biocthis Leonardo Collado Torres lcolladotor.github.io 2020-11-05

LIEBER INSTITUTE for BRAIN DEVELOPMENT usethis: helpful framework for making R packages ● https://usethis.r-lib.org/ ● usethis::create_package() https://usethis.r-lib.org/refer ence/create_package.html

LIEBER INSTITUTE for BRAIN DEVELOPMENT GitHub Actions ● Saves you time ● Enables automatically testing your package on winOS, macOS, linux, docker ○ https://docs.github.com/en/actions/reference/virtual-environments-for-github-host ed-runners ● Reproducible framework ○ Particularly when you use docker http://bioconductor.org/help/docker/ ○ powered by https://www.rocker-project.org/ ● But it’s also cutting edge ○ You might run into the latest R issues ○ Might need to figure out how to install ● https://github.com/r-lib/actions ● https://www.jimhester.com/talk/2020-rsc-github-actions/

LIEBER INSTITUTE for BRAIN DEVELOPMENT GHA machines (up to 6 hours)

LIEBER INSTITUTE for BRAIN DEVELOPMENT biocthis: helps jumpstart this process ● Includes a GitHub Actions workflow that is Bioconductor-friendly ○ https://lcolladotor.github.io/biocthis/reference/use_bioc_github_action.html ○ Bioconductor docker + macOS + winOS ○ R CMD build + check + BiocCheck ○ covr: code coverage ○ pkgdown: documentation website ● Has functions similar to usethis but that are tailored for Bioconductor’s needs (and/or mine) ○ https://lcolladotor.github.io/biocthis/reference/use_bioc_vignette.html creates a BiocStyle-based vignette with a structure that I like to use for my R/Bioconductor packages ● Includes 4 dev/*.R scripts that will guide you throughout the process of making your R/BioC package

LIEBER INSTITUTE for BRAIN DEVELOPMENT Examples: recount3 ● https://github.com/LieberInstitute/recount3 ● http://research.libd.org/recount3/ ● http://research.libd.org/recount3/reference/create_rse.ht ml ● Bookdown: http://research.libd.org/SPEAQeasy/ ● R Markdown site: https://lcolladotor.github.io/twitter-stats/CDSB2020.html ● More? https://lcolladotor.github.io/pkgs/

LIEBER INSTITUTE for BRAIN DEVELOPMENT Increased exposure to changes in R build issues ● Unlike BioC builds, you have to figure out how to deal with dependencies ○ Upstream package might not be available ● BioC 3.13 uses R-devel and CRAN has no binaries on macOS ● Compiling errors can be harder to trace ● Can use BioC 3.12 and/or focus on Bioconductor docker’s tests ● Can be directly affected by rocker/BioC docker changes

LIEBER INSTITUTE for BRAIN DEVELOPMENT Worth it (for me) ● Overall faster feedback than BioC’s builds ○ Complementary, not a replacement ● Can help notice issues with OS that you might not realize ○ Example with tests failing on megadepth on macOS ● Helped me be more productive this past round ● dev/ scripts/guides can help new users become developers