[Bioc-devel] Reducing dependencies

[Sean Davis]

Github Actions offers several advantages over travis-ci including longer
sessions and more resources. In addition, applying package caching to a
github actions workflow can essentially eliminate the time associated with
package installation after the first build. See here for an example (that
has some extra bells-and-whistles):

https://github.com/seandavi/BuildABiocWorkshop2020/blob/master/.github/workflows/basic_checks.yaml#L9-L21

Sean


On Tue, Jun 2, 2020 at 5:45 PM Koen Van den Berge <koenvdberge using berkeley.edu>
wrote:

> Dear All,
>
> We have recently extended our Bioconductor package tradeSeq <
> https://bioconductor.org/packages/devel/bioc/html/tradeSeq.html> to allow
> different input formats and accommodate extended downstream analyses, by
> building on other R/Bioconductor packages.
> However this has resulted in a significant increase in the number of
> dependencies due to relying on other packages that also have many
> dependencies, for example causing very long build times on Travis <
> https://travis-ci.com/github/statOmics/tradeSeq>.
>
> We are therefore wondering about current recommendations to reduce the
> dependency load. We have moved some larger packages from ‘Imports’ to
> ‘Suggests’, but to no avail.
>
> Best,
> Koen
>         [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Sean Davis, MD, PhD
Center for Cancer Research
National Cancer Institute
National Institutes of Health
Bethesda, MD 20892
https://seandavi.github.io/
https://twitter.com/seandavis12

	[[alternative HTML version deleted]]