Finalize changes

* fix `.lintr` (used a deprecated function)
* fix a few lints
* Call styler on test-codecov.R and test-coveralls.R
* avoid `with_mock()` in test-utils.R

Author: olivroy

.lintr

@@ -1,2 +1,2 @@
-linters: with_defaults(line_length_linter(120))
+linters: linters_with_defaults(line_length_linter(120))
 exclusions: list("inst/doc/how_it_works.R")

R/cobertura.R

@@ -14,7 +14,7 @@
 #' @param cov the coverage object returned from [package_coverage()]
 #' @param filename the name of the Cobertura XML file
 #' @export
-to_cobertura <- function(cov, filename = "cobertura.xml"){
+to_cobertura <- function(cov, filename = "cobertura.xml") {
 
   loadNamespace("xml2")
 
@@ -24,7 +24,7 @@ to_cobertura <- function(cov, filename = "cobertura.xml"){
   percent_per_function <- tapply(df$value, df$functions, FUN = function(x) (sum(x > 0) / length(x)))
   lines_valid <- nrow(df)
   lines_covered <- sum(df$value > 0)
-                                 
+
   d <- xml2::xml_new_document()
 
   xml2::xml_add_child(d, xml2::xml_dtd(
@@ -34,7 +34,7 @@ to_cobertura <- function(cov, filename = "cobertura.xml"){
   top <- xml2::xml_add_child(d,
     "coverage",
     "line-rate" = as.character(percent_overall),
-    "branch-rate" = "0", 
+    "branch-rate" = "0",
     `lines-covered` = as.character(lines_covered),
     `lines-valid` = as.character(lines_valid),
     `branches-covered` = "0",

R/compiled.R

@@ -102,7 +102,7 @@ run_gcov <- function(path, quiet = TRUE, clean = TRUE,
   res <- withr::with_dir(src_path, {
            compact(unlist(lapply(gcov_inputs, run_gcov_one), recursive = FALSE))
          })
-  if (!length(res) & length(gcov_inputs))
+  if (!length(res) && length(gcov_inputs))
     warning('parsed gcov output was empty')
   res
 }

R/covr.R

@@ -369,7 +369,7 @@ package_coverage <- function(path = ".",
                              code = character(),
                              install_path = temp_file("R_LIBS"),
                              ...,
-                             exclusions, pre_clean=TRUE) {
+                             exclusions, pre_clean = TRUE) {
 
   if (!missing(exclusions)) {
     warning(
@@ -423,8 +423,7 @@ package_coverage <- function(path = ".",
   # check for compiler
   if (!uses_icc()) {
     flags <- getOption("covr.flags")
-  }
-  else {
+  } else {
     if (length(getOption("covr.icov")) > 0L) {
       flags <- getOption("covr.icov_flags")
       # clean up old icov files
@@ -672,7 +671,7 @@ clean_coverage_tests <- function(obj) {
   for (i in seq_along(obj)) {
     if (is.null(val <- obj[[i]]$value)) next
     if (is.null(n <- nrow(obj[[i]]$tests$tally)) || n < val) next
-    obj[[i]]$tests$tally <- obj[[i]]$tests$tally[seq_len(val),,drop = FALSE]
+    obj[[i]]$tests$tally <- obj[[i]]$tests$tally[seq_len(val), , drop = FALSE]
   }
 }
 
@@ -709,7 +708,7 @@ merge_coverage_tests <- function(from, into = NULL) {
   # modify trace test tallies
   for (name in intersect(names(into), names(from))) {
     if (name == "tests") next
-    from[[name]]$tests$tally[,1L] <- test_idx[from[[name]]$tests$tally[,1L]]
+    from[[name]]$tests$tally[, 1L] <- test_idx[from[[name]]$tests$tally[, 1L]]
     into[[name]]$tests$tally <- rbind(into[[name]]$tests$tally, from[[name]]$tests$tally)
   }
 

R/icc.R

@@ -54,7 +54,7 @@ parse_icov <- function(lines, package_path = "") {
                     by = list(line=m1$line, functions=m1$functions), sum)
     names(m2) <- c("line", "functions", "coverage")
   }
-  matches <- m2[order(m2$line),]
+  matches <- m2[order(m2$line), ]
 
   values <- as.numeric(matches$coverage > 0L)
   functions <- matches$functions

R/summary_functions.R

@@ -162,7 +162,7 @@ print.coverage <- function(x, group = c("filename", "functions"), by = "line", .
 
   overall_percentage <- percent_coverage(df, by = by)
 
-  cli::cli_inform(paste(
+  cli::cli_inform(paste0(
     cli::style_bold(
       "{attr(x, 'package')$package} {to_title(type)} Coverage: "
     ),
@@ -173,7 +173,7 @@ print.coverage <- function(x, group = c("filename", "functions"), by = "line", .
 
   for (i in seq_along(by_coverage)) {
     cli::cli_inform(
-      paste(
+      paste0(
         cli::style_bold(names(by_coverage)[i], ": "),
         format_percentage(by_coverage[i])
       )

R/trace_calls.R

@@ -31,17 +31,15 @@ trace_calls <- function (x, parent_functions = NULL, parent_ref = NULL) {
   if (is.atomic(x) || is.name(x) || is.null(x)) {
     if (is.null(parent_ref)) {
       x
-    }
-    else {
+    } else {
       if (is_na(x) || is_brace(x)) {
         x
       } else {
         key <- new_counter(parent_ref, parent_functions) # nolint
         count(key, x)
       }
     }
-  }
-  else if (is.call(x)) {
+  } else if (is.call(x)) {
     src_ref <- attr(x, "srcref") %||% impute_srcref(x, parent_ref)
     if ((identical(x[[1]], as.name("<-")) || identical(x[[1]], as.name("="))) && # nolint
       (is.call(x[[3]]) && identical(x[[3]][[1]], as.name("function")))) {
@@ -59,8 +57,7 @@ trace_calls <- function (x, parent_functions = NULL, parent_ref = NULL) {
     } else {
       as.call(recurse(x))
     }
-  }
-  else if (is.function(x)) {
+  } else if (is.function(x)) {
 
     # We cannot trace primitive functions
     if (is.primitive(x)) {
@@ -83,17 +80,13 @@ trace_calls <- function (x, parent_functions = NULL, parent_ref = NULL) {
     formals(x) <- new_formals
     body(x) <- fun_body
     x
-  }
-  else if (is.pairlist(x)) {
+  } else if (is.pairlist(x)) {
     as.pairlist(recurse(x))
-  }
-  else if (is.expression(x)) {
+  } else if (is.expression(x)) {
     as.expression(recurse(x))
-  }
-  else if (is.list(x)) {
+  } else if (is.list(x)) {
     recurse(x)
-  }
-  else {
+  } else {
     message("Unknown language class: ", paste(class(x), collapse = "/"))
     x
   }

R/trace_tests.R

@@ -127,7 +127,7 @@ count_test <- function(key) {
   tests$.data[[4L]] <- .current_test$i
 
   tests$.value <- .counters[[key]]$value
-  with(tests, tally[.value,] <- .data)
+  with(tests, tally[.value, ] <- .data)
 }
 
 #' Initialize a new test counter for a coverage trace
@@ -339,9 +339,9 @@ truncate_call <- function(call_obj, limit = 1e4) {
 #'
 is_current_test_finished <- function() {
   is.null(.current_test$src) ||
-  .current_test$last_frame > sys.nframe() ||
-  !identical(.current_test$src_call, sys.call(which = .current_test$last_frame)) ||
-  !identical(.current_test$src_env, sys.frame(which = .current_test$last_frame - 1L))
+    .current_test$last_frame > sys.nframe() ||
+    !identical(.current_test$src_call, sys.call(which = .current_test$last_frame)) ||
+    !identical(.current_test$src_env, sys.frame(which = .current_test$last_frame - 1L))
 }
 
 #' Is the source bound to the expression