use rlang for errors

Author: dcangst

R/accFunctions.R

@@ -23,7 +23,7 @@
 #' @family internal
 .binToDec <- function(x){
   if (length(x[x > 1]) > 0){
-    stop("not a binary number")
+    rlang::abort("not a binary number")
   }
   power <- 2 ^ (rev(seq_along(x)) - 1)
   return(sum(x * power))
@@ -142,11 +142,11 @@ wellsFromANSII <- function(wellSelection){
   } else if (length(volumes) == 8){
     # check for mismatch between selected tips and supplied volumes
     if (sum(tipMask * volumes - volumes) < 0){
-      stop("tipMask / volumes mismatch!")
+      rlang::abort("tipMask / volumes mismatch!")
     }
     volumes12 <- c(volumes, rep(0, 4))
   } else {
-    stop("volumes vector not of length 8 (or 1)")
+    rlang::abort("volumes vector not of length 8 (or 1)")
   }
 
   volumes_str <- vector("character", 12L)
@@ -170,11 +170,11 @@ getGridSite <- function(RackLabel){
     site <- RackLabel_wt$site
   } else if (dim(RackLabel_wt)[1] < 1){
     print(gwl$worktable$worktable)
-    stop(paste0("Racklabel: "), RackLabel,
+    rlang::abort(paste0("Racklabel: "), RackLabel,
       " not defined. Define Racklabels using addToWorktable() or manually @ gwl$worktable")
   } else if (dim(RackLabel_wt)[1] > 1){
     print(gwl$worktable$worktable)
-    stop("Duplicate RackLabels? check worktable")
+    rlang::abort("Duplicate RackLabels? check worktable")
   }
   return(list(site = site, grid = grid))
 }

R/advGwlFunctions.R

@@ -468,7 +468,7 @@ moveMCA <- function(
       as.vector(matrix(1:384, 24, 16)[c(T, F), c(F, T)]),
       as.vector(matrix(1:384, 24, 16)[c(F, T), c(F, T)]))
   } else {
-    stop("must target a 96 or a 384well plate!")
+    rlang::abort("must target a 96 or a 384well plate!")
   }
   wellSelection_string <- ANSIIFromWells(wellSelection, ncol, nrow)
   GridSite <- getGridSite(RackLabel)
@@ -531,7 +531,7 @@ MCAvector <- function(
   CMadd_warning <- ""
 
   if (site == 0){
-    stop("MCAVector Sites start with 1 (from the back)!!!!")
+    rlang::abort("MCAVector Sites start with 1 (from the back)!!!!")
   }
 
   MCAVector_command <- str_c(

R/base.R

@@ -183,12 +183,12 @@ addToWorktable <- function(RackLabel = "",
       subset(worktable, RackLabel == labware_add$RackLabel[i]))[1]
 
     if (RackLabel_defined == 1){
-      stop("RackLabel already defined")
+      rlang::abort("RackLabel already defined")
     } else {
       gridSiteCheck <-
         worktable[worktable$grid == grid & worktable$site == site, ]
       if (dim(gridSiteCheck)[1] == 1){
-        stop(paste0("Grid/Site allready occupied by ", gridSiteCheck$RackLabel))
+        rlang::abort(paste0("Grid/Site allready occupied by ", gridSiteCheck$RackLabel))
       }
       worktable <- rbind(worktable, labware_add[i, ])
     }

R/pickoloFunctions.R

@@ -91,7 +91,7 @@ readColonies <- function(csv_path,
 
   growth <- unique(growth)
   if (dim(growth)[1] != n_row * n_col) {
-    stop("Data set not complete")
+    rlang::abort("Data set not complete")
   }
 
   output <- list(