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Fix atlas handling and transform file issues in bundle_seg #269

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Fix atlas handling and transform file issues in bundle_seg

Fix atlas handling and transform file issues in bundle_seg #269

Re-run triggered December 19, 2024 14:57
@AlexVCaronAlexVCaron
#80
gagnonanthony:fix/atlasbundleseg
Status Failure
Total duration 4m 1s
Artifacts –

update_pr.yml

on: pull_request
checks  /  compute - changes
17s
checks / compute - changes
checks  /  prettier
15s
checks / prettier
checks  /  editorconfig
12s
checks / editorconfig
checks  /  pre-commit
15s
checks / pre-commit
Matrix: checks / test
Matrix: checks / lint - modules
Matrix: checks / lint - subworkflows
checks  /  report
0s
checks / report
checks  /  status
0s
checks / status
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35 errors and 12 warnings
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Exit code 1 returned from process: file name '/usr/bin/docker', arguments 'version --format '{{.Server.APIVersion}}''.
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'network')
checks / test (modules/nf-neuro/registration/synthregistration) / test - modules/nf-neuro/registration/synthregistration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/ants) / test - modules/nf-neuro/registration/ants
The self-hosted runner: scilus-nf-neuro-runners-wnh9m-runner-78cf2 lost communication with the server. Verify the machine is running and has a healthy network connection. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
checks / test (subworkflows/nf-neuro/bundle_seg) / test - subworkflows/nf-neuro/bundle_seg
The self-hosted runner: scilus-nf-neuro-runners-wnh9m-runner-wc2l6 lost communication with the server. Verify the machine is running and has a healthy network connection. Anything in your workflow that terminates the runner process, starves it for CPU/Memory, or blocks its network access can cause this error.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'network')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Exit code 1 returned from process: file name '/usr/bin/docker', arguments 'version --format '{{.Server.APIVersion}}''.
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (subworkflows/nf-neuro/registration) / test - subworkflows/nf-neuro/registration
Value cannot be null. (Parameter 'ContainerId')
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 127.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 1.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
Process completed with exit code 1.
checks / status
Process completed with exit code 1.
checks / editorconfig
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / pre-commit
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / prettier
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / compute - changes
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - modules (registration/anattodwi) / lint - registration/anattodwi
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - modules (registration/ants) / lint - registration/ants
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - subworkflows (bundle_seg) / lint - bundle_seg
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - modules (registration/synthregistration) / lint - registration/synthregistration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / lint - subworkflows (registration) / lint - registration
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
No files were found with the provided path: tests_workdir/. No artifacts will be uploaded.
checks / test (modules/nf-neuro/registration/anattodwi) / test - modules/nf-neuro/registration/anattodwi
No files were found with the provided path: tests_reports/. No artifacts will be uploaded.
checks / status
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636