avoid explicit magrittr import

Author: infotroph

docker/depends/pecan_package_dependencies.csv

@@ -180,7 +180,6 @@
 "magrittr","*","base/db","Imports",FALSE
 "magrittr","*","base/utils","Imports",FALSE
 "magrittr","*","models/ed","Imports",FALSE
-"magrittr","*","modules/assim.sequential","Imports",FALSE
 "magrittr","*","modules/benchmark","Imports",FALSE
 "magrittr","*","modules/data.land","Imports",FALSE
 "magrittr","*","modules/data.remote","Imports",FALSE

modules/assim.sequential/DESCRIPTION

@@ -19,7 +19,6 @@ Imports:
     future,
     ggplot2,
     lubridate (>= 1.6.0),
-    magrittr,
     Matrix,
     ncdf4,
     nimble,

modules/assim.sequential/NAMESPACE

@@ -71,5 +71,4 @@ import(nimble)
 importFrom(dplyr,"%>%")
 importFrom(foreach,"%dopar%")
 importFrom(lubridate,"%m+%")
-importFrom(magrittr,"%>%")
 importFrom(rlang,.data)

modules/assim.sequential/R/Helper.functions.R

@@ -7,7 +7,7 @@
 #' @return A list the same dimension as X, with each column of each dataframe
 #'   modified by replacing outlier points with the column median
 #' @export
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #'
 outlier.detector.boxplot<-function(X) {
   X <- X  %>% 
@@ -86,7 +86,7 @@ SDA_control <-
 #' @description This function uses a set of scaling factors defined in the pecan XML to scale a given matrix
 #' @return rescaled Matrix
 #' @export
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 rescaling_stateVars <- function(settings, X, multiply=TRUE) {
 
   FUN <- ifelse(multiply, .Primitive('*'), .Primitive('/'))

modules/assim.sequential/R/Prep_OBS_SDA.R

@@ -7,7 +7,7 @@
 #'
 #' @return mean and covariance of observations
 #'
-#' @importFrom magrittr %>%
+#' @importFrom dplyr %>%
 #' @export
 #'
 Prep_OBS_SDA <- function(settings, out_dir, AGB_dir, Search_Window=30){

modules/assim.sequential/tests/Rcheck_reference.log

@@ -8,11 +8,7 @@
 * this is package ‘PEcAnAssimSequential’ version ‘1.7.2’
 * package encoding: UTF-8
 * checking package namespace information ... OK
-* checking package dependencies ... NOTE
-Imports includes 21 non-default packages.
-Importing from so many packages makes the package vulnerable to any of
-them becoming unavailable. Move as many as possible to Suggests and
-use conditionally.
+* checking package dependencies ... OK
 * checking if this is a source package ... OK
 * checking if there is a namespace ... OK
 * checking for executable files ... OK