v1.25.1 -- Resolve #57

This commit resolves #57
by updating the `handleMessage()` calls after the formatting check
fails. Instead of mentioning `formatR`, these messages now refer to:

* `styler`,
* `biocthis`,
* the `BiocCheck` vignette.

Furthermore, the `BiocCheck` vignette section on formatting still
mentions `formatR`, but it now also mentions in more detail:

* `styler`: how to install and run it
* `biocthis`: as a companion to `styler` with code how to run it
(but not install it since it's optional and the install instructions
will hopefully change soon once this package is submitted/reviewed).
* a quick overview of the differences between `formatR` and `styler`,
though this is mostly done by highlighting current limitations of
`formatR`.
* how RStudio Desktop's `Reformat code` button (under the magic wand)
can help break long lines which is something that `styler` cannot do
as discussed in more detail at
r-lib/styler#247. `formatR` can do this,
but personally, the fact that it broke valid R code in some of my
packages made me trust its output less.

The NEWS and DESCRIPTION files have been updated accordingly.

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: BiocCheck
-Version: 1.25.0
+Version: 1.25.1
 Title: Bioconductor-specific package checks
 Description: Executes Bioconductor-specific package checks.
 Authors@R: c(

NEWS

@@ -1,3 +1,10 @@
+CHANGES IN VERSION 1.25
+-----------------------
+
+USER SIGNIFICANT CHANGES
+
+ o (1.25.1) Suggest styler over formatR for automatic code re-formatting.
+
 CHANGES IN VERSION 1.23
 -----------------------
 
@@ -98,4 +105,4 @@ NEW FEATURES
 
 BUG FIXES
 
- o Use shell quotes to allow spaces in package paths
+ o Use shell quotes to allow spaces in package paths

R/checks.R

@@ -1431,7 +1431,11 @@ checkFormatting <- function(pkgdir, nlines=6)
  handleMessage(
  "See http://bioconductor.org/developers/how-to/coding-style/")
  handleMessage(
- "See FormatR package: https://cran.r-project.org/web/packages/formatR/index.html")
+ "See styler package: https://styler.r-lib.org/ ",
+ "as described in the BiocCheck vignette.")
+ handleMessage(
+ "See also biocthis: ",
+ "https://lcolladotor.github.io/biocthis/reference/bioc_style.html")
  }
 }
 

vignettes/BiocCheck.Rmd

@@ -550,10 +550,48 @@ The output of this check includes the first 6 offending lines of code;
 see more with `BiocCheck:::checkFormatting("path/to/YourPackage",
 nlines=Inf)`.
 
-There is a helpful package [formatR][formatR] that can be used for formatting of
-R code to particular coding standards.
+There are several helpful packages that can be used for formatting of
+R code to particular coding standards such as [formatR][formatR] and
+[styler][styler] as well as the "Reformat code" button in
+[RStudio Desktop][RStudio]. Each solution has its advantages, though 
+[styler][styler] works with `roxygen2` examples and is actively
+maintained. You can re-format your code using [styler][styler] as shown
+below:
+
+```{r reformat_code, eval = FALSE}
+## Install styler if necessary
+if (!requireNamespace("styler", quietly = TRUE)) {
+ install.packages("styler")
+}
+## Automatically re-format the R code in your package
+styler::style_pkg(transformers = styler::tidyverse_style(indent_by = 4))
+
+## If using biocthis:
+styler::style_pkg(transformers = biocthis::bioc_style())
+
+## For your Rmd vignette files:
+styler::style_dir(
+ "vignettes",
+ transformers = biocthis::bioc_style(),
+ filetype = "Rmd"
+)
+```
+
+You can also use [`biocthis::bioc_style()`][biocstyle] which adapts the
+`tidverse_style()` to make it more Bioconductor-friendly. If you are
+working with [RStudio Desktop][RStudio] use also the "Reformat code"
+button which will help you break long lines of code. Alternatively,
+use [formatR][formatR], though beware that it can break valid code
+involving both type of quotation marks (`"` and `'`) and does not
+support re-formatting `roxygen2` examples. In general,
+it is best to version control your code before applying any
+automatic re-formatting solutions and implement unit tests to
+verify that your code runs as intended after you re-format your code.
 
 [formatR]: https://cran.r-project.org/web/packages/formatR/index.html
+[styler]: https://styler.r-lib.org/
+[RStudio]: https://rstudio.com/products/rstudio/download/
+[biocstyle]: https://lcolladotor.github.io/biocthis/reference/bioc_style.html
 
 ## Duplication checks