Removing call from function errors

R/autoplot.R

@@ -147,7 +147,7 @@ autoplot.design <- function(object, rotation = 0, size = 4, margin = FALSE, pale
         colour_palette <- scales::viridis_pal(option = palette)(ntrt)
     }
     else {
-        stop("Invalid value for palette.")
+        stop("Invalid value for palette.", call. = FALSE)
     }
 
     hcl <- farver::decode_colour(colour_palette, "rgb", "hcl")

R/create_buffers.R

@@ -81,7 +81,7 @@ create_buffers <- function(design, type, blocks = FALSE) {
     }
     # Match block, blocks, or b
     else if(grepl("(^blocks?$|^b$)", tolower(type))) {
-        stop("Block buffers are not yet supported.")
+        stop("Block buffers are not yet supported.", call. = FALSE)
     }
     else {
         stop("Invalid buffer option: ", type, call. = FALSE)

R/des_info.R

@@ -105,11 +105,11 @@ des_info <- function(design.obj,
 
     # Check brows and bcols supplied if necessary
     if(design.obj$parameters$design == "rcbd" & anyNA(c(brows, bcols))) {
-        stop("Design has blocks so brows and bcols must be supplied.")
+        stop("Design has blocks so brows and bcols must be supplied.", call. = FALSE)
     }
     else if(design.obj$parameters$design == "factorial") {
         if(design.obj$parameters$applied == "rcbd" & anyNA(c(brows, bcols))) {
-            stop("Design has blocks so brows and bcols must be supplied.")
+            stop("Design has blocks so brows and bcols must be supplied.", call. = FALSE)
         }
 
         # If factorial design, and names are supplied, use them
@@ -160,7 +160,7 @@ des_info <- function(design.obj,
     }
     else if(design.obj$parameters$design == "split") {
         if(design.obj$parameters$applied == "rcbd" & anyNA(c(brows, bcols))) {
-            stop("Design has blocks so brows and bcols must be supplied.")
+            stop("Design has blocks so brows and bcols must be supplied.", call. = FALSE)
         }
 
         # If names are supplied, use them
@@ -556,7 +556,7 @@ des_info <- function(design.obj,
             # Do nothing
         }
         else {
-            stop("save must be one of 'none'/FALSE, 'both'/TRUE, 'plot', or 'workbook'.")
+            stop("save must be one of 'none'/FALSE, 'both'/TRUE, 'plot', or 'workbook'.", call. = FALSE)
         }
     }
     else if(save) {

R/design.R

@@ -104,19 +104,19 @@ design <- function(type,
 
     # Some error checking of inputs before creating design
     if(!is.na(brows) & brows > nrows) {
-        stop("brows must not be larger than nrows")
+        stop("brows must not be larger than nrows", call. = FALSE)
     }
 
     if(!is.na(bcols) & bcols > ncols) {
-        stop("bcols must not be larger than ncols")
+        stop("bcols must not be larger than ncols", call. = FALSE)
     }
 
     if(!is.numeric(size)) {
-        stop("size must be numeric")
+        stop("size must be numeric", call. = FALSE)
     }
 
     if((!is.logical(seed) | is.na(seed)) & !is.numeric(seed)) {
-        stop("seed must be numeric or TRUE/FALSE")
+        stop("seed must be numeric or TRUE/FALSE", call. = FALSE)
     }
 
     dim <- nrows*ncols
@@ -149,7 +149,7 @@ design <- function(type,
 
     else if(tolower(type) == "split") {
         if(is.null(sub_treatments) | anyNA(sub_treatments)) {
-            stop("sub_treatments are required for a split plot design")
+            stop("sub_treatments are required for a split plot design", call. = FALSE)
         }
         trs <- length(treatments)*length(sub_treatments)*reps
         outdesign <- agricolae::design.split(trt1 = treatments,
@@ -163,11 +163,11 @@ design <- function(type,
         savename <- gsub(":", "_", savename)
 
         if(type_split[2] %!in% c("crd", "rcbd", "lsd")) {
-            stop("Crossed designs of type '", type_split[2], "' are not supported")
+            stop("Crossed designs of type '", type_split[2], "' are not supported", call. = FALSE)
         }
 
         if(length(treatments) > 3) {
-            stop("Crossed designs with more than three treatment factors are not supported")
+            stop("Crossed designs with more than three treatment factors are not supported", call. = FALSE)
         }
         trs <- ifelse(tolower(type_split[2])=="lsd", prod(treatments)^2, prod(treatments)*reps)
 
@@ -178,15 +178,15 @@ design <- function(type,
     }
 
     else {
-        stop("Designs of type '", type, "' are not supported")
+        stop("Designs of type '", type, "' are not supported", call. = FALSE)
     }
 
     if(dim > trs) {
-        warning("Area provided is larger than treatments applied. Please check inputs.")
+        warning("Area provided is larger than treatments applied. Please check inputs.", call. = FALSE)
     }
 
     if(dim < trs) {
-        warning("Area provided is smaller than treatments applied. Please check inputs.")
+        warning("Area provided is smaller than treatments applied. Please check inputs.", call. = FALSE)
     }
 
     output <- des_info(design.obj = outdesign, nrows = nrows, ncols = ncols,

R/install_asreml.R

@@ -298,7 +298,7 @@ create_mac_folder <- function() {
             else {
                 stop("ASReml-R cannot be installed until the folder '/Library/Application Support/Reprise' is created with appropriate permissions.
                          Please run the following command on your terminal:
-                         sudo -S mkdir '/Library/Application Support/Reprise' && sudo -S chmod 777 '/Library/Application Support/Reprise'")
+                         sudo -S mkdir '/Library/Application Support/Reprise' && sudo -S chmod 777 '/Library/Application Support/Reprise'", call. = FALSE)
             }
         }
     }

R/logltest.R

@@ -35,11 +35,11 @@
 logl_test <- function(model.obj, rand.terms = NULL, resid.terms = NULL, decimals = 3, numeric = FALSE, quiet = FALSE) {
 
     if(!inherits(model.obj, "asreml")){
-        stop("Only asreml models are supported at this time.")
+        stop("Only asreml models are supported at this time.", call. = FALSE)
     }
 
     if(is.null(rand.terms) & is.null(resid.terms)) {
-        stop("One of rand.terms or resid.terms must be provided.")
+        stop("One of rand.terms or resid.terms must be provided.", call. = FALSE)
     }
 
     # Find terms on the boundary

R/mct.R

@@ -146,7 +146,7 @@ multiple_comparisons <- function(model.obj,
     reserved_col_names <- c("predicted.value", "std.error", "Df",
                             "groups", "PredictedValue", "ApproxSE", "ci", "low", "up")
     if(any(vars %in% reserved_col_names)) {
-        stop("Invalid column name. Please change the name of column(s): ", vars[vars %in% reserved_col_names])
+        stop("Invalid column name. Please change the name of column(s): ", vars[vars %in% reserved_col_names], call. = FALSE)
     }
 
     if(inherits(model.obj, "asreml")){
@@ -157,13 +157,13 @@ multiple_comparisons <- function(model.obj,
         }
 
         if(!missing(pred.obj)) {
-            warning("Argument `pred.obj` has been deprecated and will be removed in a future version. Predictions are now performed internally in the function.")
+            warning("Argument `pred.obj` has been deprecated and will be removed in a future version. Predictions are now performed internally in the function.", call. = FALSE)
         }
 
         pred.obj <- quiet(asreml::predict.asreml(model.obj, classify = classify, sed = TRUE, trace = FALSE, ...))
         # Check if all the predicted values are NA. If so, suggests the need of the `present` argument
         if(all(is.na(pred.obj$pvals$predicted.value)) & all(is.na(pred.obj$pvals$std.error))) {
-            stop("All predicted values are aliased. Perhaps you need the `present` argument?")
+            stop("All predicted values are aliased. Perhaps you need the `present` argument?", call. = FALSE)
         }
 
         # Check if any treatments are aliased, and remove them and print a warning
@@ -282,7 +282,7 @@ multiple_comparisons <- function(model.obj,
     }
 
     else {
-        stop("Models of type ", class(model.obj), " are not supported.")
+        stop("Models of type ", class(model.obj), " are not supported.", call. = FALSE)
     }
 
     # Check that the predicted levels don't contain a dash -, if they do replace and display warning

R/resplot.R

@@ -82,7 +82,7 @@ resplot <- function(model.obj, shapiro = TRUE, call = FALSE, label.size = 10, ax
         }
     }
     else {
-        stop("model.obj must be a linear (mixed) model object. Currently supported model types are: aov, lm, lmerMod, lmerModLmerTest, asreml, mmer or art")
+        stop("model.obj must be a linear (mixed) model object. Currently supported model types are: aov, lm, lmerMod, lmerModLmerTest, asreml, mmer or art", call. = FALSE)
     }
 
     aa <- data.frame(residuals = resids, fitted = fits, lvl = rep(1:facet, k))

R/variogram.r

@@ -36,11 +36,11 @@
 variogram <- function(model.obj, row = NA, column = NA, horizontal = TRUE, palette = "default") {
 
     if(!(inherits(model.obj, "asreml"))) {
-        stop("model.obj must be an asreml model object")
+        stop("model.obj must be an asreml model object", call. = FALSE)
     }
 
     if(attr(model.obj$formulae$residual,"term.labels") == "units") {
-        stop("Residual term must include spatial component.")
+        stop("Residual term must include spatial component.", call. = FALSE)
     }
 
     vario_points <- vario_df(model.obj, row, column)
@@ -146,7 +146,7 @@ variogram <- function(model.obj, row = NA, column = NA, horizontal = TRUE, palet
                                     col.regions = scales::brewer_pal(palette = palette)(11))
         }
         else {
-            stop("Invalid value for palette.")
+            stop("Invalid value for palette.", call. = FALSE)
         }
         output[[i]] <- cowplot::plot_grid(b, a, nrow = 2, scale = c(2, 1))
         if(!orig_row) {