Fix tests and examples

.github/workflows/R-CMD-check.yaml

@@ -26,23 +26,24 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+      NOT_CRAN: "true"
 
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@e0a5ffdf0b121aa1c2112f65e54b642a81dc29d9
 
-      - uses: r-lib/actions/setup-r@756399d909bf9c180bbdafe8025f794f51f2da02
+      - uses: r-lib/actions/setup-r@12d8dd416fec5aaa60f2f54609b713b2ec031a94
         with:
           r-version: ${{ matrix.config.r }}
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r-dependencies@813ef1cb62cf0b4b51a044419024c37807fa8095
         with:
           extra-packages: any::rcmdcheck
           needs: check
 
-      - uses: r-lib/actions/check-r-package@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/check-r-package@15dc53465b2f37cf7fc85ed97ae3e28f8e210955
         with:
           upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -31,13 +31,13 @@ jobs:
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@e0a5ffdf0b121aa1c2112f65e54b642a81dc29d9
 
-      - uses: r-lib/actions/setup-r@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r@12d8dd416fec5aaa60f2f54609b713b2ec031a94
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-r-dependencies@813ef1cb62cf0b4b51a044419024c37807fa8095
         with:
           extra-packages: any::pkgdown, local::.
           needs: website
@@ -48,7 +48,7 @@ jobs:
           file.copy(from = "./public/articles/logo.png",to = "./public/reference/logo.png")
         shell: Rscript {0}
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@64bcae551a7b18bcb9a09042ddf1960979799187
+        uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b
         with:
           path: ./public
   # Deployment job

.github/workflows/test-coverage.yaml

@@ -11,14 +11,15 @@ name: test-coverage
 jobs:
   test-coverage:
     runs-on: macOS-latest
+    env: NOT_CRAN: "true"
     steps:
       - uses: actions/checkout@c0a81a463886bb75afe234e07a9fd5bb79219196
 
-      - uses: r-lib/actions/setup-r@756399d909bf9c180bbdafe8025f794f51f2da02
+      - uses: r-lib/actions/setup-r@12d8dd416fec5aaa60f2f54609b713b2ec031a94
 
-      - uses: r-lib/actions/setup-pandoc@52330cc136b963487918a8867f948ddf954e9e63
+      - uses: r-lib/actions/setup-pandoc@e0a5ffdf0b121aa1c2112f65e54b642a81dc29d9
 
-      - uses: r-lib/actions/setup-r-dependencies@756399d909bf9c180bbdafe8025f794f51f2da02
+      - uses: r-lib/actions/setup-r-dependencies@813ef1cb62cf0b4b51a044419024c37807fa8095
         with:
           extra-packages: any::rcmdcheck
           needs: check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: toxEval
 Type: Package
 Title: Exploring Biological Relevance of Environmental Chemistry Observations
-Version: 1.4.0
+Version: 1.4.1
 Authors@R: c(person("Laura", "DeCicco", 
                      role = c("aut","cre"),
                      email = "[email protected]",
@@ -47,7 +47,8 @@ Imports:
     readxl,
     tools,
     shinyAce,
-    shinycssloaders
+    shinycssloaders,
+    utils
 Suggests:
     rmarkdown,
     testthat,
@@ -60,4 +61,4 @@ BugReports: https://github.com/DOI-USGS/toxEval/issues
 VignetteBuilder: knitr
 BuildVignettes: true
 LazyLoad: yes
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS

@@ -1,3 +1,7 @@
+toxEval 1.4.1
+===========
+* Fixed a test breaking due to ggplot2 update.
+
 toxEval 1.4.0
 ===========
 * Switched to version 4.1 of the ToxCast database

R/plot_chemical_boxplots.R

@@ -242,18 +242,31 @@ plot_chemical_boxplots <- function(chemical_summary, ...,
     )
 
   if (isTRUE(y_label == "")) {
-    toxPlot_All <- toxPlot_All +
-      scale_y_log10(
-        labels = fancyNumbers,
-        breaks = pretty_logs_new
-      ) +
-      theme(axis.title.x = element_blank())
+    if(utils::packageVersion("ggplot2") == "4.0.0"){
+      toxPlot_All <- toxPlot_All +
+        scale_y_log10() +
+        theme(axis.title.x = element_blank())       
+    } else {
+      toxPlot_All <- toxPlot_All +
+        scale_y_log10(
+          labels = fancyNumbers,
+          breaks = pretty_logs_new
+        ) +
+        theme(axis.title.x = element_blank())   
+    }
+
   } else {
-    toxPlot_All <- toxPlot_All +
-      scale_y_log10(y_label,
-        labels = fancyNumbers,
-        breaks = pretty_logs_new
-      )
+    if(utils::packageVersion("ggplot2") == "4.0.0"){
+      toxPlot_All <- toxPlot_All +
+        scale_y_log10(y_label)        
+    } else {
+      toxPlot_All <- toxPlot_All +
+        scale_y_log10(
+          y_label,
+          labels = fancyNumbers,
+          breaks = pretty_logs_new
+        )  
+    }
   }
 
   if (all(is.na(palette))) {

R/plot_group_boxplots.R

@@ -47,7 +47,7 @@
 #' @export
 #' @rdname plot_tox_boxplots
 #' @import ggplot2
-#' @examples
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # This is the example workflow:
 #' path_to_tox <- system.file("extdata", package = "toxEval")
 #' file_name <- "OWC_data_fromSup.xlsx"
@@ -61,9 +61,10 @@
 #' cleaned_ep <- clean_endPoint_info(end_point_info)
 #' filtered_ep <- filter_groups(cleaned_ep)
 #' chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)
+#' \donttest{
 #' plot_tox_boxplots(chemical_summary, "Biological")
 #' 
-#' \donttest{
+#' 
 #' plot_tox_boxplots(chemical_summary, "Chemical Class")
 #' plot_tox_boxplots(chemical_summary, "Chemical")
 #'
@@ -283,18 +284,33 @@ plot_tox_boxplots <- function(chemical_summary,
     }
 
     if (isTRUE(y_label == "")) {
-      bioPlot <- bioPlot +
-        scale_y_log10(
-          labels = fancyNumbers,
-          breaks = pretty_logs_new
-        ) +
-        theme(axis.title.x = element_blank())
+      if(utils::packageVersion("ggplot2") == "4.0.0"){
+        bioPlot <- bioPlot +
+          scale_y_log10() +
+          theme(axis.title.x = element_blank())        
+      } else {
+
+        bioPlot <- bioPlot +
+          scale_y_log10(
+            labels = fancyNumbers,
+            breaks = pretty_logs_new
+          ) +
+          theme(axis.title.x = element_blank())        
+      }
+
     } else {
-      bioPlot <- bioPlot +
-        scale_y_log10(y_label,
-          labels = fancyNumbers,
-          breaks = pretty_logs_new
-        )
+      if(utils::packageVersion("ggplot2") == "4.0.0"){
+        bioPlot <- bioPlot +
+          scale_y_log10(y_label)        
+      } else {
+        bioPlot <- bioPlot +
+          scale_y_log10(
+            y_label,
+            labels = fancyNumbers,
+            breaks = pretty_logs_new
+          ) 
+      }
+
     }
 
     bioPlot <- bioPlot +
@@ -346,7 +362,7 @@ plot_tox_boxplots <- function(chemical_summary,
           theme(plot.title = element_text(size = font_size, margin = margin(b = 5)))
       } else {
         bioPlot_w_labels <- bioPlot_w_labels +
-          theme(plot.title = element_text(size = font_size, margin = margin(b = 5)))
+          theme(plot.title = element_text(margin = margin(b = 5)))
       }
     }
 

R/plot_tox_endpoints.R

@@ -35,7 +35,7 @@
 #' endpoints will be included.
 #' @export
 #' @import ggplot2
-#' @examples
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' # This is the example workflow:
 #' path_to_tox <- system.file("extdata", package = "toxEval")
 #' file_name <- "OWC_data_fromSup.xlsx"
@@ -50,11 +50,13 @@
 #' filtered_ep <- filter_groups(cleaned_ep)
 #' chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)
 #'
+#' \donttest{
+#'
 #' plot_tox_endpoints(chemical_summary,
 #'   filterBy = "Cell Cycle",
 #'   top_num = 10
 #' )
-#' \donttest{
+#' 
 #' plot_tox_endpoints(chemical_summary,
 #'   filterBy = "Cell Cycle",
 #'   top_num = 10,
@@ -261,18 +263,30 @@ plot_tox_endpoints <- function(chemical_summary,
     }
   }
   if (isTRUE(y_label == "")) {
-    stackedPlot <- stackedPlot +
-      scale_y_log10(
-        labels = fancyNumbers,
-        breaks = pretty_logs_new
-      ) +
-      theme(axis.title.x = element_blank())
+    if(utils::packageVersion("ggplot2") == "4.0.0"){
+      stackedPlot <- stackedPlot +
+        scale_y_log10() +
+        theme(axis.title.x = element_blank())       
+    } else {
+      stackedPlot <- stackedPlot +
+        scale_y_log10(
+          labels = fancyNumbers,
+          breaks = pretty_logs_new
+        ) +
+        theme(axis.title.x = element_blank())
+    }
+
   } else {
-    stackedPlot <- stackedPlot +
-      scale_y_log10(y_label,
-        labels = fancyNumbers,
-        breaks = pretty_logs_new
-      )
+    if(utils::packageVersion("ggplot2") == "4.0.0"){
+      stackedPlot <- stackedPlot +
+        scale_y_log10(y_label)     
+    } else {
+      stackedPlot <- stackedPlot +
+        scale_y_log10(y_label,
+                      labels = fancyNumbers,
+                      breaks = pretty_logs_new
+        )
+    }
   }
 
   plot_layout <- ggplot_build(stackedPlot)$layout

R/plot_tox_endpoints2.R

@@ -32,7 +32,7 @@
 #' @param ... Additional group_by arguments. This can be handy for creating facet graphs.
 #' @export
 #' @import ggplot2
-#' @examples
+#' @examplesIf identical(Sys.getenv("NOT_CRAN"), "true")
 #' 
 #' \donttest{
 #' path_to_tox <- system.file("extdata", package = "toxEval")
@@ -185,18 +185,29 @@ plot_tox_endpoints2 <- function(cs, ...,
   }
 
   if (isTRUE(y_label == "")) {
-    stackedPlot <- stackedPlot +
-      scale_y_log10(
-        labels = fancyNumbers,
-        breaks = pretty_logs_new
-      ) +
-      theme(axis.title.x = element_blank())
+    if(utils::packageVersion("ggplot2") == "4.0.0"){
+      stackedPlot <- stackedPlot +
+        scale_y_log10() +
+        theme(axis.title.x = element_blank())    
+    } else {
+      stackedPlot <- stackedPlot +
+        scale_y_log10(
+          labels = fancyNumbers,
+          breaks = pretty_logs_new
+        ) +
+        theme(axis.title.x = element_blank())
+    }
   } else {
-    stackedPlot <- stackedPlot +
-      scale_y_log10(y_label,
-        labels = fancyNumbers,
-        breaks = pretty_logs_new
-      )
+    if(utils::packageVersion("ggplot2") == "4.0.0"){
+      stackedPlot <- stackedPlot +
+        scale_y_log10(y_label)
+    } else {
+      stackedPlot <- stackedPlot +
+        scale_y_log10(y_label,
+                      labels = fancyNumbers,
+                      breaks = pretty_logs_new
+        )
+    }
   }
 
   plot_layout <- ggplot_build(stackedPlot)$layout

inst/CITATION

@@ -9,11 +9,11 @@ bibentry(bibtype = "Manual",
               as.person("Gerald T. Ankley")),
   title = "toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks.",
   publisher = "U.S. Geological Survey",
-  version = "1.4.0",
+  version = "1.4.1",
   address="Reston, VA",
   institution = "U.S. Geological Survey",
-  year = 2024,
+  year = 2025,
   doi = "10.5066/P1CQJHJV",
   url = "https://code.usgs.gov/water/toxEval",
-  textVersion = "De Cicco, L.A., Corsi, S.R., Villeneuve D.L, Blackwell, and B.R, Ankley, G.T., 2024, toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks. R package version 1.4.0., U.S. Geological Survey software release. Reston, VA., doi:10.5066/P1CQJHJV"
+  textVersion = "De Cicco, L.A., Corsi, S.R., Villeneuve D.L, Blackwell, and B.R, Ankley, G.T., 2025, toxEval: Evaluation of measured concentration data using the ToxCast high-throughput screening database or a user-defined set of concentration benchmarks. R package version 1.4.1., U.S. Geological Survey software release. Reston, VA., doi:10.5066/P1CQJHJV"
 )