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camlab-bioml / cytomarker

Interactive design and validation of antibody panels using single-cell atlases
https://camlab.shinyapps.io/cytomarker/
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setup-r-dependencies has highly variable time to completion within larger actions workflow #78

Closed matt-sd-watson closed 1 year ago

matt-sd-watson commented 2 years ago

https://github.com/r-lib/actions/issues/621

matt-sd-watson commented 1 year ago

updates on deployment script: a shift to minor R version upgrade 4.2.2 from 4.2.1 appears to be problematic for shinyapps servers. There is apparently a delay of up to two weeks before a new R version is supported by shinyapps: https://github.com/rstudio/rsconnect/issues/633

Additionally, Bioconductor packages are now out of sync with the automatic deployment script, requiring updating of all packages in Bioconductor version 3.16, which adds about 20 minutes of time for the deployment. Will need to investigate solutions to these package errors to maintain a reasonable time to deploy (20-25 minutes).

matt-sd-watson commented 1 year ago

After discussion, time to deploy will not be as important as the loading time for the application on the shinyapps server. Closing with the potential to reopen if deployment times becomes a priority.