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Started by upstream project "Trigger" build number 1
originally caused by:
 Started by user devspace
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
Cloning the remote Git repository
Cloning repository https://github.com/ome/bio-formats-build
 > git init /home/omero/workspace/BIOFORMATS-push/bio-formats-build # timeout=10
Fetching upstream changes from https://github.com/ome/bio-formats-build
 > git --version # timeout=10
 > git --version # 'git version 2.39.3'
 > git fetch --tags --force --progress -- https://github.com/ome/bio-formats-build +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git config remote.origin.url https://github.com/ome/bio-formats-build # timeout=10
 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10
Avoid second fetch
 > git rev-parse origin/master^{commit} # timeout=10
Checking out Revision e7ea0c022f87bdf67c4090bdcd8c10c2f2014607 (origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f e7ea0c022f87bdf67c4090bdcd8c10c2f2014607 # timeout=10
Commit message: "Merge pull request #568 from ome/dependabot/submodules/bio-formats-documentation-817d09e"
First time build. Skipping changelog.
 > 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/jenkins6232610743317721656.sh
+ python3 -mvenv venv
+ source /home/omero/workspace/BIOFORMATS-push/venv/bin/activate
++ deactivate nondestructive
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' 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
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
+ pip install -U pip
Requirement already satisfied: pip in ./venv/lib/python3.9/site-packages (21.2.3)
Collecting pip
  Using cached pip-24.0-py3-none-any.whl (2.1 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-24.0
+ pip install -U scc
Collecting scc
  Using cached scc-0.19.1-py3-none-any.whl.metadata (3.6 kB)
Collecting PyGithub>=1.54 (from scc)
  Using cached PyGithub-2.2.0-py3-none-any.whl.metadata (3.8 kB)
Collecting PyYAML>=5.1 (from scc)
  Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting future (from scc)
  Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB)
Collecting ruamel.yaml (from scc)
  Using cached ruamel.yaml-0.18.6-py3-none-any.whl.metadata (23 kB)
Collecting ruamel.yaml.jinja2 (from scc)
  Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl.metadata (2.9 kB)
Collecting six (from scc)
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting urllib3<2 (from scc)
  Using cached urllib3-1.26.18-py2.py3-none-any.whl.metadata (48 kB)
Collecting yaclifw<0.3,>=0.2.0 (from scc)
  Using cached yaclifw-0.2.0-py3-none-any.whl
Collecting pynacl>=1.4.0 (from PyGithub>=1.54->scc)
  Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl.metadata (8.6 kB)
Collecting requests>=2.14.0 (from PyGithub>=1.54->scc)
  Using cached requests-2.31.0-py3-none-any.whl.metadata (4.6 kB)
Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc)
  Using cached PyJWT-2.8.0-py3-none-any.whl.metadata (4.2 kB)
Collecting typing-extensions>=4.0.0 (from PyGithub>=1.54->scc)
  Using cached typing_extensions-4.10.0-py3-none-any.whl.metadata (3.0 kB)
Collecting Deprecated (from PyGithub>=1.54->scc)
  Using cached Deprecated-1.2.14-py2.py3-none-any.whl.metadata (5.4 kB)
Collecting ruamel.yaml.clib>=0.2.7 (from ruamel.yaml->scc)
  Using cached ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl.metadata (2.2 kB)
Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc)
  Using cached cryptography-42.0.5-cp39-abi3-manylinux_2_28_x86_64.whl.metadata (5.3 kB)
Collecting cffi>=1.4.1 (from pynacl>=1.4.0->PyGithub>=1.54->scc)
  Using cached cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting charset-normalizer<4,>=2 (from requests>=2.14.0->PyGithub>=1.54->scc)
  Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)
Collecting idna<4,>=2.5 (from requests>=2.14.0->PyGithub>=1.54->scc)
  Using cached idna-3.6-py3-none-any.whl.metadata (9.9 kB)
Collecting certifi>=2017.4.17 (from requests>=2.14.0->PyGithub>=1.54->scc)
  Using cached certifi-2024.2.2-py3-none-any.whl.metadata (2.2 kB)
Collecting wrapt<2,>=1.10 (from Deprecated->PyGithub>=1.54->scc)
  Using cached wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.6 kB)
Collecting pycparser (from cffi>=1.4.1->pynacl>=1.4.0->PyGithub>=1.54->scc)
  Using cached pycparser-2.21-py2.py3-none-any.whl.metadata (1.1 kB)
Using cached scc-0.19.1-py3-none-any.whl (48 kB)
Using cached PyGithub-2.2.0-py3-none-any.whl (350 kB)
Using cached PyYAML-6.0.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (738 kB)
Using cached urllib3-1.26.18-py2.py3-none-any.whl (143 kB)
Using cached future-1.0.0-py3-none-any.whl (491 kB)
Using cached ruamel.yaml-0.18.6-py3-none-any.whl (117 kB)
Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl (5.5 kB)
Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
Using cached PyJWT-2.8.0-py3-none-any.whl (22 kB)
Using cached PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl (856 kB)
Using cached requests-2.31.0-py3-none-any.whl (62 kB)
Using cached ruamel.yaml.clib-0.2.8-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl (562 kB)
Using cached typing_extensions-4.10.0-py3-none-any.whl (33 kB)
Using cached Deprecated-1.2.14-py2.py3-none-any.whl (9.6 kB)
Using cached certifi-2024.2.2-py3-none-any.whl (163 kB)
Using cached cffi-1.16.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (443 kB)
Using cached charset_normalizer-3.3.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (142 kB)
Using cached cryptography-42.0.5-cp39-abi3-manylinux_2_28_x86_64.whl (4.6 MB)
Using cached idna-3.6-py3-none-any.whl (61 kB)
Using cached wrapt-1.16.0-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (80 kB)
Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Installing collected packages: wrapt, urllib3, typing-extensions, six, ruamel.yaml.clib, PyYAML, pyjwt, pycparser, idna, future, charset-normalizer, certifi, yaclifw, ruamel.yaml, requests, Deprecated, cffi, ruamel.yaml.jinja2, pynacl, cryptography, PyGithub, scc
Successfully installed Deprecated-1.2.14 PyGithub-2.2.0 PyYAML-6.0.1 certifi-2024.2.2 cffi-1.16.0 charset-normalizer-3.3.2 cryptography-42.0.5 future-1.0.0 idna-3.6 pycparser-2.21 pyjwt-2.8.0 pynacl-1.5.0 requests-2.31.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 ruamel.yaml.jinja2-0.2.7 scc-0.19.1 six-1.16.0 typing-extensions-4.10.0 urllib3-1.26.18 wrapt-1.16.0 yaclifw-0.2.0
+ 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
2024-03-14 15:38:16,392 [   scc.merge] INFO  Merging Pull Request(s) based on master
2024-03-14 15:38:16,392 [   scc.merge] INFO  Including Pull Request(s) opened by any public member of the organization
2024-03-14 15:38:16,392 [   scc.merge] INFO  Including Pull Request(s) labelled as include or dependencies
2024-03-14 15:38:16,392 [   scc.merge] INFO  Excluding Pull Request(s) staged as draft
2024-03-14 15:38:16,392 [   scc.merge] INFO  Excluding Pull Request(s) labelled as exclude or breaking
2024-03-14 15:38:16,392 [   scc.merge] INFO  Excluding Pull Request(s) without successful status
2024-03-14 15:38:35,320 [   scc.merge] INFO  Repository: ome/bio-formats-build
2024-03-14 15:38:35,320 [   scc.merge] INFO  Already up to date.
2024-03-14 15:38:35,320 [   scc.merge] INFO  
2024-03-14 15:38:35,320 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:38:35,320 [   scc.merge] INFO    - PR 567 dependabot[bot] 'Bump ZarrReader from `4deea8d` to `cf4f3f2`'
2024-03-14 15:38:35,320 [   scc.merge] INFO    - PR 570 dependabot[bot] 'Bump ome-common-java from `fa81e2b` to `eca9c1c`'
2024-03-14 15:38:35,320 [   scc.merge] INFO    - PR 571 dependabot[bot] 'Bump bioformats from `6815841` to `83df5ca`'
2024-03-14 15:38:35,320 [   scc.merge] INFO    - PR 572 dependabot[bot] 'Bump ome-poi from `ba0d5d2` to `1fcfd18`'
2024-03-14 15:38:35,320 [   scc.merge] INFO    - PR 573 dependabot[bot] 'Bump ome-codecs from `040c8b9` to `e092dea`'
2024-03-14 15:38:35,320 [   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 'ome-metakit': checked out '21bd75668a005effa65cb89404623d056fcee9b2'
+ 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
2024-03-14 15:38:50,822 [github.Reque] INFO  Following Github server redirection from /repos/openmicroscopy/bioformats to /repositories/2510503
2024-03-14 15:39:10,898 [   scc.merge] INFO  Merging Pull Request(s) based on master
2024-03-14 15:39:10,899 [   scc.merge] INFO  Including Pull Request(s) opened by any public member of the organization
2024-03-14 15:39:10,899 [   scc.merge] INFO  Including Pull Request(s) labelled as include or dependencies
2024-03-14 15:39:10,899 [   scc.merge] INFO  Excluding Pull Request(s) staged as draft
2024-03-14 15:39:10,899 [   scc.merge] INFO  Excluding Pull Request(s) labelled as exclude or breaking
2024-03-14 15:39:10,899 [   scc.merge] INFO  Excluding Pull Request(s) without successful status
2024-03-14 15:39:29,425 [     scc.git] INFO  Overriding base-branch from master to main
2024-03-14 15:40:03,253 [     scc.git] INFO  Overriding base-branch from master to develop
2024-03-14 15:41:29,420 [     scc.git] INFO    - PR 174 jburel 'Remove docs'
Conflicting PR. Removed from build [BIOFORMATS-push#1](https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1/). See the [console output](https://BRANCHCI.openmicroscopy.org/jenkins/job/BIOFORMATS-push/1/consoleText) for more details.
Possible conflicts:
  - Upstream changes
    - docs/sphinx/pom.xml

--conflicts

2024-03-14 15:41:44,490 [   scc.merge] INFO  Repository: ome/bio-formats-build
2024-03-14 15:41:44,490 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,490 [   scc.merge] INFO  
2024-03-14 15:41:44,490 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 567 dependabot[bot] 'Bump ZarrReader from `4deea8d` to `cf4f3f2`'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 570 dependabot[bot] 'Bump ome-common-java from `fa81e2b` to `eca9c1c`'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 571 dependabot[bot] 'Bump bioformats from `6815841` to `83df5ca`'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 572 dependabot[bot] 'Bump ome-poi from `ba0d5d2` to `1fcfd18`'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 573 dependabot[bot] 'Bump ome-codecs from `040c8b9` to `e092dea`'
2024-03-14 15:41:44,490 [   scc.merge] INFO  
2024-03-14 15:41:44,490 [   scc.merge] INFO  Repository: ome/ZarrReader
2024-03-14 15:41:44,490 [   scc.merge] INFO  Excluded PRs:
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 73 dgault 'Update ReadMe and Change Log' (status: failure)
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 20 dgault 'ZarrReader: Use chunk API' (exclude comment)
2024-03-14 15:41:44,490 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,490 [   scc.merge] INFO  
2024-03-14 15:41:44,490 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 71 sbesson 'Bump Bio-Formats to version 7.1.0'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 74 dgault 'JZarr: Add jackson.core and jackson-databind to exclsions'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 75 dgault 'Update handling and parsing of acquisition metadata'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 80 jburel 'Review action'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 81 jburel 'add Java 17 to testing matrix'
2024-03-14 15:41:44,490 [   scc.merge] INFO    - PR 82 dgault 'Reintroduce S3FileSystemStore'
2024-03-14 15:41:44,490 [   scc.merge] INFO  
2024-03-14 15:41:44,490 [   scc.merge] INFO  Repository: ome/bio-formats-documentation
2024-03-14 15:41:44,491 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Repository: ome/bio-formats-examples
2024-03-14 15:41:44,491 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 69 dgault 'Add macro examples from OME 2020 NGFF workshop'
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Repository: openmicroscopy/bioformats
2024-03-14 15:41:44,491 [   scc.merge] INFO  Excluded PRs:
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4164 melissalinkert 'Reduce DICOM write time' (stage: draft)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4131 dgault 'VirtualImagePlus: Retain B&C settings for each slice' (status: failure)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4092 NicoKiaru 'Commits an alternative Zeiss CZI Reader' (user: NicoKiaru)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4000 XLEFReaderForBioformats 'Reworking LMSMetadata package and adding a new lif reader' (user: XLEFReaderForBioformats)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 3898 melissalinkert 'InCell 1000/2000 field count and plane metadata fixes' (stage: draft)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 3794 dgault 'Chunk API: Add new API and functionality for reading and writing chunks' (label: exclude)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 3680 iwbh15 'Performance increase in writeIFD' (user: iwbh15)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 3618 dgault 'Memoizer: Persist caching to sub readers' (label: breaking)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 3537 dgault 'Flex: Merge IDR changes and add new group plate option' (label: exclude)
2024-03-14 15:41:44,491 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4117 ed-scanlon 'Work-around for breaking change in CellSens 4.1'
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4130 carandraug 'matlab/bfGetPlane.m: avoid use of makeDataArray2D when Octave (ome/bio-formats-octave-docker#29)'
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4147 TBlackmore 'Added support for ColumbusReader to import data with z stacks'
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4154 melissalinkert 'Update GitHub actions versions and add M1/Java 21 build'
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4159 melissalinkert 'Turn off file-leak-detector if tests are run with Java 21'
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4162 melissalinkert 'Remove duplicate enum check and add clarifying comment'
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 4163 melissalinkert 'SimplePCI: fix Z position handling'
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Repository: ome/ome-codecs
2024-03-14 15:41:44,491 [   scc.merge] INFO  Excluded PRs:
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 24 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (status: failure)
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 21 dgault 'Replace one-jai with jai-imageio-jpeg2000' (stage: draft)
2024-03-14 15:41:44,491 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,491 [   scc.merge] INFO    - PR 36 sbesson 'Use Maven profiles to handle different versions of TestNG'
2024-03-14 15:41:44,491 [   scc.merge] INFO  
2024-03-14 15:41:44,491 [   scc.merge] INFO  Repository: ome/ome-common-java
2024-03-14 15:41:44,491 [   scc.merge] INFO  Excluded PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 72 dependabot[bot] 'Bump testng from 6.8 to 7.7.0' (label: exclude)
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 59 NicoKiaru 'adds AverageImageScaler implementation of IImageScaler' (user: NicoKiaru)
2024-03-14 15:41:44,492 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 88 sbesson 'Use Maven profiles to handle different versions of TestNG'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Repository: ome/ome-jai
2024-03-14 15:41:44,492 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 7 melissalinkert 'Add JDK21 to build matrix'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Repository: ome/ome-mdbtools
2024-03-14 15:41:44,492 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 13 melissalinkert 'Add JDK 21 to build matrix'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Repository: ome/ome-metakit
2024-03-14 15:41:44,492 [   scc.merge] INFO  Updating 8ead2f6..21bd756
2024-03-14 15:41:44,492 [   scc.merge] INFO  Previously merged:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 20 melissalinkert 'Add JDK 21 to build matrix'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 21 sbesson 'Use Maven profiles to handle different versions of TestNG'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Repository: ome/ome-model
2024-03-14 15:41:44,492 [   scc.merge] INFO  Excluded PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 180 joshmoore 'xsd-fu: templates for linkml generation' (stage: draft)
2024-03-14 15:41:44,492 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 185 melissalinkert 'Add model object API to clear each list of associated objects'
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 187 melissalinkert 'Add JDK 21 to build matrix'
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 188 sbesson 'Use Maven profiles to handle different versions of TestNG'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Conflicting PRs (not included):
2024-03-14 15:41:44,492 [   scc.merge] INFO    - PR 174 jburel 'Remove docs'
2024-03-14 15:41:44,492 [   scc.merge] INFO  
2024-03-14 15:41:44,492 [   scc.merge] INFO  Repository: ome/ome-poi
2024-03-14 15:41:44,493 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,493 [   scc.merge] INFO  
2024-03-14 15:41:44,493 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,493 [   scc.merge] INFO    - PR 15 sbesson 'Add JDK 21 to the build matrix'
2024-03-14 15:41:44,493 [   scc.merge] INFO  
2024-03-14 15:41:44,493 [   scc.merge] INFO  Repository: ome/ome-stubs
2024-03-14 15:41:44,493 [   scc.merge] INFO  Already up to date.
2024-03-14 15:41:44,493 [   scc.merge] INFO  
2024-03-14 15:41:44,493 [   scc.merge] INFO  Merged PRs:
2024-03-14 15:41:44,493 [   scc.merge] INFO    - PR 11 melissalinkert 'Add JDK 21 to build matrix'
2024-03-14 15:41:44,493 [   scc.merge] INFO  
2024-03-14 15:42:09,828 [   scc.merge] INFO  Merged branch pushed to https://github.com/snoopycrimecop/bio-formats-build/tree/merge_ci
+ echo 'Update maven component versions'
Update maven component versions
+ update-versions
OMEZarrReader=0.4.2-SNAPSHOT bio-formats-documentation=8.0.0-SNAPSHOT bio-formats-examples=8.0.0-SNAPSHOT bio-formats_plugins=8.0.0-SNAPSHOT bio-formats-tools=8.0.0-SNAPSHOT bioformats_package=8.0.0-SNAPSHOT turbojpeg=8.0.0-SNAPSHOT formats-api=8.0.0-SNAPSHOT formats-bsd=8.0.0-SNAPSHOT formats-gpl=8.0.0-SNAPSHOT test-suite=8.0.0-SNAPSHOT pom-bio-formats=8.0.0-SNAPSHOT bioformats=8.0.0-SNAPSHOT ome-codecs=1.0.2-SNAPSHOT ome-common=6.0.22-SNAPSHOT ome-jai=0.1.3-SNAPSHOT ome-mdbtools=5.3.3-SNAPSHOT metakit=5.3.7-SNAPSHOT ome-model-doc=6.3.5-SNAPSHOT ome-xml=6.3.5-SNAPSHOT specification=6.3.5-SNAPSHOT ome-model=6.3.5-SNAPSHOT ome-poi=5.3.9-SNAPSHOT mipav-stubs=6.0.2-SNAPSHOT ome-stubs=6.0.2-SNAPSHOT
+ echo 'Commit all component version changes'
Commit all component version changes
+ git submodule foreach 'git add -u'
Entering 'ZarrReader'
Entering 'bio-formats-documentation'
Entering 'bio-formats-examples'
Entering 'bioformats'
Entering 'ome-codecs'
Entering 'ome-common-java'
Entering 'ome-jai'
Entering 'ome-mdbtools'
Entering 'ome-metakit'
Entering 'ome-model'
Entering 'ome-poi'
Entering 'ome-stubs'
+ git submodule foreach 'git commit -m '\''Update component versions'\'' || true'
Entering 'ZarrReader'
HEAD detached from cf4f3f2
nothing to commit, working tree clean
Entering 'bio-formats-documentation'
[detached HEAD 5d06aaaf] Update component versions
 1 file changed, 7 insertions(+), 7 deletions(-)
Entering 'bio-formats-examples'
[detached HEAD 7881d68] Update component versions
 1 file changed, 1 insertion(+), 1 deletion(-)
Entering 'bioformats'
[detached HEAD f94707a843] Update component versions
 1 file changed, 9 insertions(+), 9 deletions(-)
Entering 'ome-codecs'
[detached HEAD 63b8d4b] Update component versions
 1 file changed, 2 insertions(+), 2 deletions(-)
Entering 'ome-common-java'
HEAD detached from eca9c1c
nothing to commit, working tree clean
Entering 'ome-jai'
HEAD detached from 6b7e421
nothing to commit, working tree clean
Entering 'ome-mdbtools'
HEAD detached from cdb3552
nothing to commit, working tree clean
Entering 'ome-metakit'
[detached HEAD 2338588] Update component versions
 1 file changed, 1 insertion(+), 1 deletion(-)
Entering 'ome-model'
[detached HEAD a45ab065] Update component versions
 1 file changed, 1 insertion(+), 1 deletion(-)
Entering 'ome-poi'
[detached HEAD 7f9542d] Update component versions
 1 file changed, 1 insertion(+), 1 deletion(-)
Entering 'ome-stubs'
HEAD detached from a17529e
nothing to commit, working tree clean
+ echo 'Push all branches'
Push all branches
++ git config github.user
+ user=snoopycrimecop
+ git submodule foreach 'git push -f git@github.com:snoopycrimecop/${path}.git HEAD:merge_ci'
Entering 'ZarrReader'
Everything up-to-date
Entering 'bio-formats-documentation'
To github.com:snoopycrimecop/bio-formats-documentation.git
   661f1bcd..5d06aaaf  HEAD -> merge_ci
Entering 'bio-formats-examples'
To github.com:snoopycrimecop/bio-formats-examples.git
   e9ad5ed..7881d68  HEAD -> merge_ci
Entering 'bioformats'
To github.com:snoopycrimecop/bioformats.git
   1ebed53d77..f94707a843  HEAD -> merge_ci
Entering 'ome-codecs'
To github.com:snoopycrimecop/ome-codecs.git
   dbce919..63b8d4b  HEAD -> merge_ci
Entering 'ome-common-java'
Everything up-to-date
Entering 'ome-jai'
Everything up-to-date
Entering 'ome-mdbtools'
Everything up-to-date
Entering 'ome-metakit'
To github.com:snoopycrimecop/ome-metakit.git
   8ee2483..2338588  HEAD -> merge_ci
Entering 'ome-model'
To github.com:snoopycrimecop/ome-model.git
   6919ee42..a45ab065  HEAD -> merge_ci
Entering 'ome-poi'
To github.com:snoopycrimecop/ome-poi.git
   e17eedb..7f9542d  HEAD -> merge_ci
Entering 'ome-stubs'
Everything up-to-date
+ echo 'Commit all component version changes'
Commit all component version changes
+ git add -u
+ git commit -m 'Update component versions'
[detached HEAD 1612f4f] Update component versions
 7 files changed, 7 insertions(+), 7 deletions(-)
+ git push -f git@github.com:snoopycrimecop/bio-formats-build.git HEAD:merge_ci
To github.com:snoopycrimecop/bio-formats-build.git
   e24fcb2..1612f4f  HEAD -> merge_ci
[BIOFORMATS-push] $ /bin/bash -xe /tmp/jenkins9770641833888561744.sh
+ mkdir -p /home/omero/workspace/BIOFORMATS-push/target
+ cd /home/omero/workspace/BIOFORMATS-push/target
+ curl -sfL https://github.com/ome/build-infra/archive/master.tar.gz
+ tar -zxf -
+ export PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/
+ PATH=/opt/ice-3.6.5/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/home/omero/workspace/BIOFORMATS-push/target/build-infra-master/
+ cd /home/omero/workspace/BIOFORMATS-push/bio-formats-build
+ foreach-get-version
+ foreach-get-version-as-property
Archiving artifacts
Finished: SUCCESS