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AlexsLemonade / OpenPBTA-analysis

The analysis repository for the Open Pediatric Brain Tumor Atlas Project
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Remove sigfit vignette install from Dockerfile #1273

Closed sjspielman closed 2 years ago

sjspielman commented 2 years ago

As noted in #1225 there are occasional CI timeouts. The docker image may benefit from some cleanup to reduce changes of timeouts when there is no cache available.

What changes need to be made? Please provide enough detail for another participant to make the update.

In the Dockerfile, R -e "remotes::install_github('kgori/sigfit', ref = '209776ee1d2193ad4b682b2e2472f848bd7c67a6', build_vignettes = TRUE, build_opts = c('--no-resave-data', '--no-manual'), dependencies = TRUE)" takes a long time to build the vignettes but the vignettes aren't needed int he docker. We should remove build_vignettes = TRUE so the default of FALSE is used.

Who will complete the updated analysis?

@sjspielman, <1 day

sjspielman commented 2 years ago

No longer happening because PR was experiencing CI problems (probably unrelated to vignette removal), but those problems are not a compelling argument for this proceed. In addition, it doesn't really make a dent in runtime overall.