This function is very similar to usethis::use_vignette() except
that it uses a template from biocthis. This template includes
instructions for citing other packages using RefManageR, uses
sessioninfo::session_info() for displaying the R session information since
it includes GitHub installation information and other useful details. The
template also includes a section on how to ask for help and required
knowledge.
use_bioc_vignette(name, title = name)Just like in usethis::use_vignette(): base for file name to
use for new vignette. Should consist only of numbers, letters, _ and -.
Lower case is recommended.
Just like in usethis::use_vignette(): the title of the
vignette.
This function adds and/or replaces the
vignettes/<name>.Rmd file in your R package.
if (FALSE) {
## Run this function in your package
pkg <- basename(usethis::proj_get())
biocthis::use_bioc_vignette(pkg, paste("Introduction to", pkg))
}
## Create an example package for illustrative purposes.
## Note: you do not need to run this for your own package!
pkgdir <- biocthis_example_pkg()
#> ✔ Setting active project to '/tmp/RtmpTHfQjN/biocthisexample'
#> Package: biocthisexample
#> Title: What the Package Does (One Line, Title Case)
#> Version: 0.0.0.9000
#> Authors@R (parsed):
#> * First Last <first.last@example.com> [aut, cre] (YOUR-ORCID-ID)
#> Description: What the package does (one paragraph).
#> License: `use_mit_license()`, `use_gpl3_license()` or friends to
#> pick a license
#> Encoding: UTF-8
#> Roxygen: list(markdown = TRUE)
#> RoxygenNote: 7.2.3
#> ✔ Setting active project to '/tmp/RtmpTHfQjN/biocthisexample'
## Create a template vignette file that is Bioconductor-friendly
biocthis::use_bioc_vignette("biocthisexample", "Introduction to biocthisexample")
#> ✔ Adding 'knitr' to Suggests field in DESCRIPTION
#> • Use `requireNamespace("knitr", quietly = TRUE)` to test if package is installed
#> • Then directly refer to functions with `knitr::fun()`
#> ✔ Adding 'BiocStyle' to Suggests field in DESCRIPTION
#> • Use `requireNamespace("BiocStyle", quietly = TRUE)` to test if package is installed
#> • Then directly refer to functions with `BiocStyle::fun()`
#> ✔ Adding 'RefManageR' to Suggests field in DESCRIPTION
#> • Use `requireNamespace("RefManageR", quietly = TRUE)` to test if package is installed
#> • Then directly refer to functions with `RefManageR::fun()`
#> ✔ Adding 'sessioninfo' to Suggests field in DESCRIPTION
#> • Use `requireNamespace("sessioninfo", quietly = TRUE)` to test if package is installed
#> • Then directly refer to functions with `sessioninfo::fun()`
#> ✔ Adding 'testthat' to Suggests field in DESCRIPTION
#> • Use `requireNamespace("testthat", quietly = TRUE)` to test if package is installed
#> • Then directly refer to functions with `testthat::fun()`
#> ✔ Adding 'knitr' to VignetteBuilder
#> ✔ Adding 'inst/doc' to '.gitignore'
#> ✔ Creating 'vignettes/'
#> ✔ Adding '*.html', '*.R' to 'vignettes/.gitignore'
#> ✔ Adding 'rmarkdown' to Suggests field in DESCRIPTION
#> • Use `requireNamespace("rmarkdown", quietly = TRUE)` to test if package is installed
#> • Then directly refer to functions with `rmarkdown::fun()`
#> ✔ Writing 'vignettes/biocthisexample.Rmd'
#> • Edit 'vignettes/biocthisexample.Rmd'