Fix remaining check warnings from PEcAn.logger (fixes #2814)

base/logger/DESCRIPTION

@@ -2,11 +2,10 @@ Package: PEcAn.logger
 Title: Logger functions for PEcAn
 Version: 1.7.1
 Date: 2019-09-05
-Authors@R: c(person("Rob","Kooper"),
-             person("Alexey", "Shiklomanov"))
-Author: Rob Kooper, Alexey Shiklomanov
-Maintainer: Alexey Shiklomanov <ashiklom@bu.edu>
+Authors@R: c(person("Rob", "Kooper", role = c("aut", "cre"), email = "kooper@illinois.edu"),
+             person("Alexey", "Shiklomanov", role = c("aut"), email = "ashiklom@bu.edu"))
 Description: Special logger functions for tracking execution status and the environment.
+imports: utils
 Suggests: testthat
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8

base/logger/R/logger.R

@@ -140,11 +140,11 @@ logger.severe <- function(msg, ..., wrap = TRUE) {
 ##' }
 logger.message <- function(level, msg, ..., wrap = TRUE) {
   if (logger.getLevelNumber(level) >= .utils.logger$level) {
-    dump.frames(dumpto = "dump.log")
+    utils::dump.frames(dumpto = "dump.log")
     calls <- names(dump.log)
     calls <- calls[!grepl("^(#[0-9]+: )?(PEcAn\\.logger::)?logger", calls)]
     calls <- calls[!grepl("(severe|error|warn|info|debug)ifnot", calls)]
-    func <- sub("\\(.*", "", tail(calls, 1))
+    func <- sub("\\(.*", "", utils::tail(calls, 1))
     if (length(func) == 0) {
       func <- "console"
     }

base/logger/R/logifnot.R

@@ -18,7 +18,7 @@
 #' warnifnot("I would prefer it if you used lists.", is.list(a), is.list(b))
 #' errorifnot("You should definitely use lists.", is.list(a), is.list(b))
 #' try({
-#'   severeifnot("I absolutely cannot deal with the fact that something is not a list.", is.list(a), is.list(b))
+#'   severeifnot("I cannot deal with the fact that something is not a list.", is.list(a), is.list(b))
 #' })
 #' @export
 severeifnot <- function(msg, ...) {

base/logger/R/print2string.R

@@ -17,6 +17,6 @@
 #' logger.debug("Current status:\n", print2string(df, row.names = FALSE), wrap = FALSE)
 #' @export
 print2string <- function(x, ...) {
-  cout <- capture.output(print(x, ...))
+  cout <- utils::capture.output(print(x, ...))
   paste(cout, collapse = "\n")
 }