neurogenomics / rworkflows

Continuous integration for R packages. šŸ”€ Automates testing āœ…, documentation website building šŸ“¦, & containerised deployment šŸ³.
https://neurogenomics.github.io/rworkflows/
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workflow-telemetry-action: `Error: EACCES: permission denied` #128

Open bschilder opened 7 months ago

bschilder commented 7 months ago

1. Bug description

First brought to my attention by @vjcitn An error arises during the telemetry step in the rworkflows action.

Console output

https://github.com/tempbioc/parody/actions/runs/7700556648/job/20984649706

Run runforesight/workflow-telemetry-action@v1
  with:
    github_token: ***
    comment_on_pr: false
    metric_frequency: 5
    proc_trace_min_duration: -1
    proc_trace_sys_enable: false
    proc_trace_chart_show: true
    proc_trace_chart_max_count: 100
    proc_trace_table_show: false
    job_summary: true
    theme: light
/usr/bin/docker exec  6c2e97cc4a283c72fe7bf139a67a7da38acadf3432c0c132475639d0cd[27](https://github.com/tempbioc/parody/actions/runs/7700556648/job/20984649706#step:4:28)aae2 sh -c "cat /etc/*release | grep ^ID"
[Workflow Telemetry] Initializing ...
[Workflow Telemetry] Starting step tracer ...
[Workflow Telemetry] Started step tracer
[Workflow Telemetry] Starting stat collector ...
[Workflow Telemetry] Started stat collector
[Workflow Telemetry] Starting process tracer ...
[Workflow Telemetry] Using proc_tracer_ubuntu-22
Error: [Workflow Telemetry] Unable to start process tracer
Error: [Workflow Telemetry] Error
Error: Error: EACCES: permission denied, open '/__w/_temp/_runner_file_commands/save_state_ac4bd7c5-921e-48b3-b0[29](https://github.com/tempbioc/parody/actions/runs/7700556648/job/20984649706#step:4:30)-d0cb99c12220'
[Workflow Telemetry] Initialization completed
Run echo "RGL_USE_NULL=TRUE" >> $GITHUB_ENV
/__w/_temp/06874ccf-cdc5-4e06-aed4-f0e66a4aa052.sh: line 1: /__w/_temp/_runner_file_commands/set_env_1542[31](https://github.com/tempbioc/parody/actions/runs/7700556648/job/20984649706#step:4:32)dd-e084-4f24-9ded-f0a82f647c04: Permission denied
/__w/_temp/06874ccf-cdc5-4e06-aed4-f0e66a4aa052.sh: line 2: /__w/_temp/_runner_file_commands/set_env_15[42](https://github.com/tempbioc/parody/actions/runs/7700556648/job/20984649706#step:4:44)31dd-e084-4f24-9ded-f0a82f647c04: Permission denied
/__w/_temp/06874ccf-cdc5-4e06-aed4-f0e66a4aa052.sh: line 3: /__w/_temp/_runner_file_commands/set_env_154231dd-e084-4f24-9ded-f0a82f647c04: Permission denied
/__w/_temp/06874ccf-cdc5-4e06-aed4-f0e66a4aa052.sh: line 4: /__w/_temp/_runner_file_commands/set_env_154231dd-e084-4f24-9ded-f0a82f647c04: Permission denied
/__w/_temp/06874ccf-cdc5-4e06-aed4-f0e66a4aa052.sh: line 5: /__w/_temp/_runner_file_commands/set_env_154231dd-e084-4f24-9ded-f0a82f647c04: Permission denied
Error: Process completed with exit code 1.

Expected behaviour

Telemetry actions runs all the way through and produces reports.

2. Reproducible example

https://github.com/tempbioc/parody/actions/runs/7700556648/workflow

bschilder commented 7 months ago

This seems strange since there hasn't been any changes to the telemetry action in >10 months. It's possible something changed with the GH runners themselves that caused the error. Or perhaps there was some temporary bug with the GH runners. I've checked the workflow file of @vjcitn and everything seems to be ok there. Another possibility is that there's some weird interactions going on between the Docker container ghcr.io/bioconductor/bioconductor_salt:devel-jammy-bioc-3.19-r-4.4.0 and this particular action, though I have no idea what that might be.

Reached out to the telemetry action authors to investigate.

bschilder commented 7 months ago

Potentially related Issues:

bschilder commented 7 months ago

Got a suggested solution from the subaction authors: https://github.com/catchpoint/workflow-telemetry-action/issues/57#issuecomment-1916597573

Going to try see if this something I can implement in rworkflows. In the meantime, this might be something you can add directly to your rworkflows.yml file @vjcitn

bschilder commented 7 months ago

Additional examples of setting the "privileged" flag in GHA: https://github.com/actions/container-action/issues/2#issuecomment-854057781