fix: Adds add = TRUE, after = FALSE to on.exit()

as recommended by https://testthat.r-lib.org/articles/test-fixtures.html
pfmc-assessments · Jul 3, 2023 · 560769a · 560769a
1 parent b2c3422
commit 560769a
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Showing 7 changed files with 12 additions and 12 deletions.
diff --git a/R/EF1_Denominator.R b/R/EF1_Denominator.R
@@ -182,7 +182,7 @@ EF1_Denominator <- function(Pdata,
       plot <- file.path(savedir, "PacFIN_exp1_denom.png")
       plot2 <- file.path(savedir, "PacFIN_WL.png")
       grDevices::png(plot)
-      on.exit(grDevices::dev.off(), add = TRUE)
+      on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
     }
     graphics::par(mfrow = c(1, ifelse(nNA > 0, 2, 1)), mgp = c(2.5, 0.5, 0))
     graphics::boxplot(

diff --git a/R/age_representativeness_plot.R b/R/age_representativeness_plot.R
@@ -39,7 +39,7 @@ age_representativeness_plot <- function(bio,
                                         plot_panels = c(10, 2),
                                         wait2plot = FALSE) {
   if (!is.null(file)) {
-    on.exit(grDevices::dev.off(), add = TRUE)
+    on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
   }
   if (!is.null(file)) wait2plot <- FALSE
 

diff --git a/R/cleanPacFIN.R b/R/cleanPacFIN.R
@@ -195,7 +195,7 @@ cleanPacFIN <- function(Pdata,
   Pdata$year <- Pdata$SAMPLE_YEAR
   if (!missing(savedir)) {
     grDevices::png(filename = file.path(savedir, "PacFIN_comp_season.png"))
-    on.exit(grDevices::dev.off(), add = TRUE)
+    on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
   }
   Pdata <- getSeason(Pdata, verbose = verbose,
     plotResults = !missing(savedir))

diff --git a/R/doSexRatio.R b/R/doSexRatio.R
@@ -142,7 +142,7 @@ doSexRatio <- function(CompData,
   if (!missing(savedir)) {
     find = which(CompData$usamps > 0 )
     grDevices::png(file.path(savedir, "Applied_Sex_Ratio_to_Unsexed_Fish.png"))
-      on.exit(grDevices::dev.off(), add = TRUE)
+      on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
       plot(CompData[find,'lengthcm'], CompData[find, 'sexRatio'],
         xlab = "Length (cm)", ylab = "Sex Ratio",
         main = paste0("Sex Ratio Applied to Unsexed Fish (N = ", sum(CompData$usamps), ")" )

diff --git a/R/getDB.R b/R/getDB.R
@@ -76,7 +76,7 @@ getDB <- function(sql,
     uid = username,
     pw = password
   )
-  on.exit(RODBC::odbcClose(database))
+  on.exit(RODBC::odbcClose(database), add = TRUE, after = FALSE)
   out <- tryCatch(
     RODBC::sqlQuery(database, sql, as.is = asis),
     error = function(e) e

diff --git a/R/getExpansion_2.R b/R/getExpansion_2.R
@@ -210,7 +210,7 @@ getExpansion_2 <- function(Pdata,
     NA_EF2[, "FREQ"] <- 1
     if (!missing(savedir)) {
       grDevices::png(file.path(savedir, "PacFIN_exp2_NAreplace.png"))
-      on.exit(grDevices::dev.off(), add = TRUE)
+      on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
       graphics::barplot(
         stats::xtabs(NA_EF2$FREQ ~ NA_EF2$state + NA_EF2$fishyr),
         col = grDevices::rainbow(3),
@@ -223,7 +223,7 @@ getExpansion_2 <- function(Pdata,
 
   if (!missing(savedir)) {
     grDevices::png(file.path(savedir, "PacFIN_exp2_summarybyyear.png"))
-    on.exit(grDevices::dev.off(), add = TRUE)
+    on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
     graphics::boxplot(Pdata$Expansion_Factor_2 ~ Pdata$fishyr,
       main = "", xlab = "Year", ylab = "Second-stage expansion factor")
   }

diff --git a/R/plotCleaned.R b/R/plotCleaned.R
@@ -36,7 +36,7 @@ plotCleaned <- function (Pdata,
 
   #### Plot
   grDevices::png(file.path(savedir, "PacFIN_comp_Nbystate.png"))
-  on.exit(grDevices::dev.off(), add = TRUE)
+  on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
   graphics::par(mfrow = c(2, 1),
     oma = c(1, 1, 3, 0.25), mar = c(0.5, 3.25, 0, 0),
     mgp = c(1.5, 0.5, 0))
@@ -52,7 +52,7 @@ plotCleaned <- function (Pdata,
     args.legend = list(x = "topleft", bty = "n"))
 
   grDevices::png(file.path(savedir, "PacFIN_comp_distributions.png"))
-  on.exit(grDevices::dev.off(), add = TRUE)
+  on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
   graphics::par(mfrow = c(2, 1),
     oma = c(1, 1, 3, 0.25), mar = c(0.5, 3.25, 0, 0),
     mgp = c(1.5, 0.5, 0))
@@ -64,7 +64,7 @@ plotCleaned <- function (Pdata,
     frame.plot = TRUE, ylim = c(0, max(Pdata$Age, na.rm = TRUE)))
 
   grDevices::png(file.path(savedir, "PacFIN_comp_NbyGRID.png"))
-  on.exit(grDevices::dev.off(), add = TRUE)
+  on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
   graphics::par(mfrow = c(2, 1),
     oma = c(1, 1, 3, 0.25), mar = c(0.5, 3.25, 0, 0),
     mgp = c(1.5, 0.5, 0))
@@ -82,14 +82,14 @@ plotCleaned <- function (Pdata,
 
   if (!all(is.na(Pdata[, "DEPTH_AVG"]))) {
     grDevices::png(file.path(savedir, "PacFIN_comp_depth.png"))
-    on.exit(grDevices::dev.off(), add = TRUE)
+    on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
     graphics::boxplot(Pdata$DEPTH_AVG ~ Pdata$fishyr, ylab = expression(bar(Depth)),
       frame.plot = FALSE, ylim = c(0, max(Pdata$DEPTH_AVG, na.rm = TRUE)))
   }
 
   if (geargroups) {
     grDevices::png(file.path(savedir, "PacFIN_comp_geargroup.png"))
-    on.exit(grDevices::dev.off(), add = TRUE)
+    on.exit(grDevices::dev.off(), add = TRUE, after = FALSE)
     graphics::par(mfrow = c(2, 1),
       oma = c(1, 1, 3, 0.25), mar = c(0.5, 3.25, 0, 0),
       mgp = c(1.5, 0.5, 0))