Started by upstream project "Trigger" build number 35 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 2.52.0' > 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/jenkins9615354568774964204.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 (26.1.2) + 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) (2.9.1) 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 2026-07-29 10:50:30,621 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-07-29 10:50:30,622 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-07-29 10:50:30,622 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-07-29 10:50:30,622 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-07-29 10:50:30,622 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-07-29 10:50:30,622 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-07-29 10:50:34,535 [ scc.merge] INFO Repository: ome/bio-formats-build 2026-07-29 10:50:34,535 [ scc.merge] INFO Already up to date. 2026-07-29 10:50:34,535 [ scc.merge] INFO 2026-07-29 10:50:34,535 [ 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 '12f8e6bca00521f20ed3a0142740d30ca8bdb5e3' Submodule path 'bio-formats-examples': checked out '669e8f37d483c62a4f8e9da89f14b7a8220b883f' Submodule path 'bioformats': checked out 'b486f7c4b47a90af6093b56f9f6e006ad5243010' Submodule path 'ome-codecs': checked out '61a7334fea6533ba945c2279a6d62a216a365936' Submodule path 'ome-common-java': checked out '3d2f042952323757922c487ebac81edb8dafcae3' Submodule path 'ome-jai': checked out '029d825eea01e9d5f3c12528a230c95cd71a0cd1' Submodule path 'ome-mdbtools': checked out '52241813f78efa5191175a7952c0b2d89c215498' Submodule path 'ome-metakit': checked out 'b8b3a629a6dd9bf422949f6b175b9e310ba6e252' Submodule path 'ome-model': checked out '8be3f6cbeac93f1139012c309da057c1775131fd' 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 2026-07-29 10:50:59,416 [github.Reque] INFO Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503 2026-07-29 10:51:28,907 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-07-29 10:51:28,907 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-07-29 10:51:28,907 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-07-29 10:51:28,907 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-07-29 10:51:28,907 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-07-29 10:51:28,907 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-07-29 10:51:29,715 [ scc.git] INFO Overriding base-branch from master to main 2026-07-29 10:52:15,512 [ scc.git] INFO Overriding base-branch from master to develop 2026-07-29 10:53:04,946 [ scc.git] ERROR stderr (git merge --ff-only origin/develop): Updating files: 69% (87/126) Updating files: 70% (89/126) Updating files: 71% (90/126) Updating files: 72% (91/126) Updating files: 73% (92/126) Updating files: 74% (94/126) Updating files: 75% (95/126) Updating files: 76% (96/126) Updating files: 77% (98/126) Updating files: 78% (99/126) Updating files: 79% (100/126) Updating files: 80% (101/126) Updating files: 81% (103/126) Updating files: 82% (104/126) Updating files: 83% (105/126) Updating files: 84% (106/126) Updating files: 85% (108/126) Updating files: 86% (109/126) Updating files: 87% (110/126) Updating files: 88% (111/126) Updating files: 89% (113/126) Updating files: 90% (114/126) Updating files: 91% (115/126) Updating files: 92% (116/126) Updating files: 93% (118/126) Updating files: 94% (119/126) Updating files: 95% (120/126) Updating files: 96% (121/126) Updating files: 97% (123/126) Updating files: 98% (124/126) Updating files: 99% (125/126) Updating files: 100% (126/126) Updating files: 100% (126/126), done. Build was aborted Calling Pipeline was cancelled Archiving artifacts Terminated Finished: ABORTED