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