From 811baf2b0adeb7c2cc6f2e345df4944074a7481d Mon Sep 17 00:00:00 2001
From: Will Beasley <wibeasley@hotmail.com>
Date: Thu, 11 Aug 2022 23:12:20 -0500
Subject: [PATCH] lintr & other checks

ref #9
---
 .Rbuildignore                          |  1 +
 .lintr                                 |  5 ++++
 CRAN-RELEASE                           |  2 --
 documentation-for-developers/refresh.R | 38 ++++++++++++++++++++++----
 4 files changed, 39 insertions(+), 7 deletions(-)
 create mode 100644 .lintr
 delete mode 100644 CRAN-RELEASE

diff --git a/.Rbuildignore b/.Rbuildignore
index d91dc4b..d2dd944 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -12,6 +12,7 @@ documentation-for-developers/
 playgrounds/
 utility/
 ^\.github$
+^\.lintr$
 ^\.markdownlist\.json$
 ^\.travis\.yml$
 ^appveyor\.yml$
diff --git a/.lintr b/.lintr
new file mode 100644
index 0000000..7bd9b0e
--- /dev/null
+++ b/.lintr
@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    commas_linter = NULL,
+    commented_code_linter = NULL
+  )
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
deleted file mode 100644
index d780e1c..0000000
--- a/CRAN-RELEASE
+++ /dev/null
@@ -1,2 +0,0 @@
-This package was submitted to CRAN on 2018-09-12.
-Once it is accepted, delete this file and tag the release (commit de657690f5).
diff --git a/documentation-for-developers/refresh.R b/documentation-for-developers/refresh.R
index 2956958..2be540f 100644
--- a/documentation-for-developers/refresh.R
+++ b/documentation-for-developers/refresh.R
@@ -1,14 +1,36 @@
-rm(list=ls(all=TRUE))
+rm(list = ls(all = TRUE))
 # library(devtools)
-deviceType <- ifelse(R.version$os=="linux-gnu", "X11", "windows")
-options(device = deviceType) #http://support.rstudio.org/help/discussions/problems/80-error-in-function-only-one-rstudio-graphics-device-is-permitted
+# deviceType <- ifelse(R.version$os=="linux-gnu", "X11", "windows")
+# options(device = deviceType) #http://support.rstudio.org/help/discussions/problems/80-error-in-function-only-one-rstudio-graphics-device-is-permitted
+
+spelling::spell_check_package()
+# spelling::update_wordlist()
+lintr::lint_package()
+urlchecker::url_check(); urlchecker::url_update()
 
 devtools::document()
 devtools::check_man() #Should return NULL
 devtools::build_vignettes()
+
+checks_to_exclude <- c(
+  "covr",
+  # "cyclocomp"#,
+  "lintr_line_length_linter"
+)
+gp <-
+  goodpractice::all_checks() |>
+  purrr::discard(~(. %in% checks_to_exclude)) |>
+  {
+    \(checks)
+    goodpractice::gp(checks = checks)
+  }()
+goodpractice::results(gp)
+gp
+
+devtools::document()
 pkgdown::clean_site()
 pkgdown::build_site()
-system("R CMD Rd2pdf --no-preview --force --output=./documentation-peek.pdf ." )
+# system("R CMD Rd2pdf --no-preview --force --output=./documentation-peek.pdf ." )
 
 devtools::run_examples(); #dev.off() #This overwrites the NAMESPACE file too
 # devtools::run_examples(, "table-nih-enrollment.Rd")
@@ -18,7 +40,13 @@ test_results_checked <- devtools::test(filter = "table-nih-enrollment")
 test_results_not_checked <- testthat::test_dir("./tests/manual/")
 
 # devtools::check(force_suggests = FALSE)
+devtools::check(cran=TRUE)
+devtools::check( # Equivalent of R-hub
+  manual    = TRUE,
+  remote    = TRUE,
+  incoming  = TRUE
+)
+devtools::check_rhub(email="wibeasley@hotmail.com")
 # devtools::check_win_devel() #CRAN submission policies encourage the development version
-# devtools::check_rhub(email="wibeasley@hotmail.com")
 # devtools::revdep_check(pkg="codified", recursive=TRUE)
 # devtools::release(check=FALSE) #Careful, the last question ultimately uploads it to CRAN, where you can't delete/reverse your decision.