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)
2026-05-16 00:58:48,364 [ scc.config] DEBUG Found github.token
2026-05-16 00:58:48,365 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443
2026-05-16 00:58:48,610 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-16 00:58:49,043 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-16 00:58:49,438 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None
2026-05-16 00:58:49,439 [ scc.gh] DEBUG 4953 remaining from 5000 (Reset at 01:05
2026-05-16 00:58:49,439 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel'
2026-05-16 00:58:49,442 [ scc.git] DEBUG Check current status
2026-05-16 00:58:49,442 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-16 00:58:49,444 [ scc.git] DEBUG 3e9b9da Merge remote-tracking branch 'glencoe/master'
2026-05-16 00:58:49,445 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-16 00:58:49,484 [ scc.config] DEBUG Found remote.origin.url
2026-05-16 00:58:50,004 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer HTTP/1.1" 200 None
2026-05-16 00:58:50,521 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None
2026-05-16 00:58:50,998 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None
2026-05-16 00:58:51,473 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None
2026-05-16 00:58:51,923 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None
2026-05-16 00:58:51,924 [ scc.git] DEBUG Resetting...
2026-05-16 00:58:51,924 [ scc.git] DEBUG Calling 'git reset --hard HEAD'
2026-05-16 00:58:51,930 [ scc.git] DEBUG HEAD is now at 3e9b9da Merge remote-tracking branch 'glencoe/master'
2026-05-16 00:58:51,930 [ scc.git] DEBUG Calling 'git submodule update --recursive'
2026-05-16 00:58:51,968 [ scc.git] DEBUG Check current status
2026-05-16 00:58:51,968 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-16 00:58:51,970 [ scc.git] DEBUG 3e9b9da Merge remote-tracking branch 'glencoe/master'
2026-05-16 00:58:51,970 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-16 00:58:52,006 [ scc.merge] INFO Merging Pull Request(s) based on master
2026-05-16 00:58:52,007 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization
2026-05-16 00:58:52,007 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies
2026-05-16 00:58:52,007 [ scc.merge] INFO Excluding Pull Request(s) staged as draft
2026-05-16 00:58:52,007 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking
2026-05-16 00:58:52,007 [ scc.repo] DEBUG ## PRs found:
2026-05-16 00:58:52,491 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/pulls HTTP/1.1" 200 None
2026-05-16 00:58:52,953 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/issues/16 HTTP/1.1" 200 None
2026-05-16 00:58:52,953 [ scc.repo] DEBUG - PR 16 dominikl 'Zarr v3 support'
2026-05-16 00:58:52,953 [ scc.repo] DEBUG ## Branches found:
2026-05-16 00:58:52,953 [ scc.git] DEBUG Get sha1 of %s
2026-05-16 00:58:52,953 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:58:52,955 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master'
2026-05-16 00:58:52,957 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included.
2026-05-16 00:58:52,957 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master'
2026-05-16 00:58:52,960 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master'
2026-05-16 00:58:52,963 [ scc.git] DEBUG Already up to date.
2026-05-16 00:58:52,963 [ scc.git] DEBUG Calling 'git fetch origin pull/16/head'
2026-05-16 00:58:53,316 [ scc.git] DEBUG From https://github.com/ome/omero-zarr-pixel-buffer
2026-05-16 00:58:53,316 [ scc.git] DEBUG * branch refs/pull/16/head -> FETCH_HEAD
2026-05-16 00:58:53,320 [ scc.git] DEBUG ## Unique users: []
2026-05-16 00:58:53,320 [ scc.git] DEBUG Get sha1 of %s
2026-05-16 00:58:53,320 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:58:53,322 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-16 00:58:53,326 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:58:53,328 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 16 (Zarr v3 support) ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-16 00:58:53,336 [ scc.git] DEBUG Merge made by the 'ort' strategy.
2026-05-16 00:58:53,341 [ scc.git] DEBUG .github/workflows/codeql.yml | 48 -
2026-05-16 00:58:53,341 [ scc.git] DEBUG build.gradle | 42 +-
2026-05-16 00:58:53,341 [ scc.git] DEBUG config/checkstyle/checkstyle.xml | 9 +-
2026-05-16 00:58:53,341 [ scc.git] DEBUG .../com/bc/zarr/storage/OmeroFileSystemStore.java | 78 --
2026-05-16 00:58:53,341 [ scc.git] DEBUG .../omero/zarr/OmeroAmazonS3ClientFactory.java | 138 ---
2026-05-16 00:58:53,342 [ scc.git] DEBUG .../omero/zarr/OmeroS3FileSystem.java | 44 -
2026-05-16 00:58:53,342 [ scc.git] DEBUG .../zarr/OmeroS3ReadOnlySeekableByteChannel.java | 194 ----
2026-05-16 00:58:53,342 [ scc.git] DEBUG .../java/com/glencoesoftware/omero/zarr/Utils.java | 88 ++
2026-05-16 00:58:53,342 [ scc.git] DEBUG .../com/glencoesoftware/omero/zarr/ZarrPath.java | 64 ++
2026-05-16 00:58:53,342 [ scc.git] DEBUG .../omero/zarr/ZarrPixelBuffer.java | 464 ++++-----
2026-05-16 00:58:53,342 [ scc.git] DEBUG .../omero/zarr/ZarrPixelsService.java | 247 ++---
2026-05-16 00:58:53,343 [ scc.git] DEBUG .../com/glencoesoftware/omero/zarr/ZarrStore.java | 391 ++++++++
2026-05-16 00:58:53,343 [ scc.git] DEBUG .../s3fs/OmeroS3FilesystemProvider.java | 187 ----
2026-05-16 00:58:53,343 [ scc.git] DEBUG .../omero/zarr/ZarrPixelBufferTest.java | 1001 ++++----------------
2026-05-16 00:58:53,343 [ scc.git] DEBUG .../omero/zarr/ZarrPixelsServiceTest.java | 10 +-
2026-05-16 00:58:53,343 [ scc.git] DEBUG 15 files changed, 1031 insertions(+), 1974 deletions(-)
2026-05-16 00:58:53,343 [ scc.git] DEBUG delete mode 100644 .github/workflows/codeql.yml
2026-05-16 00:58:53,343 [ scc.git] DEBUG delete mode 100644 src/main/java/com/bc/zarr/storage/OmeroFileSystemStore.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG delete mode 100644 src/main/java/com/glencoesoftware/omero/zarr/OmeroAmazonS3ClientFactory.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG delete mode 100644 src/main/java/com/glencoesoftware/omero/zarr/OmeroS3FileSystem.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG delete mode 100644 src/main/java/com/glencoesoftware/omero/zarr/OmeroS3ReadOnlySeekableByteChannel.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG create mode 100644 src/main/java/com/glencoesoftware/omero/zarr/Utils.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG create mode 100644 src/main/java/com/glencoesoftware/omero/zarr/ZarrPath.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG create mode 100644 src/main/java/com/glencoesoftware/omero/zarr/ZarrStore.java
2026-05-16 00:58:53,343 [ scc.git] DEBUG delete mode 100644 src/main/java/com/upplication/s3fs/OmeroS3FilesystemProvider.java
2026-05-16 00:58:53,532 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-16 00:58:53,532 [ scc.git] DEBUG Calling 'git submodule update'
2026-05-16 00:58:53,569 [ scc.git] DEBUG Get sha1 of %s
2026-05-16 00:58:53,569 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:58:53,571 [ scc.git] DEBUG Calling 'git status --porcelain'
2026-05-16 00:58:53,575 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7fa239b9b150> has no local changes
2026-05-16 00:58:53,575 [ 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#155 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-zarr-pixel-buffer-push/155/)'
2026-05-16 00:58:53,581 [ scc.git] DEBUG [detached HEAD d13a1c9] merge master -Dorg -Snone
2026-05-16 00:58:53,581 [ scc.merge] INFO Repository: ome/omero-zarr-pixel-buffer
2026-05-16 00:58:53,581 [ scc.merge] INFO Already up to date.
2026-05-16 00:58:53,581 [ scc.merge] INFO
2026-05-16 00:58:53,581 [ scc.merge] INFO Merged PRs:
2026-05-16 00:58:53,581 [ scc.merge] INFO - PR 16 dominikl 'Zarr v3 support'
2026-05-16 00:58:53,581 [ scc.merge] INFO
2026-05-16 00:58:53,581 [ scc.merge] DEBUG Cleaning remote branches created for merging
2026-05-16 00:58:53,582 [ scc.git] DEBUG Calling 'git remote'
Merge all submodules2026-05-16 00:58:54,033 [ scc.config] DEBUG Found github.token
2026-05-16 00:58:54,035 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443
2026-05-16 00:58:54,269 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-16 00:58:54,700 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-16 00:58:55,093 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None
2026-05-16 00:58:55,093 [ scc.gh] DEBUG 4951 remaining from 5000 (Reset at 01:05
2026-05-16 00:58:55,094 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel'
2026-05-16 00:58:55,096 [ scc.git] DEBUG Check current status
2026-05-16 00:58:55,096 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-16 00:58:55,098 [ scc.git] DEBUG d13a1c9 merge master -Dorg -Snone
2026-05-16 00:58:55,099 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-16 00:58:55,137 [ scc.config] DEBUG Found remote.origin.url
2026-05-16 00:58:55,637 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer HTTP/1.1" 200 None
2026-05-16 00:58:56,136 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome HTTP/1.1" 200 None
2026-05-16 00:58:56,589 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/ome/members HTTP/1.1" 200 None
2026-05-16 00:58:57,043 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=2 HTTP/1.1" 200 None
2026-05-16 00:58:57,518 [urllib3.conn] DEBUG https://api.github.com:443 "GET /organizations/1831717/members?page=3 HTTP/1.1" 200 None
2026-05-16 00:58:57,519 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path'
2026-05-16 00:58:57,557 [ scc.git] DEBUG Resetting...
2026-05-16 00:58:57,557 [ scc.git] DEBUG Calling 'git reset --hard HEAD'
2026-05-16 00:58:57,562 [ scc.git] DEBUG HEAD is now at d13a1c9 merge master -Dorg -Snone
2026-05-16 00:58:57,562 [ scc.git] DEBUG Calling 'git submodule update --recursive'
2026-05-16 00:58:57,599 [ scc.git] DEBUG Check current status
2026-05-16 00:58:57,599 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2026-05-16 00:58:57,601 [ scc.git] DEBUG d13a1c9 merge master -Dorg -Snone
2026-05-16 00:58:57,601 [ scc.git] DEBUG Calling 'git submodule status'
2026-05-16 00:58:57,637 [ scc.merge] INFO Merging Pull Request(s) based on master
2026-05-16 00:58:57,637 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization
2026-05-16 00:58:57,637 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies
2026-05-16 00:58:57,637 [ scc.merge] INFO Excluding Pull Request(s) staged as draft
2026-05-16 00:58:57,637 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking
2026-05-16 00:58:57,637 [ scc.merge] INFO Excluding Pull Request(s) without successful status
2026-05-16 00:58:57,637 [ scc.repo] DEBUG ## PRs found:
2026-05-16 00:58:58,087 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/pulls HTTP/1.1" 200 None
2026-05-16 00:58:58,563 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/issues/16 HTTP/1.1" 200 None
2026-05-16 00:58:59,104 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/commits/ee383a347382bbc6428f5faebcc3744383d144ab?page=1 HTTP/1.1" 200 None
2026-05-16 00:58:59,639 [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
2026-05-16 00:59:00,213 [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
2026-05-16 00:59:00,730 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/ome/omero-zarr-pixel-buffer/commits/ee383a347382bbc6428f5faebcc3744383d144ab?page=1 HTTP/1.1" 200 None
2026-05-16 00:59:01,189 [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
2026-05-16 00:59:01,190 [ scc.repo] DEBUG - PR 16 dominikl 'Zarr v3 support'
2026-05-16 00:59:01,190 [ scc.repo] DEBUG ## Branches found:
2026-05-16 00:59:01,190 [ scc.git] DEBUG Get sha1 of %s
2026-05-16 00:59:01,190 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:59:01,192 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master'
2026-05-16 00:59:01,195 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included.
2026-05-16 00:59:01,195 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master'
2026-05-16 00:59:01,197 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master'
2026-05-16 00:59:01,200 [ scc.git] DEBUG Already up to date.
2026-05-16 00:59:01,200 [ scc.git] DEBUG Calling 'git fetch origin pull/16/head'
2026-05-16 00:59:01,533 [ scc.git] DEBUG From https://github.com/ome/omero-zarr-pixel-buffer
2026-05-16 00:59:01,533 [ scc.git] DEBUG * branch refs/pull/16/head -> FETCH_HEAD
2026-05-16 00:59:01,537 [ scc.git] DEBUG ## Unique users: []
2026-05-16 00:59:01,537 [ scc.git] DEBUG Get sha1 of %s
2026-05-16 00:59:01,537 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:59:01,539 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-16 00:59:01,542 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:59:01,544 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 16 (Zarr v3 support) ee383a347382bbc6428f5faebcc3744383d144ab'
2026-05-16 00:59:01,546 [ scc.git] DEBUG Already up to date.
2026-05-16 00:59:01,734 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2026-05-16 00:59:01,734 [ scc.git] DEBUG Calling 'git submodule update'
2026-05-16 00:59:01,772 [ scc.git] DEBUG Get sha1 of %s
2026-05-16 00:59:01,772 [ scc.git] DEBUG Calling 'git rev-parse HEAD'
2026-05-16 00:59:01,774 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path'
2026-05-16 00:59:01,810 [ scc.git] DEBUG Calling 'git status --porcelain'
2026-05-16 00:59:01,813 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f0957639b10> has no local changes
2026-05-16 00:59:01,813 [ 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#155 (https://merge-ci.openmicroscopy.org/jenkins/job/OMERO-zarr-pixel-buffer-push/155/)'
2026-05-16 00:59:01,819 [ scc.git] DEBUG [detached HEAD 66ff19f] merge master -Dorg -Ssuccess-only
2026-05-16 00:59:01,819 [ scc.merge] INFO Repository: ome/omero-zarr-pixel-buffer
2026-05-16 00:59:01,819 [ scc.merge] INFO Already up to date.
2026-05-16 00:59:01,819 [ scc.merge] INFO
2026-05-16 00:59:01,820 [ scc.merge] INFO Merged PRs:
2026-05-16 00:59:01,820 [ scc.merge] INFO - PR 16 dominikl 'Zarr v3 support'
2026-05-16 00:59:01,820 [ scc.merge] INFO
2026-05-16 00:59:01,820 [ scc.merge] DEBUG Cleaning remote branches created for merging
2026-05-16 00:59:01,820 [ 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
2026-05-16 00:59:08,620 [ scc.push] INFO Merged branch pushed to https://github.com/snoopycrimecop/omero-zarr-pixel-buffer/tree/merge_ci
