biocthis-TAB

Presentation about biocthis to the Bioconductor Technical Advisory Board on 2020-11-05

Transcript

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

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2. 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
   

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3. 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/
   

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

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5. 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
   

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6. 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/
   

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7. 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
   

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8. 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
   

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