Started by user devspace [Pipeline] Start of Pipeline [Pipeline] node Running on testintegration in /home/omero/workspace/IDRSITE-push [Pipeline] { [Pipeline] library Loading library recursiveMerge@master Attempting to resolve master from remote references... > git --version # timeout=10 > git --version # 'git version 2.47.3' > git ls-remote -- https://github.com/ome/jenkins-library-recursivemerge.git # timeout=10 Found match: refs/heads/master revision 654fab96d71411fab33e55b79057bcbf94eef8a2 The recommended git tool is: NONE No credentials specified > git rev-parse --resolve-git-dir /var/jenkins_home/jobs/IDRSITE-push/workspace@libs/e9d96de4efbb3e39a2ce24824e54985c7c2760a6ed46c5415ea0aa1fd1e18d41/.git # timeout=10 Fetching changes from the remote Git repository > git config remote.origin.url https://github.com/ome/jenkins-library-recursivemerge.git # timeout=10 Fetching without tags Fetching upstream changes from https://github.com/ome/jenkins-library-recursivemerge.git > git --version # timeout=10 > git --version # 'git version 2.47.3' > git fetch --no-tags --force --progress -- https://github.com/ome/jenkins-library-recursivemerge.git +refs/heads/*:refs/remotes/origin/* # timeout=10 Checking out Revision 654fab96d71411fab33e55b79057bcbf94eef8a2 (master) > git config core.sparsecheckout # timeout=10 > git checkout -f 654fab96d71411fab33e55b79057bcbf94eef8a2 # timeout=10 Commit message: "Merge pull request #18 from jburel/python_311" > git rev-list --no-walk 654fab96d71411fab33e55b79057bcbf94eef8a2 # timeout=10 [Pipeline] checkout The recommended git tool is: NONE No credentials specified Fetching changes from the remote Git repository > git rev-parse --resolve-git-dir /home/omero/workspace/IDRSITE-push/.git # timeout=10 > git config remote.origin.url https://github.com/idr/idr.openmicroscopy.org # timeout=10 Fetching upstream changes from https://github.com/idr/idr.openmicroscopy.org > git --version # timeout=10 > git --version # 'git version 2.52.0' > git fetch --tags --force --progress -- https://github.com/idr/idr.openmicroscopy.org +refs/heads/*:refs/remotes/origin/* # timeout=10 Checking out Revision 94915ef467774ab056f6df88b2b5d944a6a61c4b (refs/remotes/origin/master) > git rev-parse refs/remotes/origin/master^{commit} # timeout=10 > git config core.sparsecheckout # timeout=10 > git checkout -f 94915ef467774ab056f6df88b2b5d944a6a61c4b # timeout=10 Commit message: "Merge pull request #229 from pwalczysko/remove-mybinder" First time build. Skipping changelog. Cleaning workspace > git rev-parse --verify HEAD # timeout=10 Resetting working tree > git reset --hard # timeout=10 [Pipeline] pwd [Pipeline] sh + mkdir -p build + echo build [Pipeline] sh > git clean -fdx # timeout=10 + pushd build ~/workspace/IDRSITE-push/build ~/workspace/IDRSITE-push + tar -zxf - + curl -sfL https://github.com/ome/build-infra/archive/master.tar.gz + popd ~/workspace/IDRSITE-push + python3.11 -m venv build/venv + . 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/IDRSITE-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/IDRSITE-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 + python3.11 -m pip install -U pip Requirement already satisfied: pip in ./build/venv/lib64/python3.11/site-packages (22.3.1) Collecting pip Using cached pip-26.2.1-py3-none-any.whl (1.8 MB) Installing collected packages: pip Attempting uninstall: pip Found existing installation: pip 22.3.1 Uninstalling pip-22.3.1: Successfully uninstalled pip-22.3.1 Successfully installed pip-26.2.1 + python3.11 -m pip install scc Collecting scc Using cached scc-0.20.0-py3-none-any.whl.metadata (3.6 kB) Collecting PyGithub>=1.54 (from scc) Using cached pygithub-2.10.0-py3-none-any.whl.metadata (3.9 kB) Collecting PyYAML>=5.1 (from scc) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (2.4 kB) Collecting future (from scc) Using cached future-1.0.0-py3-none-any.whl.metadata (4.0 kB) Collecting ruamel.yaml (from scc) Using cached ruamel_yaml-0.19.1-py3-none-any.whl.metadata (16 kB) Collecting ruamel.yaml.jinja2 (from scc) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl.metadata (2.9 kB) Collecting six (from scc) Using cached six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) Collecting urllib3<2 (from scc) Using cached urllib3-1.26.20-py2.py3-none-any.whl.metadata (50 kB) Collecting yaclifw<0.3,>=0.2.0 (from scc) Using cached yaclifw-0.2.0-py3-none-any.whl Collecting pynacl>=1.4.0 (from PyGithub>=1.54->scc) Using cached pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl.metadata (10.0 kB) Collecting requests>=2.14.0 (from PyGithub>=1.54->scc) Using cached requests-2.34.2-py3-none-any.whl.metadata (4.8 kB) Collecting pyjwt>=2.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached pyjwt-2.15.1-py3-none-any.whl.metadata (3.5 kB) Collecting typing-extensions>=4.5.0 (from PyGithub>=1.54->scc) Using cached typing_extensions-4.16.0-py3-none-any.whl.metadata (3.3 kB) Collecting cryptography>=3.4.0 (from pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cryptography-50.0.2-cp311-abi3-manylinux_2_34_x86_64.whl.metadata (4.4 kB) Collecting cffi>=2.0.0 (from cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached cffi-2.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.5 kB) Collecting pycparser (from cffi>=2.0.0->cryptography>=3.4.0->pyjwt[crypto]>=2.4.0->PyGithub>=1.54->scc) Using cached pycparser-3.0-py3-none-any.whl.metadata (8.2 kB) Collecting charset_normalizer<4,>=2 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached charset_normalizer-3.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl.metadata (46 kB) Collecting idna<4,>=2.5 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached idna-3.20-py3-none-any.whl.metadata (7.2 kB) Collecting certifi>=2023.5.7 (from requests>=2.14.0->PyGithub>=1.54->scc) Using cached certifi-2026.7.22-py3-none-any.whl.metadata (2.5 kB) Using cached scc-0.20.0-py3-none-any.whl (48 kB) Using cached urllib3-1.26.20-py2.py3-none-any.whl (144 kB) Using cached pygithub-2.10.0-py3-none-any.whl (455 kB) Using cached pyjwt-2.15.1-py3-none-any.whl (33 kB) Using cached cryptography-50.0.2-cp311-abi3-manylinux_2_34_x86_64.whl (4.8 MB) Using cached cffi-2.1.1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (217 kB) Using cached pynacl-1.6.2-cp38-abi3-manylinux_2_34_x86_64.whl (1.4 MB) Using cached pyyaml-6.0.3-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (806 kB) Using cached requests-2.34.2-py3-none-any.whl (73 kB) Using cached charset_normalizer-3.5.2-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_28_x86_64.whl (269 kB) Using cached idna-3.20-py3-none-any.whl (69 kB) Using cached certifi-2026.7.22-py3-none-any.whl (136 kB) Using cached typing_extensions-4.16.0-py3-none-any.whl (45 kB) Using cached future-1.0.0-py3-none-any.whl (491 kB) Using cached pycparser-3.0-py3-none-any.whl (48 kB) Using cached ruamel_yaml-0.19.1-py3-none-any.whl (118 kB) Using cached ruamel.yaml.jinja2-0.2.7-py2.py3-none-any.whl (5.5 kB) Using cached six-1.17.0-py2.py3-none-any.whl (11 kB) Installing collected packages: urllib3, typing-extensions, six, ruamel.yaml, PyYAML, pyjwt, pycparser, idna, future, charset_normalizer, certifi, yaclifw, ruamel.yaml.jinja2, requests, cffi, pynacl, cryptography, PyGithub, scc Successfully installed PyGithub-2.10.0 PyYAML-6.0.3 certifi-2026.7.22 cffi-2.1.1 charset_normalizer-3.5.2 cryptography-50.0.2 future-1.0.0 idna-3.20 pycparser-3.0 pyjwt-2.15.1 pynacl-1.6.2 requests-2.34.2 ruamel.yaml-0.19.1 ruamel.yaml.jinja2-0.2.7 scc-0.20.0 six-1.17.0 typing-extensions-4.16.0 urllib3-1.26.20 yaclifw-0.2.0 [Pipeline] sh + export BASE_REPO=idr.openmicroscopy.org + BASE_REPO=idr.openmicroscopy.org + export BASE_BRANCH=master + BASE_BRANCH=master + export VERSION_LOG=/home/omero/workspace/IDRSITE-push/build/version.tsv + VERSION_LOG=/home/omero/workspace/IDRSITE-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/IDRSITE-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/IDRSITE-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) 2026-10-01 18:10:35,717 [ scc.config] DEBUG Found github.token 2026-10-01 18:10:35,719 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443 2026-10-01 18:10:35,984 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:36,412 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:36,852 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None 2026-10-01 18:10:36,853 [ scc.gh] DEBUG 5000 remaining from 5000 (Reset at 19:10 2026-10-01 18:10:36,854 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-01 18:10:36,865 [ scc.git] DEBUG Check current status 2026-10-01 18:10:36,865 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-01 18:10:36,883 [ scc.git] DEBUG 94915ef Merge pull request #229 from pwalczysko/remove-mybinder 2026-10-01 18:10:36,884 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-01 18:10:36,994 [ scc.config] DEBUG Found remote.origin.url 2026-10-01 18:10:37,427 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/idr/idr.openmicroscopy.org HTTP/1.1" 200 None 2026-10-01 18:10:37,965 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/IDR HTTP/1.1" 200 None 2026-10-01 18:10:38,439 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/IDR/members HTTP/1.1" 200 None 2026-10-01 18:10:38,440 [ scc.git] DEBUG Resetting... 2026-10-01 18:10:38,440 [ scc.git] DEBUG Calling 'git reset --hard HEAD' 2026-10-01 18:10:38,606 [ scc.git] DEBUG HEAD is now at 94915ef Merge pull request #229 from pwalczysko/remove-mybinder 2026-10-01 18:10:38,608 [ scc.git] DEBUG Calling 'git submodule update --recursive' 2026-10-01 18:10:38,717 [ scc.git] DEBUG Check current status 2026-10-01 18:10:38,717 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-01 18:10:38,732 [ scc.git] DEBUG 94915ef Merge pull request #229 from pwalczysko/remove-mybinder 2026-10-01 18:10:38,733 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-01 18:10:38,831 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-10-01 18:10:38,831 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-10-01 18:10:38,831 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-10-01 18:10:38,831 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-10-01 18:10:38,831 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-10-01 18:10:38,831 [ scc.repo] DEBUG ## PRs found: 2026-10-01 18:10:39,158 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/pulls HTTP/1.1" 200 None 2026-10-01 18:10:39,684 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/225 HTTP/1.1" 200 None 2026-10-01 18:10:40,182 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/225/comments HTTP/1.1" 200 None 2026-10-01 18:10:40,184 [ scc.repo] DEBUG - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' 2026-10-01 18:10:40,678 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/133 HTTP/1.1" 200 None 2026-10-01 18:10:41,196 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/133/comments HTTP/1.1" 200 None 2026-10-01 18:10:41,197 [ scc.repo] DEBUG - PR 133 jburel 'add Phindr3D' 2026-10-01 18:10:41,708 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/131 HTTP/1.1" 200 None 2026-10-01 18:10:41,709 [ scc.repo] DEBUG - PR 131 jburel 'itr update' 2026-10-01 18:10:41,709 [ scc.repo] DEBUG ## Branches found: 2026-10-01 18:10:41,709 [ scc.git] DEBUG Get sha1 of %s 2026-10-01 18:10:41,709 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:10:41,720 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-01 18:10:41,735 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-01 18:10:41,735 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-01 18:10:41,757 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-01 18:10:41,808 [ scc.git] DEBUG Already up to date. 2026-10-01 18:10:41,808 [ scc.git] DEBUG Calling 'git fetch origin pull/131/head' 2026-10-01 18:10:43,017 [ scc.git] DEBUG From https://github.com/idr/idr.openmicroscopy.org 2026-10-01 18:10:43,017 [ scc.git] DEBUG * branch refs/pull/131/head -> FETCH_HEAD 2026-10-01 18:10:43,059 [ scc.git] DEBUG Calling 'git fetch origin pull/133/head' 2026-10-01 18:10:44,159 [ scc.git] DEBUG From https://github.com/idr/idr.openmicroscopy.org 2026-10-01 18:10:44,159 [ scc.git] DEBUG * branch refs/pull/133/head -> FETCH_HEAD 2026-10-01 18:10:44,184 [ scc.git] DEBUG Calling 'git fetch origin pull/225/head' 2026-10-01 18:10:45,801 [ scc.git] DEBUG From https://github.com/idr/idr.openmicroscopy.org 2026-10-01 18:10:45,801 [ scc.git] DEBUG * branch refs/pull/225/head -> FETCH_HEAD 2026-10-01 18:10:45,823 [ scc.git] DEBUG ## Unique users: [] 2026-10-01 18:10:45,823 [ scc.git] DEBUG Get sha1 of %s 2026-10-01 18:10:45,823 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:10:45,834 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...1f880d2dc5fbf1c4bfbe479af44186dd5e15f433' 2026-10-01 18:10:45,862 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:10:45,873 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 131 (itr update) 1f880d2dc5fbf1c4bfbe479af44186dd5e15f433' 2026-10-01 18:10:46,090 [ scc.git] DEBUG Auto-merging _data/tools.json 2026-10-01 18:10:46,090 [ scc.git] DEBUG CONFLICT (content): Merge conflict in _data/tools.json 2026-10-01 18:10:46,138 [ scc.git] DEBUG Automatic merge failed; fix conflicts and then commit the result. 2026-10-01 18:10:46,139 [ scc.git] DEBUG Calling 'git diff --name-only --diff-filter=U' 2026-10-01 18:10:46,167 [ scc.git] DEBUG Calling 'git reset --hard 94915ef467774ab056f6df88b2b5d944a6a61c4b' 2026-10-01 18:10:46,282 [ scc.git] DEBUG HEAD is now at 94915ef Merge pull request #229 from pwalczysko/remove-mybinder 2026-10-01 18:10:47,477 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:47,478 [ scc.git] DEBUG Calling 'git merge-base 94915ef467774ab056f6df88b2b5d944a6a61c4b 1f880d2dc5fbf1c4bfbe479af44186dd5e15f433' 2026-10-01 18:10:47,502 [ scc.git] DEBUG Calling 'git diff --name-only 0e25fb6b33f85d7ee59961b72df500c1e35f5fe7..94915ef467774ab056f6df88b2b5d944a6a61c4b' 2026-10-01 18:10:47,556 [ scc.git] INFO - PR 131 jburel 'itr update' Conflicting PR. Removed from build [IDRSITE-push#2](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/). See the [console output](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/consoleText) for more details. Possible conflicts: - Upstream changes - _data/tools.json --conflicts 2026-10-01 18:10:47,569 [ scc.config] DEBUG Found github.token 2026-10-01 18:10:47,569 [ scc.git] DEBUG Adding comment to issue #131. 2026-10-01 18:10:48,473 [urllib3.conn] DEBUG https://api.github.com:443 "POST /repos/IDR/idr.openmicroscopy.org/issues/131/comments HTTP/1.1" 201 2031 2026-10-01 18:10:48,474 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...b3a1d6213698629bbc8b5febeaffa27121f172d7' 2026-10-01 18:10:48,505 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:10:48,517 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 133 (add Phindr3D) b3a1d6213698629bbc8b5febeaffa27121f172d7' 2026-10-01 18:10:48,670 [ scc.git] DEBUG Auto-merging _data/tools.json 2026-10-01 18:10:48,739 [ scc.git] DEBUG Merge made by the 'ort' strategy. 2026-10-01 18:10:48,807 [ scc.git] DEBUG _data/tools.json | 13 +++++++++++++ 2026-10-01 18:10:48,807 [ scc.git] DEBUG 1 file changed, 13 insertions(+) 2026-10-01 18:10:49,075 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:49,076 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8' 2026-10-01 18:10:49,120 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:10:49,164 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Snone: PR 225 (Fix idr0106 to download from ftp instead of github) f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8' 2026-10-01 18:10:49,464 [ scc.git] DEBUG Auto-merging _data/download_urls.tsv 2026-10-01 18:10:49,464 [ scc.git] DEBUG CONFLICT (content): Merge conflict in _data/download_urls.tsv 2026-10-01 18:10:49,493 [ scc.git] DEBUG Automatic merge failed; fix conflicts and then commit the result. 2026-10-01 18:10:49,494 [ scc.git] DEBUG Calling 'git diff --name-only --diff-filter=U' 2026-10-01 18:10:49,517 [ scc.git] DEBUG Calling 'git reset --hard 51a5b1c40e3b1f39a96661f035f39b31b78d3a2e' 2026-10-01 18:10:49,646 [ scc.git] DEBUG HEAD is now at 51a5b1c merge master -Dorg -Snone: PR 133 (add Phindr3D) 2026-10-01 18:10:49,882 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:49,882 [ scc.git] DEBUG Calling 'git merge-base 94915ef467774ab056f6df88b2b5d944a6a61c4b f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8' 2026-10-01 18:10:49,911 [ scc.git] DEBUG Calling 'git diff --name-only 66e98c953258a512ae5d4c288d8b1cc88a9c6fb9..94915ef467774ab056f6df88b2b5d944a6a61c4b' 2026-10-01 18:10:49,930 [ scc.git] INFO - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' Conflicting PR. Removed from build [IDRSITE-push#2](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/). See the [console output](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/consoleText) for more details. Possible conflicts: - Upstream changes - _data/download_urls.tsv --conflicts 2026-10-01 18:10:49,939 [ scc.config] DEBUG Found github.token 2026-10-01 18:10:49,939 [ scc.git] DEBUG Adding comment to issue #225. 2026-10-01 18:10:51,002 [urllib3.conn] DEBUG https://api.github.com:443 "POST /repos/IDR/idr.openmicroscopy.org/issues/225/comments HTTP/1.1" 201 2038 2026-10-01 18:10:51,003 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-01 18:10:53,100 [ scc.git] DEBUG Get sha1 of %s 2026-10-01 18:10:53,100 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:10:53,115 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-01 18:10:53,207 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7fc29a7e5a10> has no local changes 2026-10-01 18:10:53,207 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Snone Repository: idr/idr.openmicroscopy.org Already up to date. Merged PRs: - PR 133 jburel 'add Phindr3D' Conflicting PRs (not included): - PR 131 jburel 'itr update' - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' Generated by IDRSITE-push#2 (https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/)' 2026-10-01 18:10:53,364 [ scc.git] DEBUG [detached HEAD abb2911] merge master -Dorg -Snone 2026-10-01 18:10:53,366 [ scc.merge] INFO Repository: idr/idr.openmicroscopy.org 2026-10-01 18:10:53,366 [ scc.merge] INFO Already up to date. 2026-10-01 18:10:53,366 [ scc.merge] INFO 2026-10-01 18:10:53,366 [ scc.merge] INFO Merged PRs: 2026-10-01 18:10:53,366 [ scc.merge] INFO - PR 133 jburel 'add Phindr3D' 2026-10-01 18:10:53,366 [ scc.merge] INFO 2026-10-01 18:10:53,366 [ scc.merge] INFO Conflicting PRs (not included): 2026-10-01 18:10:53,366 [ scc.merge] INFO - PR 131 jburel 'itr update' 2026-10-01 18:10:53,366 [ scc.merge] INFO - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' 2026-10-01 18:10:53,366 [ scc.merge] INFO 2026-10-01 18:10:53,366 [ scc.merge] DEBUG Cleaning remote branches created for merging 2026-10-01 18:10:53,366 [ scc.git] DEBUG Calling 'git remote' Merge all submodules2026-10-01 18:10:54,860 [ scc.config] DEBUG Found github.token 2026-10-01 18:10:54,862 [urllib3.conn] DEBUG Starting new HTTPS connection (1): api.github.com:443 2026-10-01 18:10:55,118 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:55,549 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:10:56,000 [urllib3.conn] DEBUG https://api.github.com:443 "GET /rate_limit HTTP/1.1" 200 None 2026-10-01 18:10:56,001 [ scc.gh] DEBUG 5000 remaining from 5000 (Reset at 19:10 2026-10-01 18:10:56,002 [ scc.git] DEBUG Calling 'git rev-parse --show-toplevel' 2026-10-01 18:10:56,013 [ scc.git] DEBUG Check current status 2026-10-01 18:10:56,014 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-01 18:10:56,033 [ scc.git] DEBUG abb2911 merge master -Dorg -Snone 2026-10-01 18:10:56,034 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-01 18:10:56,185 [ scc.config] DEBUG Found remote.origin.url 2026-10-01 18:10:56,554 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/idr/idr.openmicroscopy.org HTTP/1.1" 200 None 2026-10-01 18:10:57,102 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/IDR HTTP/1.1" 200 None 2026-10-01 18:10:57,563 [urllib3.conn] DEBUG https://api.github.com:443 "GET /orgs/IDR/members HTTP/1.1" 200 None 2026-10-01 18:10:57,564 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-01 18:10:57,668 [ scc.git] DEBUG Resetting... 2026-10-01 18:10:57,668 [ scc.git] DEBUG Calling 'git reset --hard HEAD' 2026-10-01 18:10:57,782 [ scc.git] DEBUG HEAD is now at abb2911 merge master -Dorg -Snone 2026-10-01 18:10:57,784 [ scc.git] DEBUG Calling 'git submodule update --recursive' 2026-10-01 18:10:57,911 [ scc.git] DEBUG Check current status 2026-10-01 18:10:57,911 [ scc.git] DEBUG Calling 'git log --oneline -n 1 HEAD' 2026-10-01 18:10:57,930 [ scc.git] DEBUG abb2911 merge master -Dorg -Snone 2026-10-01 18:10:57,931 [ scc.git] DEBUG Calling 'git submodule status' 2026-10-01 18:10:58,041 [ scc.merge] INFO Merging Pull Request(s) based on master 2026-10-01 18:10:58,041 [ scc.merge] INFO Including Pull Request(s) opened by any public member of the organization 2026-10-01 18:10:58,041 [ scc.merge] INFO Including Pull Request(s) labelled as include or dependencies 2026-10-01 18:10:58,041 [ scc.merge] INFO Excluding Pull Request(s) staged as draft 2026-10-01 18:10:58,041 [ scc.merge] INFO Excluding Pull Request(s) labelled as exclude or breaking 2026-10-01 18:10:58,041 [ scc.merge] INFO Excluding Pull Request(s) without successful status 2026-10-01 18:10:58,041 [ scc.repo] DEBUG ## PRs found: 2026-10-01 18:10:58,372 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/pulls HTTP/1.1" 200 None 2026-10-01 18:10:58,867 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/225 HTTP/1.1" 200 None 2026-10-01 18:10:59,372 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/225/comments HTTP/1.1" 200 None 2026-10-01 18:10:59,989 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8?page=1 HTTP/1.1" 200 None 2026-10-01 18:11:00,606 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-01 18:11:01,226 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8/check-suites?app_id=15368 HTTP/1.1" 200 None 2026-10-01 18:11:01,936 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8?page=1 HTTP/1.1" 200 None 2026-10-01 18:11:02,394 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/statuses/f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8?per_page=1 HTTP/1.1" 200 2 2026-10-01 18:11:02,395 [ scc.repo] DEBUG - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' 2026-10-01 18:11:02,957 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/133 HTTP/1.1" 200 None 2026-10-01 18:11:03,474 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/133/comments HTTP/1.1" 200 None 2026-10-01 18:11:04,077 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/b3a1d6213698629bbc8b5febeaffa27121f172d7?page=1 HTTP/1.1" 200 None 2026-10-01 18:11:04,644 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/b3a1d6213698629bbc8b5febeaffa27121f172d7/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-01 18:11:05,183 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/b3a1d6213698629bbc8b5febeaffa27121f172d7?page=1 HTTP/1.1" 200 None 2026-10-01 18:11:05,644 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/statuses/b3a1d6213698629bbc8b5febeaffa27121f172d7?per_page=1 HTTP/1.1" 200 2 2026-10-01 18:11:05,644 [ scc.repo] DEBUG - PR 133 jburel 'add Phindr3D' 2026-10-01 18:11:06,142 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/131 HTTP/1.1" 200 None 2026-10-01 18:11:06,698 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/issues/131/comments HTTP/1.1" 200 None 2026-10-01 18:11:07,367 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/1f880d2dc5fbf1c4bfbe479af44186dd5e15f433?page=1 HTTP/1.1" 200 None 2026-10-01 18:11:07,893 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/1f880d2dc5fbf1c4bfbe479af44186dd5e15f433/check-suites?app_id=15368&per_page=1 HTTP/1.1" 200 None 2026-10-01 18:11:08,401 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/commits/1f880d2dc5fbf1c4bfbe479af44186dd5e15f433?page=1 HTTP/1.1" 200 None 2026-10-01 18:11:08,870 [urllib3.conn] DEBUG https://api.github.com:443 "GET /repos/IDR/idr.openmicroscopy.org/statuses/1f880d2dc5fbf1c4bfbe479af44186dd5e15f433?per_page=1 HTTP/1.1" 200 2 2026-10-01 18:11:08,871 [ scc.repo] DEBUG - PR 131 jburel 'itr update' 2026-10-01 18:11:08,871 [ scc.repo] DEBUG ## Branches found: 2026-10-01 18:11:08,871 [ scc.git] DEBUG Get sha1 of %s 2026-10-01 18:11:08,871 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:11:08,885 [ scc.git] DEBUG Calling 'git show-ref --verify --quiet refs/remotes/origin/master' 2026-10-01 18:11:08,900 [ scc.git] DEBUG ## Merging base to ensure closed PRs are included. 2026-10-01 18:11:08,900 [ scc.git] DEBUG Calling 'git log --oneline --first-parent HEAD..origin/master' 2026-10-01 18:11:08,920 [ scc.git] DEBUG Calling 'git merge --ff-only origin/master' 2026-10-01 18:11:08,971 [ scc.git] DEBUG Already up to date. 2026-10-01 18:11:08,972 [ scc.git] DEBUG Calling 'git fetch origin pull/131/head' 2026-10-01 18:11:09,714 [ scc.git] DEBUG From https://github.com/idr/idr.openmicroscopy.org 2026-10-01 18:11:09,714 [ scc.git] DEBUG * branch refs/pull/131/head -> FETCH_HEAD 2026-10-01 18:11:09,741 [ scc.git] DEBUG Calling 'git fetch origin pull/133/head' 2026-10-01 18:11:10,406 [ scc.git] DEBUG From https://github.com/idr/idr.openmicroscopy.org 2026-10-01 18:11:10,406 [ scc.git] DEBUG * branch refs/pull/133/head -> FETCH_HEAD 2026-10-01 18:11:10,434 [ scc.git] DEBUG Calling 'git fetch origin pull/225/head' 2026-10-01 18:11:11,162 [ scc.git] DEBUG From https://github.com/idr/idr.openmicroscopy.org 2026-10-01 18:11:11,162 [ scc.git] DEBUG * branch refs/pull/225/head -> FETCH_HEAD 2026-10-01 18:11:11,189 [ scc.git] DEBUG ## Unique users: [] 2026-10-01 18:11:11,189 [ scc.git] DEBUG Get sha1 of %s 2026-10-01 18:11:11,189 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:11:11,199 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...1f880d2dc5fbf1c4bfbe479af44186dd5e15f433' 2026-10-01 18:11:11,235 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:11:11,245 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 131 (itr update) 1f880d2dc5fbf1c4bfbe479af44186dd5e15f433' 2026-10-01 18:11:11,475 [ scc.git] DEBUG Auto-merging _data/tools.json 2026-10-01 18:11:11,475 [ scc.git] DEBUG CONFLICT (content): Merge conflict in _data/tools.json 2026-10-01 18:11:11,502 [ scc.git] DEBUG Automatic merge failed; fix conflicts and then commit the result. 2026-10-01 18:11:11,504 [ scc.git] DEBUG Calling 'git diff --name-only --diff-filter=U' 2026-10-01 18:11:11,528 [ scc.git] DEBUG Calling 'git reset --hard abb291127607b31b307120f384874ff0b4d59442' 2026-10-01 18:11:11,674 [ scc.git] DEBUG HEAD is now at abb2911 merge master -Dorg -Snone 2026-10-01 18:11:11,892 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:11:11,893 [ scc.git] DEBUG Calling 'git merge-base abb291127607b31b307120f384874ff0b4d59442 1f880d2dc5fbf1c4bfbe479af44186dd5e15f433' 2026-10-01 18:11:11,921 [ scc.git] DEBUG Calling 'git diff --name-only 0e25fb6b33f85d7ee59961b72df500c1e35f5fe7..abb291127607b31b307120f384874ff0b4d59442' 2026-10-01 18:11:11,950 [ scc.git] INFO - PR 131 jburel 'itr update' Conflicting PR. Removed from build [IDRSITE-push#2](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/). See the [console output](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/consoleText) for more details. Possible conflicts: - Upstream changes - _data/tools.json --conflicts 2026-10-01 18:11:11,958 [ scc.config] DEBUG Found github.token 2026-10-01 18:11:11,958 [ scc.git] DEBUG Not adding comment to issue #131, already --conflicts. 2026-10-01 18:11:11,958 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...b3a1d6213698629bbc8b5febeaffa27121f172d7' 2026-10-01 18:11:11,983 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:11:11,995 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 133 (add Phindr3D) b3a1d6213698629bbc8b5febeaffa27121f172d7' 2026-10-01 18:11:12,050 [ scc.git] DEBUG Already up to date. 2026-10-01 18:11:12,383 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:11:12,384 [ scc.git] DEBUG Calling 'git diff --name-only HEAD...f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8' 2026-10-01 18:11:12,431 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:11:12,471 [ scc.git] DEBUG Calling 'git merge --no-ff -m merge master -Dorg -Ssuccess-only: PR 225 (Fix idr0106 to download from ftp instead of github) f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8' 2026-10-01 18:11:12,620 [ scc.git] DEBUG Auto-merging _data/download_urls.tsv 2026-10-01 18:11:12,620 [ scc.git] DEBUG CONFLICT (content): Merge conflict in _data/download_urls.tsv 2026-10-01 18:11:12,649 [ scc.git] DEBUG Automatic merge failed; fix conflicts and then commit the result. 2026-10-01 18:11:12,650 [ scc.git] DEBUG Calling 'git diff --name-only --diff-filter=U' 2026-10-01 18:11:12,673 [ scc.git] DEBUG Calling 'git reset --hard abb291127607b31b307120f384874ff0b4d59442' 2026-10-01 18:11:12,797 [ scc.git] DEBUG HEAD is now at abb2911 merge master -Dorg -Snone 2026-10-01 18:11:13,003 [urllib3.conn] DEBUG https://api.github.com:443 "GET /user HTTP/1.1" 200 None 2026-10-01 18:11:13,003 [ scc.git] DEBUG Calling 'git merge-base abb291127607b31b307120f384874ff0b4d59442 f920c7f9b05e5c62b08a3d667e95bb4ee9112ab8' 2026-10-01 18:11:13,040 [ scc.git] DEBUG Calling 'git diff --name-only 66e98c953258a512ae5d4c288d8b1cc88a9c6fb9..abb291127607b31b307120f384874ff0b4d59442' 2026-10-01 18:11:13,062 [ scc.git] INFO - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' Conflicting PR. Removed from build [IDRSITE-push#2](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/). See the [console output](https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/consoleText) for more details. Possible conflicts: - Upstream changes - _data/download_urls.tsv --conflicts 2026-10-01 18:11:13,072 [ scc.config] DEBUG Found github.token 2026-10-01 18:11:13,072 [ scc.git] DEBUG Not adding comment to issue #225, already --conflicts. 2026-10-01 18:11:13,072 [ scc.git] DEBUG Calling 'git submodule update' 2026-10-01 18:11:13,174 [ scc.git] DEBUG Get sha1 of %s 2026-10-01 18:11:13,174 [ scc.git] DEBUG Calling 'git rev-parse HEAD' 2026-10-01 18:11:13,184 [ scc.git] DEBUG Calling 'git submodule --quiet foreach echo $path' 2026-10-01 18:11:13,283 [ scc.git] DEBUG Calling 'git status --porcelain' 2026-10-01 18:11:13,350 [ scc.git] DEBUG <scc.git.GitRepository object at 0x7f17f98eba50> has no local changes 2026-10-01 18:11:13,350 [ scc.git] DEBUG Calling 'git commit --allow-empty -a -n -m merge master -Dorg -Ssuccess-only Repository: idr/idr.openmicroscopy.org Already up to date. Merged PRs: - PR 133 jburel 'add Phindr3D' Conflicting PRs (not included): - PR 131 jburel 'itr update' - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' Generated by IDRSITE-push#2 (https://merge-ci.openmicroscopy.org/jenkins/job/IDRSITE-push/2/)' 2026-10-01 18:11:13,501 [ scc.git] DEBUG [detached HEAD 59832bd] merge master -Dorg -Ssuccess-only 2026-10-01 18:11:13,503 [ scc.merge] INFO Repository: idr/idr.openmicroscopy.org 2026-10-01 18:11:13,503 [ scc.merge] INFO Already up to date. 2026-10-01 18:11:13,503 [ scc.merge] INFO 2026-10-01 18:11:13,503 [ scc.merge] INFO Merged PRs: 2026-10-01 18:11:13,503 [ scc.merge] INFO - PR 133 jburel 'add Phindr3D' 2026-10-01 18:11:13,503 [ scc.merge] INFO 2026-10-01 18:11:13,503 [ scc.merge] INFO Conflicting PRs (not included): 2026-10-01 18:11:13,503 [ scc.merge] INFO - PR 131 jburel 'itr update' 2026-10-01 18:11:13,503 [ scc.merge] INFO - PR 225 will-moore 'Fix idr0106 to download from ftp instead of github' 2026-10-01 18:11:13,503 [ scc.merge] INFO 2026-10-01 18:11:13,503 [ scc.merge] DEBUG Cleaning remote branches created for merging 2026-10-01 18:11:13,503 [ scc.git] DEBUG Calling 'git remote' Update component versions grep: build.gradle: No such file or directory grep: settings.gradle: No such file or directory grep: build.gradle: No such file or directory grep: build.gradle: No such file or directory Up-to-date: Commit all component version changes HEAD detached from 94915ef nothing to commit, working tree clean 2026-10-01 18:11:21,713 [ scc.push] INFO Merged branch pushed to https://github.com/snoopycrimecop/idr.openmicroscopy.org/tree/merge_ci [Pipeline] archiveArtifacts Archiving artifacts [Pipeline] } [Pipeline] // node [Pipeline] End of Pipeline Finished: SUCCESS