Started by upstream project "Trigger" build number 5 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 2.47.3' > 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 9e8c9ff560c2beea8ec33cc8a45a192d8a2f8fe0 (origin/master) > git config core.sparsecheckout # timeout=10 > git checkout -f 9e8c9ff560c2beea8ec33cc8a45a192d8a2f8fe0 # timeout=10 Commit message: "Merge pull request #731 from pwalczysko/fix-build-no-ant" > git rev-list --no-walk 9e8c9ff560c2beea8ec33cc8a45a192d8a2f8fe0 # 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/jenkins1891768889790957271.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 (25.3) + 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) (2.8.1) Requirement already satisfied: PyYAML>=5.1 in ./venv/lib64/python3.11/site-packages (from scc) (6.0.3) 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) (0.18.16) 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) (1.6.1) Requirement already satisfied: requests>=2.14.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (2.32.5) 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>=4.5.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (4.15.0) Requirement already satisfied: cryptography>=3.4.0 in ./venv/lib64/python3.11/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (46.0.3) Requirement already satisfied: cffi>=2.0.0 in ./venv/lib64/python3.11/site-packages (from cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.0.0) Requirement already satisfied: pycparser in ./venv/lib64/python3.11/site-packages (from cffi>=2.0.0->cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.23) Requirement already satisfied: charset_normalizer<4,>=2 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.4.4) Requirement already satisfied: idna<4,>=2.5 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.11) Requirement already satisfied: certifi>=2017.4.17 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (2025.11.12) Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in ./venv/lib64/python3.11/site-packages (from ruamel.yaml->scc) (0.2.15) + 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 2025-12-19 00:00:19,347 [ scc.merge] INFO Merging Pull Request(s) based on master 2025-12-19 00:00:19,347 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2025-12-19 00:00:19,347 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2025-12-19 00:00:19,347 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2025-12-19 00:00:19,347 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2025-12-19 00:00:19,347 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2025-12-19 00:00:19,746 [ scc.merge] INFO Repository: ome/bio-formats-build 2025-12-19 00:00:19,747 [ scc.merge] INFO Already up to date. 2025-12-19 00:00:19,747 [ scc.merge] INFO 2025-12-19 00:00:19,747 [ 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 'ZarrReader': checked out '5f3faa45fef73473bce6e4fc732a9cccc05c105d' Submodule path 'bio-formats-documentation': checked out '56211d70211301a587788e031691f5d8495761bc' Submodule path 'bio-formats-examples': checked out '1e4408bdccf1da4506d2b060010d134094d86dde' Submodule path 'bioformats': checked out '3fa05af5a63128aec8ff5c1cc57ac6cf7def1e67' Submodule path 'ome-codecs': checked out '1f655e61d0a7e02217a1bbff46dc54f205c8ea37' Submodule path 'ome-common-java': checked out 'd22ba6097e15edbfe2389fdcc093fd8efecc1523' Submodule path 'ome-jai': checked out '9f1b4efff4c048da02bc6634ed3325cb38b41f0f' Submodule path 'ome-mdbtools': checked out '9c3c3e268e1e76dd602daa88788403073b532e24' Submodule path 'ome-metakit': checked out '55abb777df3ebcd3d201ab0c6621b331a2731c37' Submodule path 'ome-model': checked out '3120dc4f0bf13c1ffaba04f67f738ee0d5e445aa' Submodule path 'ome-poi': checked out 'd727828f8f30ce7a97d13b58dba97580e75bab5d' 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 2025-12-19 00:00:34,306 [github.Reque] INFO Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2025-12-19 00:00:55,144 [ scc.merge] INFO Merging Pull Request(s) based on master 2025-12-19 00:00:55,144 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2025-12-19 00:00:55,144 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2025-12-19 00:00:55,144 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2025-12-19 00:00:55,144 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2025-12-19 00:00:55,144 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2025-12-19 00:00:55,403 [ scc.git] INFO Overriding base-branch from master to main 2025-12-19 00:01:18,111 [ scc.git] INFO Overriding base-branch from master to develop 2025-12-19 00:03:03,858 [ scc.merge] INFO Repository: ome/bio-formats-build 2025-12-19 00:03:03,858 [ scc.merge] INFO Already up to date. 2025-12-19 00:03:03,858 [ scc.merge] INFO 2025-12-19 00:03:03,858 [ scc.merge] INFO 2025-12-19 00:03:03,858 [ scc.merge] INFO Repository: ome/ZarrReader 2025-12-19 00:03:03,858 [ scc.merge] INFO Excluded PRs: 2025-12-19 00:03:03,858 [ scc.merge] INFO - PR 113 dominikl 'Zarr v3' (stage: draft) 2025-12-19 00:03:03,858 [ scc.merge] INFO - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment) 2025-12-19 00:03:03,858 [ scc.merge] INFO Updating 31d6d95..5f3faa4 2025-12-19 00:03:03,858 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,858 [ scc.merge] INFO - PR 111 Tom-TBT 'Fixed typo in README env var name to set' 2025-12-19 00:03:03,858 [ scc.merge] INFO 2025-12-19 00:03:03,858 [ scc.merge] INFO 2025-12-19 00:03:03,858 [ scc.merge] INFO Repository: ome/bio-formats-documentation 2025-12-19 00:03:03,858 [ scc.merge] INFO Updating db99c10d..56211d70 2025-12-19 00:03:03,858 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 450 melissalinkert 'Update a couple of outdated lines in about page' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 445 melissalinkert 'Update ome-common to 6.1.1' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 442 will-moore 'Link to Receipt of Sample Data' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 441 melissalinkert 'Update external readers page based upon feedback' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 439 melissalinkert 'Start describing external reader usage' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 438 will-moore 'Fix netcdf-java links' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 437 pwalczysko 'Nis elements and cibc-datasets' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 434 sbesson 'Add format page for Zeiss XRM format' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 431 pwalczysko 'Fix limited javadoc syntax' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 430 pwalczysko 'Fix sourceforge' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 426 jburel 'Update EMAN2 URL' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 427 jburel 'Checking linkcheck config' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 422 melissalinkert 'Add page for JDCE' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 425 melissalinkert 'Release notes for 8.2.0' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 418 sbesson 'Update MATLAB documentation for colormap return value' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 421 dominikl 'Exclude merckmillipore.com from link check' 2025-12-19 00:03:03,859 [ scc.merge] INFO 2025-12-19 00:03:03,859 [ scc.merge] INFO 2025-12-19 00:03:03,859 [ scc.merge] INFO Repository: ome/bio-formats-examples 2025-12-19 00:03:03,859 [ scc.merge] INFO Updating 3aa7013..1e4408b 2025-12-19 00:03:03,859 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 136 melissalinkert 'Add precompressed tile writing example' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 137 melissalinkert 'Fix output path for in-memory writing test' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 135 melissalinkert 'Bump logback version to 1.3.16' 2025-12-19 00:03:03,859 [ scc.merge] INFO - PR 134 sbesson 'POM: cleanup outdated metadata' 2025-12-19 00:03:03,859 [ scc.merge] INFO 2025-12-19 00:03:03,860 [ scc.merge] INFO 2025-12-19 00:03:03,860 [ scc.merge] INFO Repository: openmicroscopy/bioformats 2025-12-19 00:03:03,860 [ scc.merge] INFO Excluded PRs: 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' (stage: draft) 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude) 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking) 2025-12-19 00:03:03,860 [ scc.merge] INFO Updating 3f70394503..3fa05af5a6 2025-12-19 00:03:03,860 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4388 melissalinkert 'Update to CodeQL v4' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4384 melissalinkert 'Update ome-common to 6.1.1' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4383 melissalinkert 'Bump logback version to 1.3.16' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4374 melissalinkert 'CellH5: reduce memory usage' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' 2025-12-19 00:03:03,860 [ scc.merge] INFO - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4360 melissalinkert 'Fix several OIR issues' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4365 melissalinkert 'Fix array sizes in Octave' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4361 melissalinkert 'Remove unused detector linking logic' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4353 melissalinkert 'Fix tag encoding for LEO files' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4348 sbesson 'FakeReader: link instrument to all images' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4307 jburel 'Build report' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4338 sbesson 'org.openmicroscopy component updates' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4327 melissalinkert 'Check modulo values in repository tests' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4284 ptahmose 'fix for garbled images with CZIs' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' 2025-12-19 00:03:03,861 [ scc.merge] INFO - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4303 melissalinkert 'Fix Unidata repository URLs' 2025-12-19 00:03:03,862 [ scc.merge] INFO 2025-12-19 00:03:03,862 [ scc.merge] INFO Merged PRs: 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4362 ngladitz 'OBF: Support complex data stacks' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 4392 melissalinkert 'A few more ND2 dimension fixes' 2025-12-19 00:03:03,862 [ scc.merge] INFO 2025-12-19 00:03:03,862 [ scc.merge] INFO Repository: ome/ome-codecs 2025-12-19 00:03:03,862 [ scc.merge] INFO Updating fab1a01..1f655e6 2025-12-19 00:03:03,862 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 43 melissalinkert 'Update to ome-common 6.1.1' 2025-12-19 00:03:03,862 [ scc.merge] INFO - PR 42 sbesson 'Update publication build system to use Central Portal' 2025-12-19 00:03:03,862 [ scc.merge] INFO 2025-12-19 00:03:03,862 [ scc.merge] INFO 2025-12-19 00:03:03,862 [ scc.merge] INFO Repository: ome/ome-common-java 2025-12-19 00:03:03,863 [ scc.merge] INFO Excluded PRs: 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 109 dominikl 'Remove jackson dependency' (stage: draft) 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 108 dominikl 'Remove S3 handling' (stage: draft) 2025-12-19 00:03:03,863 [ scc.merge] INFO Updating 2cb0b7b..d22ba60 2025-12-19 00:03:03,863 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 107 sbesson 'Add GitHub release creation to Maven workflow' 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 99 melissalinkert 'Fix type of skipped bytes counter' 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' 2025-12-19 00:03:03,863 [ scc.merge] INFO 2025-12-19 00:03:03,863 [ scc.merge] INFO Merged PRs: 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' 2025-12-19 00:03:03,863 [ scc.merge] INFO 2025-12-19 00:03:03,863 [ scc.merge] INFO Repository: ome/ome-jai 2025-12-19 00:03:03,863 [ scc.merge] INFO Updating e70c2ab..9f1b4ef 2025-12-19 00:03:03,863 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 8 sbesson 'Update publication build system to use Central Portal ' 2025-12-19 00:03:03,863 [ scc.merge] INFO - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' 2025-12-19 00:03:03,864 [ scc.merge] INFO 2025-12-19 00:03:03,864 [ scc.merge] INFO 2025-12-19 00:03:03,864 [ scc.merge] INFO Repository: ome/ome-mdbtools 2025-12-19 00:03:03,864 [ scc.merge] INFO Updating 9193930..9c3c3e2 2025-12-19 00:03:03,864 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,864 [ scc.merge] INFO - PR 14 sbesson 'Update publication system to use Central Portal' 2025-12-19 00:03:03,864 [ scc.merge] INFO 2025-12-19 00:03:03,864 [ scc.merge] INFO 2025-12-19 00:03:03,864 [ scc.merge] INFO Repository: ome/ome-metakit 2025-12-19 00:03:03,864 [ scc.merge] INFO Updating 1ba6cf1..55abb77 2025-12-19 00:03:03,864 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,864 [ scc.merge] INFO - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2025-12-19 00:03:03,864 [ scc.merge] INFO - PR 30 melissalinkert 'Update ome-common to 6.1.1' 2025-12-19 00:03:03,864 [ scc.merge] INFO - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' 2025-12-19 00:03:03,864 [ scc.merge] INFO - PR 27 sbesson 'Update publication build system to use Central Portal' 2025-12-19 00:03:03,864 [ scc.merge] INFO 2025-12-19 00:03:03,864 [ scc.merge] INFO 2025-12-19 00:03:03,864 [ scc.merge] INFO Repository: ome/ome-model 2025-12-19 00:03:03,864 [ scc.merge] INFO Updating 3d70a1f9..3120dc4f 2025-12-19 00:03:03,865 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 225 melissalinkert 'Update ome-common to 6.1.1' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 224 sbesson 'Add release step to GitHub Maven workflow' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 222 sbesson 'Update publication build system to use Central Portal' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' 2025-12-19 00:03:03,865 [ scc.merge] INFO 2025-12-19 00:03:03,865 [ scc.merge] INFO 2025-12-19 00:03:03,865 [ scc.merge] INFO Repository: ome/ome-poi 2025-12-19 00:03:03,865 [ scc.merge] INFO Updating da3a5f3..d727828 2025-12-19 00:03:03,865 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 20 melissalinkert 'Update to ome-common 6.1.1' 2025-12-19 00:03:03,865 [ scc.merge] INFO - PR 19 sbesson 'Update publication system to use Central Portal' 2025-12-19 00:03:03,865 [ scc.merge] INFO 2025-12-19 00:03:03,865 [ scc.merge] INFO 2025-12-19 00:03:03,865 [ scc.merge] INFO Repository: ome/ome-stubs 2025-12-19 00:03:03,865 [ scc.merge] INFO Updating 1559997..6a87342 2025-12-19 00:03:03,865 [ scc.merge] INFO Previously merged: 2025-12-19 00:03:03,866 [ scc.merge] INFO - PR 12 sbesson 'Update publication build system to use Central Portal' 2025-12-19 00:03:03,866 [ scc.merge] INFO 2025-12-19 00:03:03,866 [ scc.merge] INFO Traceback (most recent call last): File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/main.py", line 64, in entry_point main("scc", items=[ File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/yaclifw/framework.py", line 188, in main ns.func(ns) File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 3339, in __call__ self.push(args, self.main_repo) File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 2210, in push main_repo.rpush(branch_name, remote, force=True) File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 2041, in rpush submodule_repo.rpush(branch_name, remote, force=force) File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 2047, in rpush self.push_branch(branch_name, remote=full_remote, force=force) File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 126, in wrapper error = check_exception_message(e) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 115, in wrapper return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 1296, in push_branch self.call("git", "push", "-f", remote, name) File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 1162, in call return self.wrap_call(self.debugWrap, *command, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/omero/workspace/BIOFORMATS-push/venv/lib64/python3.11/site-packages/scc/git.py", line 1187, in wrap_call raise Exception("rc=%s" % rc) Exception: rc=1 Build step 'Execute shell' marked build as failure Archiving artifacts Finished: FAILURE