Deprecate packages to "avoid" rate limit

AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project

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Deprecate packages to "avoid" rate limit #1472

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

This PR comments out a deprecated analysis module, and no longer installs some of that specific module's R package dependencies to speed up CI and/or possibly avoid a github API rate limit.

sjspielman commented 2 years ago

LGTM, but maybe change DEPRECATE to Deprecated for a bit less yelling.

I'm just very enthusiastic! Changes made :)

jashapiro commented 2 years ago

I think we can pause/close this PR in favor of #1477 which incorporates the same changes plus the PAT fix (and it does work when a cache is used and it can finish in under 3 hours)

sjspielman commented 2 years ago

@jashapiro I'll add a don't merge tag here then.

jashapiro commented 2 years ago

Closing now that #1477 is in.