Console Output
+ export BASE_REPO=omero-zarr-pixel-buffer.git
+ BASE_REPO=omero-zarr-pixel-buffer.git
+ export BASE_BRANCH=master
+ BASE_BRANCH=master
+ export VERSION_LOG=/home/omero/workspace/OMERO-zarr-pixel-buffer-push/build/version.tsv
+ VERSION_LOG=/home/omero/workspace/OMERO-zarr-pixel-buffer-push/build/version.tsv
+ . build/venv/bin/activate
++ deactivate nondestructive
++ '[' -n '' ']'
++ '[' -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ unset VIRTUAL_ENV_PROMPT
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/home/omero/workspace/OMERO-zarr-pixel-buffer-push/build/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/OMERO-zarr-pixel-buffer-push/build/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
+ '[' merge_ci '!=' null ']'
+ export PUSH_BRANCH=merge_ci
+ PUSH_BRANCH=merge_ci
+ '[' null '!=' null ']'
+ export STATUS=success-only 'MERGE_OPTIONS=-vvv --no-ask --reset --comment'
+ STATUS=success-only
+ MERGE_OPTIONS='-vvv --no-ask --reset --comment'
+ bash build/build-infra-master/recursive-merge
Merge base repository (no submodule updates)
2026-05-19 00:59:14,071 [ scc.config] DEBUG Found github.token
2026-05-19 00:59:14,073 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443
2026-05-19 00:59:14,337 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-19 00:59:14,773 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-19 00:59:15,164 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None
2026-05-19 00:59:15,164 [ scc.gh] DEBUG 4663 remaining from 5000 (Reset at 01:05
2026-05-19 00:59:15,165 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel'
2026-05-19 00:59:15,167 [ scc.git] DEBUG Check current status
2026-05-19 00:59:15,167 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-19 00:59:15,170 [ scc.git] DEBUG 3e9b9da Merge remote-tracking branch 'glencoe/master'
2026-05-19 00:59:15,170 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-19 00:59:15,208 [ scc.config] DEBUG Found remote.origin.url
2026-05-19 00:59:15,775 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer HTTP/1.1" 200 None
2026-05-19 00:59:16,283 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None
2026-05-19 00:59:16,738 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None
2026-05-19 00:59:17,190 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None
2026-05-19 00:59:17,660 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None
2026-05-19 00:59:17,661 [ scc.git] DEBUG Resetting...
2026-05-19 00:59:17,661 [ scc.git] DEBUG Calling 'git reset --hard HEAD'
2026-05-19 00:59:17,667 [ scc.git] DEBUG HEAD is now at 3e9b9da Merge remote-tracking branch 'glencoe/master'
2026-05-19 00:59:17,667 [ scc.git] DEBUG Calling 'git submodule update --recursive'
2026-05-19 00:59:17,703 [ scc.git] DEBUG Check current status
2026-05-19 00:59:17,703 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-19 00:59:17,706 [ scc.git] DEBUG 3e9b9da Merge remote-tracking branch 'glencoe/master'
2026-05-19 00:59:17,706 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-19 00:59:17,742 [ scc.merge] INFO Merging Pull Request(s) based on master
2026-05-19 00:59:17,742 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization
2026-05-19 00:59:17,742 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies
2026-05-19 00:59:17,742 [ scc.merge] INFO Excluding Pull Request(s) staged as draft
2026-05-19 00:59:17,742 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking
2026-05-19 00:59:17,742 [ scc.repo] DEBUG ## PRs found:
2026-05-19 00:59:18,199 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/pulls HTTP/1.1" 200 None
2026-05-19 00:59:18,671 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/issues/16 HTTP/1.1" 200 None
2026-05-19 00:59:18,671 [ scc.repo] DEBUG - PR 16 dominikl 'Zarr v3 support'
2026-05-19 00:59:18,671 [ scc.repo] DEBUG ## Branches found:
2026-05-19 00:59:18,671 [ scc.git] DEBUG Get sha1 of %s
2026-05-19 00:59:18,672 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:18,673 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master'
2026-05-19 00:59:18,675 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included.
2026-05-19 00:59:18,676 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master'
2026-05-19 00:59:18,678 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master'
2026-05-19 00:59:18,681 [ scc.git] DEBUG Already up to date.
2026-05-19 00:59:18,681 [ scc.git] DEBUG Calling 'git fetch origin pull/16/head'
2026-05-19 00:59:19,047 [ scc.git] DEBUG From https://github.com/ome/omero-zarr-pixel-buffer
2026-05-19 00:59:19,047 [ scc.git] DEBUG * branch refs/pull/16/head -> FETCH_HEAD
2026-05-19 00:59:19,051 [ scc.git] DEBUG ## Unique users: []
2026-05-19 00:59:19,051 [ scc.git] DEBUG Get sha1 of %s
2026-05-19 00:59:19,051 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:19,053 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-19 00:59:19,057 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:19,059 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 16 (Zarr v3 support) ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-19 00:59:19,067 [ scc.git] DEBUG Merge made by the 'ort' strategy.
2026-05-19 00:59:19,073 [ scc.git] DEBUG .github/workflows/codeql.yml | 48 -
2026-05-19 00:59:19,073 [ scc.git] DEBUG build.gradle | 42 +-
2026-05-19 00:59:19,073 [ scc.git] DEBUG config/checkstyle/checkstyle.xml | 9 +-
2026-05-19 00:59:19,073 [ scc.git] DEBUG .../com/bc/zarr/storage/OmeroFileSystemStore.java | 78 --
2026-05-19 00:59:19,073 [ scc.git] DEBUG .../omero/zarr/OmeroAmazonS3ClientFactory.java | 138 ---
2026-05-19 00:59:19,073 [ scc.git] DEBUG .../omero/zarr/OmeroS3FileSystem.java | 44 -
2026-05-19 00:59:19,073 [ scc.git] DEBUG .../zarr/OmeroS3ReadOnlySeekableByteChannel.java | 194 ----
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../java/com/glencoesoftware/omero/zarr/Utils.java | 88 ++
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../com/glencoesoftware/omero/zarr/ZarrPath.java | 64 ++
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../omero/zarr/ZarrPixelBuffer.java | 464 ++++-----
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../omero/zarr/ZarrPixelsService.java | 247 ++---
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../com/glencoesoftware/omero/zarr/ZarrStore.java | 391 ++++++++
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../s3fs/OmeroS3FilesystemProvider.java | 187 ----
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../omero/zarr/ZarrPixelBufferTest.java | 1001 ++++----------------
2026-05-19 00:59:19,074 [ scc.git] DEBUG .../omero/zarr/ZarrPixelsServiceTest.java | 10 +-
2026-05-19 00:59:19,074 [ scc.git] DEBUG 15 files changed, 1031 insertions(+), 1974 deletions(-)
2026-05-19 00:59:19,074 [ scc.git] DEBUG delete mode 100644 .github/workflows/codeql.yml
2026-05-19 00:59:19,074 [ scc.git] DEBUG delete mode 100644 src/main/java/com/bc/zarr/storage/OmeroFileSystemStore.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG delete mode 100644 src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG delete mode 100644 src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG delete mode 100644 src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG create mode 100644 src/main/java/com/glencoesoftware/omero/zarr/Utils.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG create mode 100644 src/main/java/com/glencoesoftware/omero/zarr/ZarrPath.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG create mode 100644 src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java
2026-05-19 00:59:19,074 [ scc.git] DEBUG delete mode 100644 src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java
2026-05-19 00:59:19,303 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-19 00:59:19,304 [ scc.git] DEBUG Calling 'git submodule update'
2026-05-19 00:59:19,340 [ scc.git] DEBUG Get sha1 of %s
2026-05-19 00:59:19,340 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:19,342 [ scc.git] DEBUG Calling 'git status --porcelain'
2026-05-19 00:59:19,346 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f09ce8f3d90> has no local changes
2026-05-19 00:59:19,346 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Snone
Repository: ome/omero-zarr-pixel-buffer
Already up to date.
Merged PRs:
- PR 16 dominikl 'Zarr v3 support'
Generated by OMERO-zarr-pixel-buffer-push#158 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-zarr-pixel-buffer-push/158/)'
2026-05-19 00:59:19,352 [ scc.git] DEBUG [detached HEAD e3c3b33] merge master -Dorg -Snone
2026-05-19 00:59:19,353 [ scc.merge] INFO Repository: ome/omero-zarr-pixel-buffer
2026-05-19 00:59:19,353 [ scc.merge] INFO Already up to date.
2026-05-19 00:59:19,353 [ scc.merge] INFO
2026-05-19 00:59:19,353 [ scc.merge] INFO Merged PRs:
2026-05-19 00:59:19,353 [ scc.merge] INFO - PR 16 dominikl 'Zarr v3 support'
2026-05-19 00:59:19,353 [ scc.merge] INFO
2026-05-19 00:59:19,353 [ scc.merge] DEBUG Cleaning remote branches created for merging
2026-05-19 00:59:19,353 [ scc.git] DEBUG Calling 'git remote'
Merge all submodules2026-05-19 00:59:19,820 [ scc.config] DEBUG Found github.token
2026-05-19 00:59:19,821 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443
2026-05-19 00:59:20,294 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-19 00:59:20,723 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-19 00:59:21,119 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None
2026-05-19 00:59:21,120 [ scc.gh] DEBUG 4661 remaining from 5000 (Reset at 01:05
2026-05-19 00:59:21,120 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel'
2026-05-19 00:59:21,123 [ scc.git] DEBUG Check current status
2026-05-19 00:59:21,123 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-19 00:59:21,125 [ scc.git] DEBUG e3c3b33 merge master -Dorg -Snone
2026-05-19 00:59:21,125 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-19 00:59:21,164 [ scc.config] DEBUG Found remote.origin.url
2026-05-19 00:59:21,741 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer HTTP/1.1" 200 None
2026-05-19 00:59:22,241 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None
2026-05-19 00:59:22,706 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None
2026-05-19 00:59:23,158 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None
2026-05-19 00:59:23,772 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None
2026-05-19 00:59:23,774 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path'
2026-05-19 00:59:23,810 [ scc.git] DEBUG Resetting...
2026-05-19 00:59:23,810 [ scc.git] DEBUG Calling 'git reset --hard HEAD'
2026-05-19 00:59:23,814 [ scc.git] DEBUG HEAD is now at e3c3b33 merge master -Dorg -Snone
2026-05-19 00:59:23,815 [ scc.git] DEBUG Calling 'git submodule update --recursive'
2026-05-19 00:59:23,851 [ scc.git] DEBUG Check current status
2026-05-19 00:59:23,851 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-19 00:59:23,853 [ scc.git] DEBUG e3c3b33 merge master -Dorg -Snone
2026-05-19 00:59:23,853 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-19 00:59:23,888 [ scc.merge] INFO Merging Pull Request(s) based on master
2026-05-19 00:59:23,889 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization
2026-05-19 00:59:23,889 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies
2026-05-19 00:59:23,889 [ scc.merge] INFO Excluding Pull Request(s) staged as draft
2026-05-19 00:59:23,889 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking
2026-05-19 00:59:23,889 [ scc.merge] INFO Excluding Pull Request(s) without successful status
2026-05-19 00:59:23,889 [ scc.repo] DEBUG ## PRs found:
2026-05-19 00:59:24,346 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/pulls HTTP/1.1" 200 None
2026-05-19 00:59:24,873 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/issues/16 HTTP/1.1" 200 None
2026-05-19 00:59:25,453 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/commits/ee383a347382bbc6428f5faebcc3744383d144ab?page=1 HTTP/1.1" 200 None
2026-05-19 00:59:26,000 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/commits/ee383a347382bbc6428f5faebcc3744383d144ab/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None
2026-05-19 00:59:26,565 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/commits/ee383a347382bbc6428f5faebcc3744383d144ab/check-suites?app_id=15368 HTTP/1.1" 200 None
2026-05-19 00:59:27,079 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/commits/ee383a347382bbc6428f5faebcc3744383d144ab?page=1 HTTP/1.1" 200 None
2026-05-19 00:59:27,538 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/statuses/ee383a347382bbc6428f5faebcc3744383d144ab?per_page=1 HTTP/1.1" 200 2
2026-05-19 00:59:27,538 [ scc.repo] DEBUG - PR 16 dominikl 'Zarr v3 support'
2026-05-19 00:59:27,538 [ scc.repo] DEBUG ## Branches found:
2026-05-19 00:59:27,538 [ scc.git] DEBUG Get sha1 of %s
2026-05-19 00:59:27,538 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:27,541 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master'
2026-05-19 00:59:27,543 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included.
2026-05-19 00:59:27,543 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master'
2026-05-19 00:59:27,546 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master'
2026-05-19 00:59:27,549 [ scc.git] DEBUG Already up to date.
2026-05-19 00:59:27,549 [ scc.git] DEBUG Calling 'git fetch origin pull/16/head'
2026-05-19 00:59:27,894 [ scc.git] DEBUG From https://github.com/ome/omero-zarr-pixel-buffer
2026-05-19 00:59:27,894 [ scc.git] DEBUG * branch refs/pull/16/head -> FETCH_HEAD
2026-05-19 00:59:27,898 [ scc.git] DEBUG ## Unique users: []
2026-05-19 00:59:27,898 [ scc.git] DEBUG Get sha1 of %s
2026-05-19 00:59:27,899 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:27,901 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-19 00:59:27,904 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:27,906 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 16 (Zarr v3 support) ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-19 00:59:27,909 [ scc.git] DEBUG Already up to date.
2026-05-19 00:59:28,100 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-19 00:59:28,100 [ scc.git] DEBUG Calling 'git submodule update'
2026-05-19 00:59:28,135 [ scc.git] DEBUG Get sha1 of %s
2026-05-19 00:59:28,136 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-19 00:59:28,138 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path'
2026-05-19 00:59:28,172 [ scc.git] DEBUG Calling 'git status --porcelain'
2026-05-19 00:59:28,175 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7fd2c1b110d0> has no local changes
2026-05-19 00:59:28,175 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only
Repository: ome/omero-zarr-pixel-buffer
Already up to date.
Merged PRs:
- PR 16 dominikl 'Zarr v3 support'
Generated by OMERO-zarr-pixel-buffer-push#158 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-zarr-pixel-buffer-push/158/)'
2026-05-19 00:59:28,308 [ scc.git] DEBUG [detached HEAD 283c786] merge master -Dorg -Ssuccess-only
2026-05-19 00:59:28,309 [ scc.merge] INFO Repository: ome/omero-zarr-pixel-buffer
2026-05-19 00:59:28,309 [ scc.merge] INFO Already up to date.
2026-05-19 00:59:28,309 [ scc.merge] INFO
2026-05-19 00:59:28,309 [ scc.merge] INFO Merged PRs:
2026-05-19 00:59:28,309 [ scc.merge] INFO - PR 16 dominikl 'Zarr v3 support'
2026-05-19 00:59:28,309 [ scc.merge] INFO
2026-05-19 00:59:28,309 [ scc.merge] DEBUG Cleaning remote branches created for merging
2026-05-19 00:59:28,309 [ scc.git] DEBUG Calling 'git remote'
Update component versions
grep: settings.gradle: No such file or directory
Updating formats-api from formatsVersion to 8.6.0-SNAPSHOT
Updating formats-gpl from formatsVersion to 8.6.0-SNAPSHOT
Commit all component version changes
HEAD detached from 3e9b9da
nothing to commit, working tree clean
2026-05-19 00:59:35,591 [ scc.push] INFO Merged branch pushed to https://github.com/snoopycrimecop/omero-zarr-pixel-buffer/tree/merge_ci
