Fix #262 and other R CMD check issues

DESCRIPTION

@@ -82,7 +82,7 @@ ByteCompile: true
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 SystemRequirements: pandoc (>= 1.18) - http://pandoc.org
 Config/testthat/parallel: true
 Config/testthat/edition: 2

R/chunk-header.R

@@ -81,11 +81,19 @@ chunk_header_contains <- function(header, option){
 #' "needs_trans = TRUE" then the text in `option` will be added with a
 #' preceeding comma and space, at the end of the list of options that is
 #' already present:
-#' ```{r example, eval = !fr()}`
+#'
+#' ```
+#' eval = !fr()
+#' ```
+#'
 #' would become
-#' ```{r example, eval = !fr(), needs_trans = TRUE}`
+#'
+#' ```
+#' eval = !fr(), needs_trans = TRUE
+#' ```
+#'
 #' If `header` is not matched by the regular expression used by knitr for
-#' beginning chunks [knitr::all_patterns$md$chunk.begin] then a
+#' beginning chunks `knitr::all_patterns$md$chunk.begin` then a
 #' warning will be issued and `header` will be returned.
 #' If `option` already exists in `header` and `ovr` is `TRUE`, it will be
 #' overwritten with the new `option` value

R/csasdown.R

@@ -5,11 +5,11 @@
 #' PDF or Word format. The package is based on Chester Ismay's thesisdown
 #' package and Ben Marwick's huskydown package.
 #'
-#' @docType package
 #' @name csasdown
+#' @keywords internal
+"_PACKAGE"
 NULL
 
-# hack because I can't suppress this package data warning!?
 if(getRversion() >= "2.15.1")
   utils::globalVariables(c("region_info", ".x", ".y",
                            "fn", "num_lines", "post_num",

R/set-citations.R

@@ -5,7 +5,6 @@
 #' must have a YAML option called 'french' set to either 'true' or 'false'
 #' @param verbose Logical. If `TRUE`, print messages
 #'
-#' @return
 #' @export
 set_citations <- function(fn = get_index_filename(
   system.file("rmarkdown",
@@ -32,15 +31,15 @@ set_citations <- function(fn = get_index_filename(
 
   if(fr()){
     if(!length(ca_ind)){
-      warning("You are missing the `citation_english:` tag in your YAML file:\n",
+      message("You are missing the `citation_english:` tag in your YAML file:\n",
               fn, ". This citation is required when you build in French as it ",
               "is set to the other language citation on page 2 of ",
               "the document")
       return(invisible())
     }
   }else{
     if(!length(cf_ind)){
-      warning("You are missing the `citation_french:` tag in your YAML file:\n",
+      message("You are missing the `citation_french:` tag in your YAML file:\n",
               fn, ". This citation is required when you build in English as it ",
               "is set to the other language citation on page 2 of ",
               "the document")

inst/rmarkdown/templates/manureport/skeleton/skeleton.Rmd

@@ -37,6 +37,7 @@ french_abstract: |
 # both be absent from all tables. If it is missing or any other value than
 # `false`, it will be assumed to be `true`
 show_continued_text: true
+citation_french: ""
 output:
  csasdown::manureport_pdf:
    french: false

inst/rmarkdown/templates/techreport/skeleton/skeleton.Rmd

@@ -36,6 +36,7 @@ french_abstract: |
 # with `csas_table()` that cross page boundaries. If `false`, these will
 # both be absent from all tables. If it is missing or any other value than
 # `false`, it will be assumed to be `true`
+citation_french: ""
 show_continued_text: true
 output:
  csasdown::techreport_pdf:

tests/testthat/test-fix-envs.R

@@ -19,7 +19,7 @@ test_that("fix_envs() works", {
   en_region_ind <- grep("^\\s*region:", rmd)
   rmd[en_region_ind] <- paste0("region: ", fr_region)
   writeLines(rmd, "index.Rmd")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists("_book/sr-english.pdf"))
   expect_true(file.exists("_book/sr-english.tex"))
   tex <- readLines("_book/sr-english.tex")
@@ -46,7 +46,7 @@ test_that("fix_envs() works", {
   rmd_after <- rmd[(french_abs_ind - 1):length(rmd)]
   rmd <- c(rmd_prev, "abstract:", rmd_after)
   writeLines(rmd, "index.Rmd")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists("_book/resdoc-english.pdf"))
   expect_true(file.exists("_book/resdoc-english.tex"))
 
@@ -72,7 +72,7 @@ test_that("fix_envs() works", {
   prepub_ind <- grep("prepub", rmd)
   rmd[prepub_ind] <- "   prepub: true"
   writeLines(rmd, "index.Rmd")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists("_book/sr-english.pdf"))
   expect_true(file.exists("_book/sr-english.tex"))
 
@@ -115,7 +115,7 @@ test_that("fix_envs() works", {
   ind <- grep("include_section_nums:", rmd)
   rmd[ind] <- "   include_section_nums: false"
   writeLines(rmd, "index.Rmd")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists("_book/resdoc-english.pdf"))
   expect_true(file.exists("_book/resdoc-english.tex"))
 

tests/testthat/test-render-manureport.R

@@ -20,7 +20,7 @@ expect_message(csasdown::check_yaml(type = "manureport", verbose = TRUE),
 test_that("csasdown::render generates the PDF of the manureport", {
   csasdown::set_french(val = FALSE)
   csasdown:::set_render_type(doc_type = "pdf")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists(file.path(testing_path, "_book",
                                     "manureport-english.pdf")))
 })
@@ -30,7 +30,7 @@ test_that("csasdown::render generates the PDF of the manureport", {
 test_that("csasdown::render generates the .docx of the manureport", {
   csasdown::set_french(val = FALSE)
   csasdown:::set_render_type(doc_type = "word")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists(file.path(testing_path, "_book",
                                     "manureport-english.docx")))
 })
@@ -89,7 +89,7 @@ test_that("csasdown::render detects cover page missing", {
   ind <- grep("line_nums_mod:", rmd)
   rmd[ind] <- "   line_nums_mod: 1"
   writeLines(rmd, "index.Rmd")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists(file.path(testing_path, "_book",
                                     "manureport-english.pdf")))
   expect_true(file.exists(file.path(testing_path,

tests/testthat/test-render-techreport.R

@@ -20,7 +20,7 @@ expect_message(csasdown::check_yaml(type = "techreport", verbose = TRUE),
 test_that("csasdown::render generates the PDF of the techreport", {
   csasdown::set_french(val = FALSE)
   csasdown:::set_render_type(doc_type = "pdf")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists(file.path(testing_path, "_book",
                                     "techreport-english.pdf")))
 })
@@ -30,7 +30,7 @@ test_that("csasdown::render generates the PDF of the techreport", {
 test_that("csasdown::render generates the .docx of the techreport", {
   csasdown::set_french(val = FALSE)
   csasdown:::set_render_type(doc_type = "word")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists(file.path(testing_path, "_book",
                                     "techreport-english.docx")))
 })
@@ -102,7 +102,7 @@ test_that("csasdown::render detects cover page missing", {
   ind <- grep("line_nums_mod:", rmd)
   rmd[ind] <- "   line_nums_mod: 1"
   writeLines(rmd, "index.Rmd")
-  csasdown::render()
+  csasdown::render(suppress_warnings = TRUE)
   expect_true(file.exists(file.path(testing_path, "_book",
                                     "techreport-english.pdf")))
   expect_true(file.exists(file.path(testing_path,