Started by upstream project "ha:////4PuJpIb7Sfk0tlXxIiPwuGUGFxyfYBTVf2KwutkHKFZpAAAAmR+LCAAAAAAAAP9b85aBtbiIQTGjNKU4P08vOT+vOD8nVc83PyU1x6OyILUoJzMv2y+/JJUBAhiZGBgqihhk0NSjKDWzXb3RdlLBUSYGJk8GtpzUvPSSDB8G5tKinBIGIZ+sxLJE/ZzEvHT94JKizLx0a6BxUmjGOUNodHsLgAz2EgZe/az8JP2Qosz09NQifQAk1DzAwgAAAA==Trigger" build number ha:////4LHgamFx5KAGfecXHv2IPI8riskS0sOw9dQH4xvX+jhIAAAAmx+LCAAAAAAAAP9b85aBtbiIQTGjNKU4P08vOT+vOD8nVc83PyU1x6OyILUoJzMv2y+/JJUBAhiZGBgqihhk0NSjKDWzXb3RdlLBUSYGJk8GtpzUvPSSDB8G5tKinBIGIZ+sxLJE/ZzEvHT94JKizLx0a6BxUmjGOUNodHsLgAymEgZ+/az8JP2Qosz09NQifRNzAInbMovEAAAA47 originally caused by: Started by timer Running as SYSTEM Building remotely on ha:////4MSFFwZhvKyaZKGejjoKFo+3SCj+z+JFRMNqFO6ZjC+wAAAAph+LCAAAAAAAAP9b85aBtbiIQTGjNKU4P08vOT+vOD8nVc83PyU1x6OyILUoJzMv2y+/JJUBAhiZGBgqihhk0NSjKDWzXb3RdlLBUSYGJk8GtpzUvPSSDB8G5tKinBIGIZ+sxLJE/ZzEvHT94JKizLx0a6BxUmjGOUNodHsLgAz+EgYp/eT83ILSktQi/ZLU4pLMvJLU9KLEksz8PH0Arhz8Fc8AAAA=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 2.52.0' > 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/jenkins10278432783415722096.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 (26.2.1) + 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) (2.9.1) 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) (0.19.1) 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) (1.6.2) Requirement already satisfied: requests>=2.14.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (2.34.2) Requirement already satisfied: pyjwt>=2.4.0 in ./venv/lib64/python3.11/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.13.0) Requirement already satisfied: typing-extensions>=4.5.0 in ./venv/lib64/python3.11/site-packages (from PyGithub>=1.54->scc) (4.16.0) Requirement already satisfied: cryptography>=3.4.0 in ./venv/lib64/python3.11/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (49.0.0) 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) (3.0) Requirement already satisfied: charset_normalizer<4,>=2 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.4.7) Requirement already satisfied: idna<4,>=2.5 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.18) Requirement already satisfied: certifi>=2023.5.7 in ./venv/lib64/python3.11/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (2026.6.17) + 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 2026-08-07 00:01:08,600 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-08-07 00:01:08,600 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-08-07 00:01:08,600 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-08-07 00:01:08,600 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-08-07 00:01:08,601 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-08-07 00:01:08,601 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-08-07 00:01:12,911 [ scc.merge] INFO Repository: ome/bio-formats-build 2026-08-07 00:01:12,911 [ scc.merge] INFO Already up to date. 2026-08-07 00:01:12,911 [ scc.merge] INFO 2026-08-07 00:01:12,911 [ 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 'f5e5c947ce39860f3da4a39817e8778ca0cde841' Submodule path 'bio-formats-examples': checked out '669e8f37d483c62a4f8e9da89f14b7a8220b883f' Submodule path 'bioformats': checked out '61116e46d3095f62dfef4d88612ca0943b8fe233' Submodule path 'ome-codecs': checked out '61a7334fea6533ba945c2279a6d62a216a365936' Submodule path 'ome-common-java': checked out 'a704a2abe26d165bc53bd5cd0da5a5c464f53987' Submodule path 'ome-jai': checked out '029d825eea01e9d5f3c12528a230c95cd71a0cd1' Submodule path 'ome-mdbtools': checked out '52241813f78efa5191175a7952c0b2d89c215498' Submodule path 'ome-metakit': checked out 'b953d0b0b8b7eabae84e98c262f2ac7049ffb92a' Submodule path 'ome-model': checked out '1957bd781d54ea4fde815912f27ee94b950beb2c' Submodule path 'ome-poi': checked out 'f179bf4f5fcc0499d065a0e0b40141a2834e1751' Submodule path 'ome-stubs': checked out '5a2fdd0aa37fef5d34942d367f57de6f5916fc06' + 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 2026-08-07 00:01:41,218 [github.Reque] INFO Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2026-08-07 00:02:12,886 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-08-07 00:02:12,886 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-08-07 00:02:12,886 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-08-07 00:02:12,886 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-08-07 00:02:12,886 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-08-07 00:02:12,886 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-08-07 00:02:13,808 [ scc.git] INFO Overriding base-branch from master to main 2026-08-07 00:03:06,608 [ scc.git] INFO Overriding base-branch from master to develop 2026-08-07 00:03:58,058 [ scc.git] ERROR stderr (git merge --ff-only origin/develop): Updating files: 60% (77/127) Updating files: 61% (78/127) Updating files: 62% (79/127) Updating files: 63% (81/127) Updating files: 64% (82/127) Updating files: 65% (83/127) Updating files: 66% (84/127) Updating files: 67% (86/127) Updating files: 68% (87/127) Updating files: 69% (88/127) Updating files: 70% (89/127) Updating files: 71% (91/127) Updating files: 72% (92/127) Updating files: 73% (93/127) Updating files: 74% (94/127) Updating files: 75% (96/127) Updating files: 76% (97/127) Updating files: 77% (98/127) Updating files: 78% (100/127) Updating files: 79% (101/127) Updating files: 80% (102/127) Updating files: 81% (103/127) Updating files: 82% (105/127) Updating files: 83% (106/127) Updating files: 84% (107/127) Updating files: 85% (108/127) Updating files: 86% (110/127) Updating files: 87% (111/127) Updating files: 88% (112/127) Updating files: 89% (114/127) Updating files: 90% (115/127) Updating files: 91% (116/127) Updating files: 92% (117/127) Updating files: 93% (119/127) Updating files: 94% (120/127) Updating files: 95% (121/127) Updating files: 96% (122/127) Updating files: 97% (124/127) Updating files: 98% (125/127) Updating files: 99% (126/127) Updating files: 100% (127/127) Updating files: 100% (127/127), done. 2026-08-07 00:06:41,247 [ scc.merge] INFO Repository: ome/bio-formats-build 2026-08-07 00:06:41,247 [ scc.merge] INFO Already up to date. 2026-08-07 00:06:41,247 [ scc.merge] INFO 2026-08-07 00:06:41,247 [ scc.merge] INFO 2026-08-07 00:06:41,247 [ scc.merge] INFO Repository: ome/ZarrReader 2026-08-07 00:06:41,247 [ scc.merge] INFO Updating 31d6d95..5f3faa4 2026-08-07 00:06:41,247 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 111 Tom-TBT 'Fixed typo in README env var name to set' 2026-08-07 00:06:41,247 [ scc.merge] INFO 2026-08-07 00:06:41,247 [ scc.merge] INFO 2026-08-07 00:06:41,247 [ scc.merge] INFO Repository: ome/bio-formats-documentation 2026-08-07 00:06:41,247 [ scc.merge] INFO Updating db99c10d..f5e5c947 2026-08-07 00:06:41,247 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 480 will-moore 'Exclude www.bdbiosciences.com from link checker' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 476 melissalinkert 'Update logback to 1.5.37' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 477 melissalinkert 'Replace Olympus SIS link' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 471 dominikl 'Replace faqs.org links' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 474 dominikl 'exclude unidata' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 473 melissalinkert 'Update `-tilex`/`-tiley` description to reference compression type' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 472 dominikl 'ignore nih.gov' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 456 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.16 to 1.5.25' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 469 sbesson 'Update Unidata releases URL' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 468 melissalinkert 'Require Java 11 at runtime, build on Java 21' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 465 pwalczysko 'Ignore umassmed.edu, 403' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 463 pwalczysko 'Ignore zenodo 403' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 461 melissalinkert 'Release notes for 8.5.0' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 462 sbesson 'Update dependency list documentation page for Bio-Formats 8.5.0' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 460 sbesson 'Replace third-party application pages by image.sc Community Partners links' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 459 sbesson 'Replace velocity dependency by velocity-engine-core' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 458 pwalczysko 'Konica olympus' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 455 melissalinkert 'Add TFCYTO page' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 454 melissalinkert 'Release notes for 8.4.0' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 453 pwalczysko 'Fix links' 2026-08-07 00:06:41,247 [ scc.merge] INFO - PR 451 sbesson 'Re-organize user section to differentiate end-user facing applications' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 450 melissalinkert 'Update a couple of outdated lines in about page' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 446 sbesson 'Add labelPlanes to the list of flags for fake images' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 445 melissalinkert 'Update ome-common to 6.1.1' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 444 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 442 will-moore 'Link to Receipt of Sample Data' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 440 dominikl 'Exclude https://www.mail-archive.com/tiff from linkcheck' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 441 melissalinkert 'Update external readers page based upon feedback' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 439 melissalinkert 'Start describing external reader usage' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 438 will-moore 'Fix netcdf-java links' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 437 pwalczysko 'Nis elements and cibc-datasets' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 436 pwalczysko 'Replace broken link in lemkesoft with working one' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 435 pwalczysko 'Replace nikoninstruments link with redirect' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 434 sbesson 'Add format page for Zeiss XRM format' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 432 sbesson 'Add release notes for upcoming Bio-Formats 8.3.0 release' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 433 sbesson 'Review list of dependencies for Bio-Formats 8.3.0' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 431 pwalczysko 'Fix limited javadoc syntax' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 430 pwalczysko 'Fix sourceforge' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 426 jburel 'Update EMAN2 URL' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 427 jburel 'Checking linkcheck config' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 422 melissalinkert 'Add page for JDCE' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 425 melissalinkert 'Release notes for 8.2.0' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 423 pwalczysko 'Replace link to Vaa3D for a relevant one and fix peng lab link' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 409 melissalinkert 'Link to Farsight GitHub instead of wiki' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 418 sbesson 'Update MATLAB documentation for colormap return value' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 421 dominikl 'Exclude merckmillipore.com from link check' 2026-08-07 00:06:41,248 [ scc.merge] INFO 2026-08-07 00:06:41,248 [ scc.merge] INFO Merged PRs: 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 481 melissalinkert 'Remove dependencies associated with minio and jackson' 2026-08-07 00:06:41,248 [ scc.merge] INFO 2026-08-07 00:06:41,248 [ scc.merge] INFO Repository: ome/bio-formats-examples 2026-08-07 00:06:41,248 [ scc.merge] INFO Updating 3aa7013..669e8f3 2026-08-07 00:06:41,248 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 139 melissalinkert 'Fix markers for tile conversion example' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 138 sbesson 'Fix reST inclusion markers in ReadWriteInMemory example' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 136 melissalinkert 'Add precompressed tile writing example' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 137 melissalinkert 'Fix output path for in-memory writing test' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 135 melissalinkert 'Bump logback version to 1.3.16' 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 134 sbesson 'POM: cleanup outdated metadata' 2026-08-07 00:06:41,248 [ scc.merge] INFO 2026-08-07 00:06:41,248 [ scc.merge] INFO 2026-08-07 00:06:41,248 [ scc.merge] INFO Repository: openmicroscopy/bioformats 2026-08-07 00:06:41,248 [ scc.merge] INFO Excluded PRs: 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4467 Darlokt 'Make no-JHDF tests opt-in' (user: Darlokt) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4466 Darlokt 'formats-bsd tests resource cleanup fix' (user: Darlokt) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4464 Darlokt 'Memoizer fixes' (user: Darlokt) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4463 Darlokt 'Quicktime fixes' (user: Darlokt) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4457 ebenolson 'NDPI: Add writer support' (user: ebenolson) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4450 Darlokt 'New CV7000 reader' (user: Darlokt) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4448 maartenpaul 'fix Nd2 wellinfo missing' (user: maartenpaul) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4447 cgohlke 'Fix LIF row padding with mixed memory blocks' (user: cgohlke) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4434 melissalinkert 'Refine series count calculation for .vsi data with no pyramids' (label: exclude) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4412 tlambert03 'fix: Fix null pointer exception on reopen (for some readers)' (user: tlambert03) 2026-08-07 00:06:41,248 [ scc.merge] INFO - PR 4397 kwiechen '.vmic WSI reader' (user: kwiechen) 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4260 melissalinkert 'UpgradeChecker: more thorough check of upgrade check result and HTTP response code' (stage: draft) 2026-08-07 00:06:41,249 [ scc.merge] INFO Updating 3f70394503..61116e46d3 2026-08-07 00:06:41,249 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4451 melissalinkert 'Make `DicomTile` objects more accessible' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4439 melissalinkert 'Leica SCN: update list of scanner models without color correction' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4458 melissalinkert 'Update `codeql` and `report` to use checkout v6' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4452 melissalinkert 'Update logback to 1.5.37' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4427 PEEKPerformer 'VSI: surface CALIBRATION lookup table as named slope/origin/final keys' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4446 melissalinkert 'Update netcdf-java to 5.10.0' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4444 melissalinkert 'TIFF: only adjust strip/tile byte counts for uncompressed data' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4438 melissalinkert 'Remove unnecessary negative checks' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4436 melissalinkert 'xmlvalid cleanup' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4428 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4421 melissalinkert 'Imaris HDF: allow paths to be in a subdirectory' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4430 melissalinkert 'Remove unnecessary dead store to local variable' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4379 melissalinkert 'DICOM: fix width of values with DS VR' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4403 melissalinkert 'Zeiss CZI: calculate phase, illumination, rotation counts based on both min and max indexes' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4373 melissalinkert 'CZI: ignore plate information if not activated' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4354 melissalinkert 'DICOM: use `Study Time` tag as an extra check on whether files should be grouped' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4419 melissalinkert 'Update to ome-common 6.2.1' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4417 melissalinkert 'VSI: recognize calibration function tag' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4418 melissalinkert 'Update to ome-codecs 1.1.3' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4395 melissalinkert 'Refine estimate of bytes needed to write a TIFF plane' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4415 melissalinkert 'Remove explicit aircompressor dependency from formats-gpl' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4405 melissalinkert 'NDPIS: don't overwrite image names from NDPIReader' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4409 melissalinkert 'Open NetcdfFile from a RandomAccessFile instead of a String path' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4410 melissalinkert 'Amira: fix encoding and parse physical size units when possible' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4408 melissalinkert 'Remove use of DocumentBuilderFactory in favor of relevant XMLTools method' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4406 sbesson 'Fix Javadoc warnings' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4394 sbesson 'Bump org.openmicroscopy:ome-model from 6.5.1 to 6.5.3' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4402 sbesson 'Review the list of cdm-core exclusions in formats-gpl' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4399 sbesson 'Bump org.openmicroscopy:ome-common from 6.1.1 to 6.1.2' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4392 melissalinkert 'A few more ND2 dimension fixes' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4380 melissalinkert 'Calculate resolution counts when generating pyramids with `bfconvert`' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4371 melissalinkert 'Fix and refactor ModuloC handling in ImageJ plugins' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4391 melissalinkert 'Add lens IDs 18113 and 18114' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4382 melissalinkert 'bfconvert: make sure plane indexes are correct when writing single Z/C/T' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4387 melissalinkert 'Parse .vsi timestamps similar to Z positions' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4388 melissalinkert 'Update to CodeQL v4' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4385 melissalinkert 'Update ome-model, ome-codecs, ome-poi, ome-metakit to latest versions' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4384 melissalinkert 'Update ome-common to 6.1.1' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4383 melissalinkert 'Bump logback version to 1.3.16' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4381 melissalinkert 'ND2: preserve pixel type when setting dimensions' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4378 melissalinkert 'Unify emission wavelength handling in NDPI and NDPIS readers' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4375 melissalinkert 'FV1000: fix some small ROI parsing issues' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4374 melissalinkert 'CellH5: reduce memory usage' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4370 melissalinkert 'ND2: don't reset pixel type when the bits per pixel doesn't make sense' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4368 odinsbane 'Put the scanline padding to 4 bytes on the non-compressed reading.' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4360 melissalinkert 'Fix several OIR issues' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4365 melissalinkert 'Fix array sizes in Octave' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4358 melissalinkert 'OMEXMLReader: escape values when re-assembling OME-XML' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4363 melissalinkert 'Metamorph: read plane positions from multiple files' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4361 melissalinkert 'Remove unused detector linking logic' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4357 melissalinkert 'Add reader for TissueFAXS (.tfcyto) data' 2026-08-07 00:06:41,249 [ scc.merge] INFO - PR 4359 sbesson 'Report workflow: delay the first execution by 1 h' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4355 zacsimile 'Fix DCIMG indexing over multiple files' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4350 sbesson 'Build report workflow: fix failure when no tests failed' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4339 melissalinkert 'Fake: add `labelPlanes` option to add human-readable labels to planes' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4353 melissalinkert 'Fix tag encoding for LEO files' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4348 sbesson 'FakeReader: link instrument to all images' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4349 sbesson 'Add unit tests for ChannelMerger and ChannelSeparator' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4351 sbesson 'GH release workflow: add flag to automatically generate notes' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4345 melissalinkert 'ChannelMerger: correct number of Channels in MetadataStore' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4347 melissalinkert 'Fix Metamorph .nd encoding' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4341 melissalinkert 'Don't use position metadata when distinguishing between T and series' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4307 jburel 'Build report' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4343 sbesson 'Upgrade from commons-lang:commons-lang to org.apache.commons:commons-lang3' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4332 melissalinkert 'ND2: add TextInfoItems to original metadata before parsing' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4322 melissalinkert 'Metamorph: don't reset dimensions if the well count and series count match' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4316 sbesson 'xmlvalid: consume OMEXMLServiceImpl.SCHEMA_CLASSPATH_READER' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4338 sbesson 'org.openmicroscopy component updates' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4294 nicolapapp 'Miscellaneous fixes to SlideBook7Reader.java' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4336 sbesson 'TecanReader: use try-with-resources when opening SQL connection' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4337 melissalinkert 'Metamorph TIFF: throw more explicit exceptions if parsing invalid TIFF' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4331 melissalinkert 'Zeiss CZI: fix a few ID/reference issues' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4319 melissalinkert 'Zeiss CZI: use millisecond units for exposure times attached to channels' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4306 melissalinkert 'CZI: LightSource fixes, set LightSourceSettings.Attenuation' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4328 melissalinkert 'Ventana .bif: fix LEFT overlap and add Z stack support' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4317 melissalinkert 'Fix OME-TIFF optimal tile size if an IFD is not linked to an Image' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4323 melissalinkert 'showinf: configure logging for `-omexml-only` after all arguments parsed' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4327 melissalinkert 'Check modulo values in repository tests' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4326 sbesson 'LiFlimReader: cast integers to double for division accuracy' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4314 melissalinkert 'Operetta/Harmony: fix case where index XML is in the parent of the image directory' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4309 odinsbane 'ND2Reader Changed the padding for a specific condition to pad to 4 byte boundaries.' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4308 melissalinkert 'Add support for Zeiss XRM (.txm/.txrm) data' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4311 sbesson 'Review declaration of Maven Scijava as a repository' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4284 ptahmose 'fix for garbled images with CZIs' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4289 melissalinkert 'ImageJ export plugin: add some checks to prevent file appending' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4304 melissalinkert 'Leica LIF: map offsets to images by memory block ID' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4305 melissalinkert 'Add reader for Molecular Devices JDCE' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4293 sbesson 'Remove unnecessary Python script for bumping component versions' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4302 sbesson 'Olympus ScanR: check getCurrentFile is the first value of getUsedFiles' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4299 foxmja 'Added Multi-Page TIFF Support for Prairie Technologies TIFFs' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4298 zacsimile 'Add frameFooterBytes to image stride for DCIMG >=0x1000000' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4303 melissalinkert 'Fix Unidata repository URLs' 2026-08-07 00:06:41,250 [ scc.merge] INFO 2026-08-07 00:06:41,250 [ scc.merge] INFO Merged PRs: 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4243 melissalinkert 'Update IExtraMetadataWriter.setExtraMetadata(...) to accept an Object' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4254 melissalinkert 'Memoizer: ask any ImageReader instances to remove all but the current reader' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4362 ngladitz 'OBF: Support complex data stacks' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4429 melissalinkert 'Check for null when calling TiffParser.checkHeader()' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4437 melissalinkert 'Allow slices to be deleted from a virtual stack' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4440 melissalinkert 'BDV: store relative path instead of absolute' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4445 melissalinkert '.vsi fill color fixes' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4454 melissalinkert 'Add API and implementations to provide axis orientation' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4455 melissalinkert 'JPEG: reshape internal tiles if calculated tile width exceeds max short value' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4465 PEEKPerformer 'OIR: fix two parse failures on Olympus LEXT (OLS) acquisitions' 2026-08-07 00:06:41,250 [ scc.merge] INFO - PR 4468 melissalinkert 'Add `omitIniFromUsedFiles` option to `FakeReader`' 2026-08-07 00:06:41,250 [ scc.merge] INFO 2026-08-07 00:06:41,250 [ scc.merge] INFO Repository: ome/ome-codecs 2026-08-07 00:06:41,250 [ scc.merge] INFO Updating fab1a01..61a7334 2026-08-07 00:06:41,251 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 47 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 46 dependabot[bot] 'Bump io.airlift:aircompressor from 0.27 to 2.0.3' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 44 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 43 melissalinkert 'Update to ome-common 6.1.1' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 42 sbesson 'Update publication build system to use Central Portal' 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO Repository: ome/ome-common-java 2026-08-07 00:06:41,251 [ scc.merge] INFO Updating 2cb0b7b..a704a2a 2026-08-07 00:06:41,251 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 108 dominikl 'Remove S3 handling' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 117 melissalinkert 'Update logback to 1.5.37' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 115 sbesson 'Bump ch.qos.logback:logback-classic from 1.3.16 to 1.5.34' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 114 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 113 melissalinkert 'Make sure length() returns the correct value when Location represents a mapped file' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 112 melissalinkert 'Standardize XML parsing' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 111 sbesson 'XMLTools: use try-with-resources statement' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 110 sbesson 'Deprecate the S3 interfaces, implementations and services' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 107 sbesson 'Add GitHub release creation to Maven workflow' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 106 melissalinkert 'Bump logback-classic to 1.3.16' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 100 melissalinkert 'Add DataTools.readFile signature that accepts an encoding name' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 101 sbesson 'Update deployment infrastructure to publish to Central Portal' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 99 melissalinkert 'Fix type of skipped bytes counter' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 98 sbesson 'Add CodeQL workflow running on push and pull request events' 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO Repository: ome/ome-jai 2026-08-07 00:06:41,251 [ scc.merge] INFO Updating e70c2ab..029d825 2026-08-07 00:06:41,251 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 11 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 8 sbesson 'Update publication build system to use Central Portal ' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 9 sbesson 'Replace usage of sun.security.action by PrivilegedAction' 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO Repository: ome/ome-mdbtools 2026-08-07 00:06:41,251 [ scc.merge] INFO Updating 9193930..5224181 2026-08-07 00:06:41,251 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 15 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 14 sbesson 'Update publication system to use Central Portal' 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO Repository: ome/ome-metakit 2026-08-07 00:06:41,251 [ scc.merge] INFO Updating 1ba6cf1..b953d0b 2026-08-07 00:06:41,251 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 34 melissalinkert 'Update logback to 1.5.37' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 33 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 31 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 30 melissalinkert 'Update ome-common to 6.1.1' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 29 dependabot[bot] 'Bump ch.qos.logback:logback-core from 1.3.15 to 1.3.16' 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 27 sbesson 'Update publication build system to use Central Portal' 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO 2026-08-07 00:06:41,251 [ scc.merge] INFO Repository: ome/ome-model 2026-08-07 00:06:41,251 [ scc.merge] INFO Excluded PRs: 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 235 Darlokt 'Add dependabot' (user: Darlokt) 2026-08-07 00:06:41,251 [ scc.merge] INFO - PR 234 Darlokt 'Python cleanup' (user: Darlokt) 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 233 Darlokt 'Expose MetadataOnly through metadata APIs' (user: Darlokt) 2026-08-07 00:06:41,252 [ scc.merge] INFO Updating 3d70a1f9..1957bd78 2026-08-07 00:06:41,252 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 232 melissalinkert 'Update logback to 1.5.37' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 230 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 229 sbesson 'OMEXMLMetadata: prevent IndexOutOfBoundsException when setting references' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 226 rleigh-codelibre 'OMEXMLMetadata: Correct indexed access to annotation references' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 225 melissalinkert 'Update ome-common to 6.1.1' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 223 melissalinkert 'Bump logback-classic to 1.3.16' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 224 sbesson 'Add release step to GitHub Maven workflow' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 222 sbesson 'Update publication build system to use Central Portal' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 221 melissalinkert 'Replace mailing lists and QA with forum.image.sc and Zenodo' 2026-08-07 00:06:41,252 [ scc.merge] INFO 2026-08-07 00:06:41,252 [ scc.merge] INFO 2026-08-07 00:06:41,252 [ scc.merge] INFO Repository: ome/ome-poi 2026-08-07 00:06:41,252 [ scc.merge] INFO Updating da3a5f3..f179bf4 2026-08-07 00:06:41,252 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 22 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 21 sbesson 'GitHub actions: add step to auto-create GitHub release on tags' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 20 melissalinkert 'Update to ome-common 6.1.1' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 19 sbesson 'Update publication system to use Central Portal' 2026-08-07 00:06:41,252 [ scc.merge] INFO 2026-08-07 00:06:41,252 [ scc.merge] INFO 2026-08-07 00:06:41,252 [ scc.merge] INFO Repository: ome/ome-stubs 2026-08-07 00:06:41,252 [ scc.merge] INFO Updating 1559997..5a2fdd0 2026-08-07 00:06:41,252 [ scc.merge] INFO Previously merged: 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 13 melissalinkert 'Require Java 11 at runtime, build on Java 21/25' 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 12 sbesson 'Update publication build system to use Central Portal' 2026-08-07 00:06:41,252 [ scc.merge] INFO 2026-08-07 00:06:41,252 [ scc.merge] INFO Merged PRs: 2026-08-07 00:06:41,252 [ scc.merge] INFO - PR 14 sbesson 'Automate the publication of the artifact to Maven Central' 2026-08-07 00:06:41,252 [ scc.merge] INFO 2026-08-07 00:07:11,055 [ 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 + 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' HEAD detached from db99c10d It took 2.29 seconds to enumerate untracked files. See 'git help status' for information on how to improve this. nothing to commit, working tree clean Entering 'bio-formats-examples' HEAD detached from 3aa7013 nothing to commit, working tree clean Entering 'bioformats' HEAD detached from 3f70394503 nothing to commit, working tree clean Entering 'ome-codecs' HEAD detached from fab1a01 nothing to commit, working tree clean 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' HEAD detached from 1ba6cf1 nothing to commit, working tree clean Entering 'ome-model' HEAD detached from 3d70a1f9 nothing to commit, working tree clean Entering 'ome-poi' HEAD detached from da3a5f3 nothing to commit, working tree clean 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' Everything up-to-date Entering 'bio-formats-examples' Everything up-to-date Entering 'bioformats' Everything up-to-date Entering 'ome-codecs' Everything up-to-date 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' Everything up-to-date Entering 'ome-model' Everything up-to-date Entering 'ome-poi' Everything up-to-date 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' HEAD detached from 9e8c9ff nothing to commit, working tree clean + true + git push -f git@github.com:snoopycrimecop/bio-formats-build.git HEAD:merge_ci Everything up-to-date [BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins9781444575869492380.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 + sed -i s/9.0.0-SNAPSHOT/8.5.0/ /home/omero/workspace/BIOFORMATS-push/target/version.properties + sed -i s/9.0.0-SNAPSHOT/8.5.0/ /home/omero/workspace/BIOFORMATS-push/target/version.tsv Archiving artifacts Finished: SUCCESS