In phylotastic/datelife: Scientific Data on Time of Lineage Divergence for Your Taxa

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(datelife)

Tools for package development

And other tips that I used to get datelife on CRAN

https://www.r-bloggers.com/2020/12/top-10-tips-to-make-your-r-package-even-more-awesome/

Dependencies on packages outside of CRAN

Bioconductor packages:

I was having trouble declaring Bioconductor packages.

Most people suggested that adding "BiocViews:" to the Description file would solve the issue. But it did not, and I kept on finding unanswered posts about packages being rejected fromx CRAN because of dependencies from Bioconductor using the "biocviews" trick. So I did a reverse dependencie search on Bioconductor packages. Surely at least one package in CRAN must have a dependency from Bioconductor. Indeed, the msa package has bio3d as a reverse dependency:

devtools::revdep("msa")

#> [1] "bio3d"

Going into the CRAN mirror of the bio3d package on GitHib, I found their solution:

if (!requireNamespace("msa", quietly=TRUE)) {
  stop("msa package missing: Please install it from Bioconductor, see: ?BiocManager::install")
}

Calling Bioconductor packages conditionally allows us to move them into "Suggests" on the DESCRIPTION file. I found out you also have to add them to "Remotes":

Suggests:
    msa,
    Biostrings
Remotes:
    bioc::release/msa,
    bioc::release/Biostrings

The Remotes part had to be removed for CRAN submission. Because some of my tests depend on these packages being installed, I added helper file with a call to package installation of msa and Biostrings if they are not already installed.

Note checking CRAN incoming feasibility Maintainer:

It is safe to ignore this note: https://stackoverflow.com/questions/23829978/checking-cran-incoming-feasibility-note-maintainer

Automated R CMD checks with GitHub actions:

remotes::install_github("aaronpeikert/repro")

repro::check_git()
repro::check_github_ssh()
usethis::create_github_token()

gitcreds_set() Choose option 2) Replace credentials. It will prompt your for the
new token, and you will be all set.

usethis::use_github_actions()

Building package website

pkgdown::build_site()

pkgdown::build_home_index(); pkgdown::init_site()

phylotastic/datelife documentation built on June 9, 2024, 6:50 p.m.