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Started by user devspace
Running as SYSTEM
Building remotely on testintegration (swarm rocky9 ice36 java11) in workspace /uod/idr-scratch/merge-ci
The recommended git tool is: NONE
No credentials specified
 > git rev-parse --resolve-git-dir /uod/idr-scratch/merge-ci/.git # timeout=10
Fetching changes from the remote Git repository
 > git config remote.origin.url git@github.com:openmicroscopy/data_repo_config.git # timeout=10
Fetching upstream changes from git@github.com:openmicroscopy/data_repo_config.git
 > git --version # timeout=10
 > git --version # 'git version 2.43.5'
 > git fetch --tags --force --progress -- git@github.com:openmicroscopy/data_repo_config.git +refs/heads/*:refs/remotes/origin/* # timeout=10
 > git rev-parse refs/remotes/origin/master^{commit} # timeout=10
Checking out Revision fcef0176a797de7fe87bb767a31ebf1415506b82 (refs/remotes/origin/master)
 > git config core.sparsecheckout # timeout=10
 > git checkout -f fcef0176a797de7fe87bb767a31ebf1415506b82 # timeout=10
Commit message: "Merge pull request #629 from melissalinkert/oir-timestep"
 > git rev-list --no-walk fcef0176a797de7fe87bb767a31ebf1415506b82 # timeout=10
[merge-ci] $ /bin/bash -xe /tmp/jenkins14121612528060843091.sh
+ python3 -mvenv /tmp/venv
+ source /tmp/venv/bin/activate
++ deactivate nondestructive
++ '[' -n '' ']'
++ '[' -n '' ']'
++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
++ '[' -n '' ']'
++ unset VIRTUAL_ENV
++ '[' '!' nondestructive = nondestructive ']'
++ VIRTUAL_ENV=/tmp/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=/tmp/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
+ /tmp/venv/bin/pip install -U pip
Requirement already satisfied: pip in /tmp/venv/lib/python3.9/site-packages (24.3.1)
+ /tmp/venv/bin/pip install -U scc
Requirement already satisfied: scc in /tmp/venv/lib/python3.9/site-packages (0.20.0)
Requirement already satisfied: PyGithub>=1.54 in /tmp/venv/lib/python3.9/site-packages (from scc) (2.5.0)
Requirement already satisfied: PyYAML>=5.1 in /tmp/venv/lib/python3.9/site-packages (from scc) (6.0.2)
Requirement already satisfied: future in /tmp/venv/lib/python3.9/site-packages (from scc) (1.0.0)
Requirement already satisfied: ruamel.yaml in /tmp/venv/lib/python3.9/site-packages (from scc) (0.18.10)
Requirement already satisfied: ruamel.yaml.jinja2 in /tmp/venv/lib/python3.9/site-packages (from scc) (0.2.7)
Requirement already satisfied: six in /tmp/venv/lib/python3.9/site-packages (from scc) (1.17.0)
Requirement already satisfied: urllib3<2 in /tmp/venv/lib/python3.9/site-packages (from scc) (1.26.20)
Requirement already satisfied: yaclifw<0.3,>=0.2.0 in /tmp/venv/lib/python3.9/site-packages (from scc) (0.2.0)
Requirement already satisfied: pynacl>=1.4.0 in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (1.5.0)
Requirement already satisfied: requests>=2.14.0 in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (2.32.3)
Requirement already satisfied: pyjwt>=2.4.0 in /tmp/venv/lib/python3.9/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (2.10.1)
Requirement already satisfied: typing-extensions>=4.0.0 in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (4.12.2)
Requirement already satisfied: Deprecated in /tmp/venv/lib/python3.9/site-packages (from PyGithub>=1.54->scc) (1.2.15)
Requirement already satisfied: ruamel.yaml.clib>=0.2.7 in /tmp/venv/lib/python3.9/site-packages (from ruamel.yaml->scc) (0.2.12)
Requirement already satisfied: cryptography>=3.4.0 in /tmp/venv/lib/python3.9/site-packages (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) (44.0.0)
Requirement already satisfied: cffi>=1.4.1 in /tmp/venv/lib/python3.9/site-packages (from pynacl>=1.4.0->PyGithub>=1.54->scc) (1.17.1)
Requirement already satisfied: charset-normalizer<4,>=2 in /tmp/venv/lib/python3.9/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.4.1)
Requirement already satisfied: idna<4,>=2.5 in /tmp/venv/lib/python3.9/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (3.10)
Requirement already satisfied: certifi>=2017.4.17 in /tmp/venv/lib/python3.9/site-packages (from requests>=2.14.0->PyGithub>=1.54->scc) (2024.12.14)
Requirement already satisfied: wrapt<2,>=1.10 in /tmp/venv/lib/python3.9/site-packages (from Deprecated->PyGithub>=1.54->scc) (1.17.2)
Requirement already satisfied: pycparser in /tmp/venv/lib/python3.9/site-packages (from cffi>=1.4.1->pynacl>=1.4.0->PyGithub>=1.54->scc) (2.22)
+ test -e src
+ /tmp/venv/bin/scc merge master --no-ask --reset --comment -vv --push merge_ci
2025-01-21 09:56:14,608 [  scc.config] DEBUG Found github.token
2025-01-21 09:56:14,610 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443
2025-01-21 09:56:14,800 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2025-01-21 09:56:15,213 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2025-01-21 09:56:15,583 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None
2025-01-21 09:56:15,584 [      scc.gh] DEBUG 4922 remaining from 5000 (Reset at 10:01
2025-01-21 09:56:15,584 [     scc.git] DEBUG Calling 'git rev-parse --show-toplevel'
2025-01-21 09:56:15,591 [     scc.git] DEBUG Check current status
2025-01-21 09:56:15,591 [     scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2025-01-21 09:56:15,604 [     scc.git] DEBUG fcef0176 Merge pull request #629 from melissalinkert/oir-timestep
2025-01-21 09:56:15,605 [     scc.git] DEBUG Calling 'git submodule status'
2025-01-21 09:56:15,670 [  scc.config] DEBUG Found remote.origin.url
2025-01-21 09:56:16,081 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config HTTP/1.1" 200 None
2025-01-21 09:56:16,529 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/openmicroscopy HTTP/1.1" 200 None
2025-01-21 09:56:16,932 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/openmicroscopy/members HTTP/1.1" 200 None
2025-01-21 09:56:16,933 [     scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path'
2025-01-21 09:56:16,995 [     scc.git] DEBUG Resetting...
2025-01-21 09:56:16,996 [     scc.git] DEBUG Calling 'git reset --hard HEAD'
2025-01-21 09:56:17,406 [     scc.git] DEBUG HEAD is now at fcef0176 Merge pull request #629 from melissalinkert/oir-timestep
2025-01-21 09:56:17,408 [     scc.git] DEBUG Calling 'git submodule update --recursive'
2025-01-21 09:56:17,476 [     scc.git] DEBUG Check current status
2025-01-21 09:56:17,476 [     scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD'
2025-01-21 09:56:17,490 [     scc.git] DEBUG fcef0176 Merge pull request #629 from melissalinkert/oir-timestep
2025-01-21 09:56:17,490 [     scc.git] DEBUG Calling 'git submodule status'
2025-01-21 09:56:17,551 [   scc.merge] INFO  Merging Pull Request(s) based on master
2025-01-21 09:56:17,551 [   scc.merge] INFO  Including Pull Request(s) opened by any public member of the organization
2025-01-21 09:56:17,551 [   scc.merge] INFO  Including Pull Request(s) labelled as include or dependencies
2025-01-21 09:56:17,551 [   scc.merge] INFO  Excluding Pull Request(s) staged as draft
2025-01-21 09:56:17,551 [   scc.merge] INFO  Excluding Pull Request(s) labelled as exclude or breaking
2025-01-21 09:56:17,551 [    scc.repo] DEBUG ## PRs found:
2025-01-21 09:56:17,850 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/pulls HTTP/1.1" 200 None
2025-01-21 09:56:18,285 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/632 HTTP/1.1" 200 None
2025-01-21 09:56:18,286 [    scc.repo] DEBUG   - PR 632 sbesson 'Reconfigure CellSens datasets to use vsi as the primary file'
2025-01-21 09:56:18,751 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/631 HTTP/1.1" 200 None
2025-01-21 09:56:18,752 [    scc.repo] DEBUG   - PR 631 sbesson 'Regenerate configuration file for FujiReader sample'
2025-01-21 09:56:19,214 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/630 HTTP/1.1" 200 None
2025-01-21 09:56:19,674 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/630/comments HTTP/1.1" 200 None
2025-01-21 09:56:19,675 [    scc.repo] DEBUG   - PR 630 melissalinkert 'Add public data for new DCIMG reader'
2025-01-21 09:56:20,121 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/628 HTTP/1.1" 200 None
2025-01-21 09:56:20,561 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/628/comments HTTP/1.1" 200 None
2025-01-21 09:56:20,561 [    scc.repo] DEBUG   - PR 628 melissalinkert 'Add public LZ4 samples from Bitplane'
2025-01-21 09:56:21,059 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/612 HTTP/1.1" 200 None
2025-01-21 09:56:21,060 [    scc.repo] DEBUG   # ... Exclude label: exclude
2025-01-21 09:56:21,523 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/openmicroscopy/data_repo_config/issues/546 HTTP/1.1" 200 None
2025-01-21 09:56:21,524 [    scc.repo] DEBUG   # ... Exclude label: exclude
2025-01-21 09:56:21,524 [    scc.repo] DEBUG ## Branches found:
2025-01-21 09:56:21,524 [     scc.git] DEBUG Get sha1 of %s
2025-01-21 09:56:21,524 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:21,532 [     scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master'
2025-01-21 09:56:21,540 [     scc.git] DEBUG ## Merging base to ensure closed PRs are included.
2025-01-21 09:56:21,540 [     scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master'
2025-01-21 09:56:21,558 [     scc.git] DEBUG Calling 'git merge --ff-only origin/master'
2025-01-21 09:56:21,585 [     scc.git] DEBUG Already up to date.

2025-01-21 09:56:21,585 [     scc.git] DEBUG Calling 'git fetch origin pull/628/head'
2025-01-21 09:56:22,870 [     scc.git] DEBUG From github.com:openmicroscopy/data_repo_config
2025-01-21 09:56:22,870 [     scc.git] DEBUG  * branch              refs/pull/628/head -> FETCH_HEAD
2025-01-21 09:56:22,978 [     scc.git] DEBUG Calling 'git fetch origin pull/630/head'
2025-01-21 09:56:24,254 [     scc.git] DEBUG From github.com:openmicroscopy/data_repo_config
2025-01-21 09:56:24,254 [     scc.git] DEBUG  * branch              refs/pull/630/head -> FETCH_HEAD
2025-01-21 09:56:24,362 [     scc.git] DEBUG Calling 'git fetch origin pull/631/head'
2025-01-21 09:56:25,566 [     scc.git] DEBUG From github.com:openmicroscopy/data_repo_config
2025-01-21 09:56:25,566 [     scc.git] DEBUG  * branch              refs/pull/631/head -> FETCH_HEAD
2025-01-21 09:56:25,672 [     scc.git] DEBUG Calling 'git fetch origin pull/632/head'
2025-01-21 09:56:26,910 [     scc.git] DEBUG From github.com:openmicroscopy/data_repo_config
2025-01-21 09:56:26,910 [     scc.git] DEBUG  * branch              refs/pull/632/head -> FETCH_HEAD
2025-01-21 09:56:27,016 [     scc.git] DEBUG ## Unique users: []
2025-01-21 09:56:27,016 [     scc.git] DEBUG Get sha1 of %s
2025-01-21 09:56:27,016 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:27,023 [     scc.git] DEBUG Calling 'git diff --name-only HEAD...f2542c9cbc15deedcd1c8307979007274ed29180'
2025-01-21 09:56:27,061 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:27,067 [     scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 628 (Add public LZ4 samples from Bitplane) f2542c9cbc15deedcd1c8307979007274ed29180'
2025-01-21 09:56:27,329 [     scc.git] DEBUG Merge made by the 'ort' strategy.
2025-01-21 09:56:27,377 [     scc.git] DEBUG  curated/imaris/public/bitplane/lz4/.bioformats     | 109 +++++++++++++++++
2025-01-21 09:56:27,377 [     scc.git] DEBUG  .../imaris/public/bitplane/performance/.bioformats | 134 +++++++++++++++++++++
2025-01-21 09:56:27,377 [     scc.git] DEBUG  2 files changed, 243 insertions(+)
2025-01-21 09:56:27,377 [     scc.git] DEBUG  create mode 100755 curated/imaris/public/bitplane/lz4/.bioformats
2025-01-21 09:56:27,377 [     scc.git] DEBUG  create mode 100644 curated/imaris/public/bitplane/performance/.bioformats
2025-01-21 09:56:27,521 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2025-01-21 09:56:27,522 [     scc.git] DEBUG Calling 'git diff --name-only HEAD...d14f4d77107ce047fd1838c36524ec47ffe13829'
2025-01-21 09:56:27,572 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:27,578 [     scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 630 (Add public data for new DCIMG reader) d14f4d77107ce047fd1838c36524ec47ffe13829'
2025-01-21 09:56:27,973 [     scc.git] DEBUG Merge made by the 'ort' strategy.
2025-01-21 09:56:28,025 [     scc.git] DEBUG  .../zenodo-14268554/bead_bot4_018/.bioformats      | 32 ++++++++++++++++++++++
2025-01-21 09:56:28,025 [     scc.git] DEBUG  curated/dcimg/public/zenodo-14281237/.bioformats   | 32 ++++++++++++++++++++++
2025-01-21 09:56:28,025 [     scc.git] DEBUG  .../public/zenodo-14287640/Cell09/.bioformats      | 32 ++++++++++++++++++++++
2025-01-21 09:56:28,025 [     scc.git] DEBUG  3 files changed, 96 insertions(+)
2025-01-21 09:56:28,025 [     scc.git] DEBUG  create mode 100755 curated/dcimg/public/zenodo-14268554/bead_bot4_018/.bioformats
2025-01-21 09:56:28,025 [     scc.git] DEBUG  create mode 100755 curated/dcimg/public/zenodo-14281237/.bioformats
2025-01-21 09:56:28,025 [     scc.git] DEBUG  create mode 100755 curated/dcimg/public/zenodo-14287640/Cell09/.bioformats
2025-01-21 09:56:28,167 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2025-01-21 09:56:28,168 [     scc.git] DEBUG Calling 'git diff --name-only HEAD...08f402f21e39b13f08c2a41d3cf9a11499f789f2'
2025-01-21 09:56:28,213 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:28,220 [     scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 631 (Regenerate configuration file for FujiReader sample) 08f402f21e39b13f08c2a41d3cf9a11499f789f2'
2025-01-21 09:56:28,500 [     scc.git] DEBUG Merge made by the 'ort' strategy.
2025-01-21 09:56:28,539 [     scc.git] DEBUG  curated/fuji/venu/.bioformats | 72 +++++++++++++------------------------------
2025-01-21 09:56:28,539 [     scc.git] DEBUG  1 file changed, 22 insertions(+), 50 deletions(-)
2025-01-21 09:56:28,676 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2025-01-21 09:56:28,677 [     scc.git] DEBUG Calling 'git diff --name-only HEAD...a8671480f6fafea8ed894a51b604a665a6beb86a'
2025-01-21 09:56:28,742 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:28,749 [     scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 632 (Reconfigure CellSens datasets to use vsi as the primary file) a8671480f6fafea8ed894a51b604a665a6beb86a'
2025-01-21 09:56:29,301 [     scc.git] DEBUG Merge made by the 'ort' strategy.
2025-01-21 09:56:29,378 [     scc.git] DEBUG  curated/cellsens/gh-3822/.bioformats               |  188 +-
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../cellsens/gh-3822/_image_/stack1/.bioformats    |  180 -
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../14-09-2012/_Image_07_/stack1/.bioformats       |  555 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../14-09-2012/_Image_07_/stack10000/.bioformats   |  555 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../14-09-2012/_Image_07_/stack10002/.bioformats   |  554 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_06_/stack1/.bioformats       |  525 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_27_/stack1/.bioformats       |  503 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_27_/stack10000/.bioformats   |  503 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_27_/stack10002/.bioformats   |  503 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_27_2_/stack1/.bioformats     |  503 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_27_2_/stack10000/.bioformats |  503 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../26-10-2014/_Image_27_2_/stack10002/.bioformats |  503 ---
2025-01-21 09:56:29,378 [     scc.git] DEBUG  .../olivier/_7262 wt col_/stack1/.bioformats       |  399 ---
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../olivier/_7262 wt col_/stack10001/.bioformats   |  399 ---
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack1/.bioformats                             | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10000/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10002/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10005/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10008/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10011/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10014/.bioformats                         | 3691 -------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10017/.bioformats                         | 3691 -------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10020/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10023/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10026/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10029/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10032/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10035/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10038/.bioformats                         | 3691 -------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10041/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10044/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10047/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10050/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10053/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10056/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10059/.bioformats                         | 3691 -------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10062/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10065/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10068/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10071/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10074/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10077/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10080/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10083/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack10086/.bioformats                         | 3692 --------------------
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../qa-11039/_Image_01_/stack1/.bioformats         |  632 ----
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../qa-11039/_Image_01_/stack10000/.bioformats     |  633 ----
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../qa-11039/_Image_01_/stack10003/.bioformats     |  633 ----
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../stack1/.bioformats                             |  216 --
2025-01-21 09:56:29,379 [     scc.git] DEBUG  curated/cellsens/samples/Deconvolution/.bioformats |  224 ++
2025-01-21 09:56:29,379 [     scc.git] DEBUG  .../_chroma liver 40x 8 planes_/stack1/.bioformats |  174 -
2025-01-21 09:56:29,380 [     scc.git] DEBUG  .../{_islets_40X_2_/stack1 => }/.bioformats        |  438 ++-
2025-01-21 09:56:29,380 [     scc.git] DEBUG  curated/olympus-oir/olympus/.bioformats            | 1056 ++++++
2025-01-21 09:56:29,380 [     scc.git] DEBUG  .../_calcium sparks_XYt_/stack1/.bioformats        |  864 -----
2025-01-21 09:56:29,380 [     scc.git] DEBUG  .../stack1/.bioformats                             |  148 -
2025-01-21 09:56:29,380 [     scc.git] DEBUG  55 files changed, 1896 insertions(+), 123943 deletions(-)
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100755 curated/cellsens/gh-3822/_image_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/14-09-2012/_Image_07_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/14-09-2012/_Image_07_/stack10000/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/14-09-2012/_Image_07_/stack10002/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_06_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_27_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_27_/stack10000/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_27_/stack10002/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_27_2_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_27_2_/stack10000/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/26-10-2014/_Image_27_2_/stack10002/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/_7262 wt col_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/_7262 wt col_/stack10001/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack1/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10000/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10002/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10005/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10008/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10011/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10014/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10017/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10020/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10023/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10026/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10029/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10032/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10035/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10038/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10041/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10044/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10047/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10050/.bioformats
2025-01-21 09:56:29,380 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10053/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10056/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10059/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10062/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10065/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10068/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10071/.bioformats
2025-01-21 09:56:29,381 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10074/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10077/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10080/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10083/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/olivier/small-tiles/_esgTS-+;Sox21a[6]-+_30D25_09_/stack10086/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/qa-11039/_Image_01_/stack1/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/qa-11039/_Image_01_/stack10000/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/qa-11039/_Image_01_/stack10003/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/qa-11394/_f1 lateral 25hpf yen4 20X timelapse_/stack1/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/cellsens/samples/Deconvolution/_chroma liver 40x 8 planes_/stack1/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  rename curated/cellsens/samples/Deconvolution/_islets_40X_2_/{_islets_40X_2_/stack1 => }/.bioformats (65%)
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/olympus-oir/olympus/_calcium sparks_XYt_/stack1/.bioformats
2025-01-21 09:56:29,388 [     scc.git] DEBUG  delete mode 100644 curated/olympus-oir/olympus/_stitched 4x4 zstack 10X_XYZ_/stack1/.bioformats
2025-01-21 09:56:29,519 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None
2025-01-21 09:56:29,520 [     scc.git] DEBUG Calling 'git submodule update'
2025-01-21 09:56:29,592 [     scc.git] DEBUG Get sha1 of %s
2025-01-21 09:56:29,593 [     scc.git] DEBUG Calling 'git rev-parse HEAD'
2025-01-21 09:56:29,600 [     scc.git] DEBUG Calling 'git status --porcelain'
2025-01-21 09:56:31,135 [     scc.git] DEBUG <scc.git.GitRepository object at 0x7f16e6fd67c0> has local changes
2025-01-21 09:56:31,136 [     scc.git] DEBUG Calling 'git commit -a -n -m merge master -Dorg -Snone

Repository: openmicroscopy/data_repo_config
Excluded PRs:
  - PR 612 melissalinkert 'DICOM: swap Z and T for datasets newly detected as timelapse' (label: exclude)
  - PR 546 melissalinkert 'InCell updates' (label: exclude)
Already up to date.

Merged PRs:
  - PR 628 melissalinkert 'Add public LZ4 samples from Bitplane'
  - PR 630 melissalinkert 'Add public data for new DCIMG reader'
  - PR 631 sbesson 'Regenerate configuration file for FujiReader sample'
  - PR 632 sbesson 'Reconfigure CellSens datasets to use vsi as the primary file'

Generated by DATA_REPO_CONFIG-merge#420 (https://merge-ci.openmicroscopy.org/jenkins/job/DATA_REPO_CONFIG-merge/420/)'
2025-01-21 09:56:32,680 [     scc.git] DEBUG HEAD detached from fcef0176
2025-01-21 09:56:32,680 [     scc.git] DEBUG Untracked files:
2025-01-21 09:56:32,680 [     scc.git] DEBUG   (use "git add <file>..." to include in what will be committed)
2025-01-21 09:56:32,681 [     scc.git] DEBUG 	curated/olympus-oir/olympus/.nfs0000008383f7738d00000002
2025-01-21 09:56:32,681 [     scc.git] DEBUG 
2025-01-21 09:56:32,681 [     scc.git] DEBUG nothing added to commit but untracked files present (use "git add" to track)
2025-01-21 09:56:32,681 [   scc.merge] DEBUG Cleaning remote branches created for merging
2025-01-21 09:56:32,682 [     scc.git] DEBUG Calling 'git remote'
Traceback (most recent call last):
  File "/tmp/venv/lib64/python3.9/site-packages/scc/main.py", line 64, in entry_point
    main("scc", items=[
  File "/tmp/venv/lib64/python3.9/site-packages/yaclifw/framework.py", line 188, in main
    ns.func(ns)
  File "/tmp/venv/lib64/python3.9/site-packages/scc/git.py", line 3332, in __call__
    self.merge(args, self.main_repo)
  File "/tmp/venv/lib64/python3.9/site-packages/scc/git.py", line 3357, in merge
    updated, merge_msg = main_repo.rmerge(
  File "/tmp/venv/lib64/python3.9/site-packages/scc/git.py", line 1861, in rmerge
    summary_update = self.summary_commit(
  File "/tmp/venv/lib64/python3.9/site-packages/scc/git.py", line 1924, in summary_commit
    self.call("git", "commit", "-a", "-n", "-m", commit_message)
  File "/tmp/venv/lib64/python3.9/site-packages/scc/git.py", line 1162, in call
    return self.wrap_call(self.debugWrap, *command, **kwargs)
  File "/tmp/venv/lib64/python3.9/site-packages/scc/git.py", line 1187, in wrap_call
    raise Exception("rc=%s" % rc)
Exception: rc=1
Build step 'Execute shell' marked build as failure
Finished: FAILURE