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

base/logger/DESCRIPTION

@@ -1,15 +1,19 @@
 Package: PEcAn.logger
-Title: Logger functions for PEcAn
+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"),
+             person("Shashank", "Singh", role = c("aut"),
+                email = "shashanksingh819@gmail.com"),
+             person("Chris", "Black", role = c("ctb")))
 Description: Special logger functions for tracking execution status and the environment.
+BugReports: https://github.com/PecanProject/pecan/issues
+Imports: utils
 Suggests: testthat
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
-LazyData: true
 RoxygenNote: 7.0.2
 Roxygen: list(markdown = TRUE)

base/logger/NEWS.md

@@ -0,0 +1,9 @@
+# PEcAn.logger 1.7.1.9000
+## Fixed
+
+* Logger calls no longer create a stray `dump.log` object in the global environment
+
+#PEcAn.logger 1.7.1
+
+* All changes in 1.7.1 and earlier were recorded in a single file for all of the PEcAn packages; please see 
+https://github.com/PecanProject/pecan/blob/v1.7.1/CHANGELOG.md for details.

base/logger/R/logger.R

@@ -88,9 +88,9 @@ logger.error <- function(msg, ...) {
 ##' Prints an severe message and stops execution.
 ##' 
 ##' This function will print a message and stop execution of the code. This
-##' should only be used if the application should terminate. 
+##' should only be used if the application should terminate.
 ##' 
-##' set \code{\link{logger.setQuitOnSevere(FALSE)}}. To avoid terminating
+##' set \code{\link{logger.setQuitOnSevere}(FALSE)} to avoid terminating
 ##' the session. This is set by default to TRUE if interactive or running
 ##' inside Rstudio.
 ##'
@@ -140,11 +140,10 @@ 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")
-    calls <- names(dump.log)
+    calls <- utils::limitedLabels(sys.calls())
     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"
     }
@@ -191,18 +190,15 @@ logger.setLevel <- function(level) {
 } # logger.setLevel
 
 
-##' Returns numeric value for string
-##'
-##' Given the string representation this will return the numeric value
-##' ALL   =  0
-##' DEBUG = 10
-##' INFO  = 20
-##' WARN  = 30
-##' ERROR = 40
-##' ALL   = 99
-##'
-##' @return level the level of the message
-##' @author Rob Kooper
+## Given the string representation this will return the numeric value
+## DEBUG = 10
+## INFO  = 20
+## WARN  = 30
+## ERROR = 40
+## ALL   = 99
+##
+##@return level the level of the message
+##@author Rob Kooper
 logger.getLevelNumber <- function(level) {
   if (toupper(level) == "ALL") {
     return(0)

base/logger/R/logifnot.R

@@ -1,14 +1,14 @@
 #' Logger message if conditions are not met
 #'
-#' Similar to [base::stopifnot], but allows you to use a custom message and 
+#' Similar to [base::stopifnot], but allows you to use a custom message and
 #' logger level. If all conditions are `TRUE`, silently exit.
 #'
-#' Conditions can be vectorized, or can return non-logical values.The 
-#' underlying function automatically applies `isTRUE(all(.))` to the 
+#' Conditions can be vectorized, or can return non-logical values.The
+#' underlying function automatically applies `isTRUE(all(.))` to the
 #' conditions.
 #'
 #' @param msg Logger message to write, as a single character string.
-#' @param ... Conditions to evaluate 
+#' @param ... Conditions to evaluate
 #' @return Invisibly, `TRUE` if conditions are met, `FALSE` otherwise
 #' @examples
 #' a <- 1:5
@@ -18,7 +18,9 @@
 #' 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, ...) {
@@ -73,14 +75,14 @@ debugifnot <- function(msg, ...) {
   }
 }
 
-#' Check a list of conditions
+# Check a list of conditions
 check_conditions <- function(...) {
   dots <- list(...)
   conditions <- vapply(dots, is_definitely_true, logical(1))
   all(conditions)
 }
 
-#' Robust logical check
+# Robust logical check
 is_definitely_true <- function(x) {
   if (is.null(x) || length(x) == 0 || !is.logical(x)) {
     return(FALSE)

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")
 }