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AlexsLemonade / refinebio

Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.
https://www.refine.bio/
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Fix affymetrix "no space left on device" error #3187

Closed arkid15r closed 1 year ago

arkid15r commented 1 year ago

Context

In order to restore staging/prod deploy process CI/CD tests need to be fixed.

Problem or idea

5078d9394dfc: Verifying Checksum
5078d9394dfc: Download complete
failed to register layer: ApplyLayer exit status 1 stdout:  stderr: write /root/.cache/R/renv/cache/v5/R-3.6/x86_64-pc-linux-gnu/pd.huex.1.0.st.v2/3.14.1/0f4628027cc7c9e99d6113fbcbe905ad/pd.huex.1.0.st.v2/data/pmSequence.rda: no space left on device
Error: Process completed with exit code 1.

Solution or next step

It seems that renv migration may have caused the image size increase. Figure out what takes the extra space and apply appropriate solution.

arkid15r commented 1 year ago

It seems we should consider using larger runners.

arkid15r commented 1 year ago

With --cache-from/--cache-to enabled the error message changed to:

ERROR: failed to solve: failed to compute cache key: write /var/lib/buildkit/runc-overlayfs/snapshots/snapshots/1141/fs/root/.cache/R/renv/source/bioconductor/pd.rta.1.0/pd.rta.1.0_3.12.2.tar.gz: no space left on device
Could not build ccdlstaging/dr_affymetrix_local after 3 attempts.
arkid15r commented 1 year ago

No longer an issue w/ the larger runners available