-java' Entering 'ome-jai' Entering 'ome-mdbtools' Entering 'ome-metakit' Entering 'ome-model' Entering 'ome-poi' Entering 'ome-stubs' + git submodule foreach 'git commit -m '\''Update component versions'\'' || true' Entering 'ZarrReader' HEAD detached from 31d6d95 nothing to commit, working tree clean Entering 'bio-formats-documentation' [detached HEAD 1dfc5897] Update component versions 1 file changed, 7 insertions(+), 7 deletions(-) Entering 'bio-formats-examples' [detached HEAD bed7249] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'bioformats' [detached HEAD 5aa0f4bedd] Update component versions 1 file changed, 9 insertions(+), 9 deletions(-) Entering 'ome-codecs' [detached HEAD d8a2440] Update component versions 1 file changed, 2 insertions(+), 2 deletions(-) Entering 'ome-common-java' HEAD detached from 2cb0b7b nothing to commit, working tree clean Entering 'ome-jai' HEAD detached from e70c2ab nothing to commit, working tree clean Entering 'ome-mdbtools' HEAD detached from 9193930 nothing to commit, working tree clean Entering 'ome-metakit' [detached HEAD 574c75d] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'ome-model' [detached HEAD 934a7988] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'ome-poi' [detached HEAD 195189e] Update component versions 1 file changed, 1 insertion(+), 1 deletion(-) Entering 'ome-stubs' HEAD detached from 1559997 nothing to commit, working tree clean + echo 'Push all branches' Push all branches ++ git config github.user + user=snoopycrimecop + git submodule foreach 'git push -f git@github.com:snoopycrimecop/${path}.git HEAD:merge_ci' Entering 'ZarrReader' Everything up-to-date Entering 'bio-formats-documentation' To github.com:snoopycrimecop/bio-formats-documentation.git 2c06dbe7..1dfc5897 HEAD -> merge_ci Entering 'bio-formats-examples' To github.com:snoopycrimecop/bio-formats-examples.git 9553290..bed7249 HEAD -> merge_ci Entering 'bioformats' To github.com:snoopycrimecop/bioformats.git 4d967febdb..5aa0f4bedd HEAD -> merge_ci Entering 'ome-codecs' To github.com:snoopycrimecop/ome-codecs.git c2f85a8..d8a2440 HEAD -> merge_ci Entering 'ome-common-java' Everything up-to-date Entering 'ome-jai' Everything up-to-date Entering 'ome-mdbtools' Everything up-to-date Entering 'ome-metakit' To github.com:snoopycrimecop/ome-metakit.git 9e0e4ec..574c75d HEAD -> merge_ci Entering 'ome-model' To github.com:snoopycrimecop/ome-model.git e9ec8d9e..934a7988 HEAD -> merge_ci Entering 'ome-poi' To github.com:snoopycrimecop/ome-poi.git db38b41..195189e HEAD -> merge_ci Entering 'ome-stubs' Everything up-to-date + echo 'Commit all component version changes' Commit all component version changes + git add -u + git commit -m 'Update component versions' [detached HEAD 06ea7a1] Update component versions 7 files changed, 7 insertions(+), 7 deletions(-) + git push -f git@github.com:snoopycrimecop/bio-formats-build.git HEAD:merge_ci To github.com:snoopycrimecop/bio-formats-build.git d8f9d38..06ea7a1 HEAD -> merge_ci [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins12426783672654586626.sh + mkdir -p /home/omero/workspace/BIOFORMATS-push/target + cd /home/omero/workspace/BIOFORMATS-push/target + curl -sfL https://github.com/ome/build-infra/archive/master.tar.gz + tar -zxf - + export PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/ + PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/ + cd /home/omero/workspace/BIOFORMATS-push/bio-formats-build + foreach-get-version + foreach-get-version-as-property Archiving artifacts Finished: SUCCESS