Fix tests for cran (#418)

Co-authored-by: Joseph <[email protected]> Co-authored-by: Barret Schloerke <[email protected]>
ggobi · Jun 19, 2021 · 01a2c67 · 01a2c67
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -19,16 +19,18 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          # - { os: macOS-latest,   r: 'devel',   force_suggests: "0" }
-          - { os: windows-latest, r: 'devel',   force_suggests: "1" }
+          - { os: macOS-latest,   r: 'devel',   force_suggests: "0" }
+          # - { os: window-latest,   r: 'devel',   force_suggests: "1" }
 
           - { os: macOS-latest,   r: 'release', force_suggests: "1" }
           - { os: windows-latest, r: 'release', force_suggests: "1" }
           - { os: ubuntu-16.04,   r: 'release', force_suggests: "1",  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
+          - { os: ubuntu-20.04,   r: 'release', force_suggests: "1",  rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
 
           - { os: macOS-latest,   r: 'oldrel',  force_suggests: "1" }
           - { os: windows-latest, r: 'oldrel',  force_suggests: "1" }
           - { os: ubuntu-16.04,   r: 'oldrel',  force_suggests: "1" , rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest" }
+          - { os: ubuntu-20.04,   r: 'oldrel',  force_suggests: "1" , rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,7 @@ Description:
     plot networks.
 Depends:
     R (>= 3.1),
-    ggplot2 (>= 3.3.0)
+    ggplot2 (>= 3.3.4)
 Imports:
     dplyr (>= 1.0.0),
     forcats,
@@ -58,7 +58,7 @@ Suggests:
     maps (>= 3.1.0),
     mapproj,
     nnet,
-    network (>= 1.12.0),
+    network (>= 1.17.1),
     scagnostics,
     sna (>= 2.3-2),
     survival,

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,10 @@
 # GGally (development version)
 
+### Bug fixes
+
+* Replace `ggplot2` usage of `*_guide = FALSE` with `*_guide = "none"` (@larmarange, #418)
+* Require `network >= 1.17.1` (#418)
+
 # GGally 2.1.1
 
 ### Bug fixes

diff --git a/R/gg-plots.R b/R/gg-plots.R
@@ -1087,7 +1087,7 @@ ggally_text <- function(
   if (!is.null(mapping$colour)) {
     p <- p +
        geom_text( label = label, mapping = mapping, ...) +
-       guides(colour = FALSE)
+       guides(colour = "none")
   } else if ("colour" %in% names(aes(...))) {
     p <- p +
        geom_text( label = label, mapping = mapping, ...)

diff --git a/R/ggcoef_model.R b/R/ggcoef_model.R
@@ -363,7 +363,7 @@ ggcoef_compare <- function (
 #'   p_(ggcoef_multinom(mod, type = "faceted"))
 #'   p_(ggcoef_multinom(
 #'     mod, type = "faceted",
-#'     y.level = c(
+#'     y.level_label = c(
 #'       "pretty happy" = "pretty happy\n(ref: very happy)",
 #'       "very happy" = "very happy"
 #'     )
@@ -713,16 +713,22 @@ ggcoef_plot <- function (
     )
 
   if(!is.null(colour) && colour %in% names(data)) {
-    if (colour_guide)
+    if (colour_guide) {
       colour_guide <- guide_legend()
+    } else {
+      colour_guide <- "none"
+    }
     p <- p +
       scale_colour_discrete(guide = colour_guide, labels = colour_labels) +
       labs(colour = colour_lab)
   }
 
   if(!is.null(shape) && shape %in% names(data)) {
-    if (shape_guide)
+    if (shape_guide) {
       shape_guide <- guide_legend()
+    } else {
+      shape_guide <- "none"
+    }
     p <- p +
       scale_shape_manual(
         values = shape_values,

diff --git a/R/ggcorr.R b/R/ggcorr.R
@@ -323,7 +323,7 @@ ggcorr <- function(
 
     p = p +
       scale_size_continuous(range = c(min_size, max_size)) +
-      guides(size = FALSE)
+      guides(size = "none")
 
     r = list(size = (min_size + max_size) / 2)
 

diff --git a/R/ggnet2.R b/R/ggnet2.R
@@ -946,7 +946,7 @@ ggnet2 <- function(
     names(v_alpha) = unique(data$alpha)
 
     p = p +
-      scale_alpha_manual("", values = v_alpha) + guides(alpha = FALSE)
+      scale_alpha_manual("", values = v_alpha) + guides(alpha = "none")
 
   } else {
 
@@ -974,7 +974,7 @@ ggnet2 <- function(
     names(v_color) = unique(data$color)
 
     p = p +
-      scale_color_manual("", values = v_color) + guides(color = FALSE)
+      scale_color_manual("", values = v_color) + guides(color = "none")
 
   }
 
@@ -986,7 +986,7 @@ ggnet2 <- function(
     names(v_shape) = unique(data$shape)
 
     p = p +
-      scale_shape_manual("", values = v_shape) + guides(shape = FALSE)
+      scale_shape_manual("", values = v_shape) + guides(shape = "none")
 
   } else {
 
@@ -1009,7 +1009,7 @@ ggnet2 <- function(
 
       v_size = as.numeric(names(v_size))
       p = p +
-        scale_size_manual("", values = v_size) + guides(size = FALSE)
+        scale_size_manual("", values = v_size) + guides(size = "none")
 
     } else {
 

diff --git a/R/ggnetworkmap.R b/R/ggnetworkmap.R
@@ -63,7 +63,10 @@ if(getRversion() >= "2.15.1") {
 #' )
 #'
 #' # convert to network
-#' flights <- network(flights, directed = TRUE)
+#' flights <- network(
+#'   flights[-114,], # remove loop
+#'   directed = TRUE
+#' )
 #'
 #' # add geographic coordinates
 #' flights %v% "lat" <- airports[ network.vertex.names(flights), "lat" ]

diff --git a/R/ggsurv.R b/R/ggsurv.R
@@ -51,7 +51,7 @@ if(getRversion() >= "2.15.1") {
 #'
 #'   # Adjusting the legend of the ggsurv fit
 #'   p_(pl.sex +
-#'     ggplot2::guides(linetype = FALSE) +
+#'     ggplot2::guides(linetype = "none") +
 #'     ggplot2::scale_colour_discrete(
 #'       name   = 'Sex',
 #'       breaks = c(1,2),
@@ -92,7 +92,7 @@ if(getRversion() >= "2.15.1") {
 #'         direction = 1
 #'       )(4)
 #'     ) +
-#'     ggplot2::guides(color = FALSE, linetype = FALSE))
+#'     ggplot2::guides(color = "none", linetype = "none"))
 #' }
 ggsurv <- function(
   s,

diff --git a/man/ggcoef_model.Rd b/man/ggcoef_model.Rd
diff --git a/man/ggnetworkmap.Rd b/man/ggnetworkmap.Rd
diff --git a/man/ggsurv.Rd b/man/ggsurv.Rd
diff --git a/tests/testthat/test-gg-plots.R b/tests/testthat/test-gg-plots.R
@@ -129,7 +129,7 @@ test_that("dates", {
   expect_equal(get("aes_params", envir = p$layers[[1]])$label, "Corr:\n0.278***")
   p <- ggally_barDiag(nas, ggplot2::aes(x = date))
   expect_equal(mapping_string(p$mapping$x), "date")
-  expect_equal(p$labels$y, "count")
+  expect_equal(as.character(p$labels$y), "count")
 
 })
 

diff --git a/tests/testthat/test-ggcoef_model.R b/tests/testthat/test-ggcoef_model.R
@@ -11,6 +11,13 @@ test_that("example of ggcoef_model", {
   mod_simple <- lm(tip ~ day + time + total_bill, data = tips)
   expect_print(ggcoef_model(mod_simple))
 
+  expect_warning(
+    print(
+      ggcoef_model(mod_simple, shape_guide = FALSE, colour_guide = FALSE)
+    ),
+    NA
+  )
+
   # custom variable labels
   # you can use to define variable labels before computing model
   if (require(labelled)) {
@@ -121,7 +128,7 @@ test_that("example of ggcoef_model", {
   expect_print(ggcoef_multinom(mod, type = "faceted"))
   expect_print(ggcoef_multinom(
     mod, type = "faceted",
-    y.level = c(
+    y.level_label = c(
       "pretty happy" = "pretty happy\n(ref: very happy)"
     )
   ))

diff --git a/tests/testthat/test-ggnet.R b/tests/testthat/test-ggnet.R
@@ -209,10 +209,10 @@ test_that("examples", {
 
   # weighted bipartite network
   bip <- network(
-    bip,
+    bip[-4,], # remove "loop"
     matrix.type = "bipartite",
-    ignore.eval = FALSE,
-    names.eval = "weights"
+    ignore.eval = FALSE
+    # names.eval = "weights"
   )
 
   # test bipartite mode
@@ -223,7 +223,7 @@ test_that("examples", {
   expect_warning(ggnet(network(matrix(1, nrow = 2, ncol = 2), loops = TRUE)), "self-loops")
 
   expect_error(ggnet(1:2), "network object")
-  expect_error(ggnet(network(data.frame(1:2, 3:4), hyper = TRUE)), "hyper graphs")
+  expect_error(ggnet(network(data.frame(1:2, 3:4), hyper = TRUE)), "hyper")
   expect_error(ggnet(network(data.frame(1:2, 3:4), multiple = TRUE)), "multiplex graphs")
 
   ### --- test igraph functionality

diff --git a/tests/testthat/test-ggnet2.R b/tests/testthat/test-ggnet2.R
@@ -21,6 +21,7 @@ rq(RColorBrewer) # test ColorBrewer palettes
 test_that("examples", {
 
   ### --- start: documented examples
+  set.seed(54321)
 
   # random adjacency matrix
   x           <- 10
@@ -242,10 +243,10 @@ test_that("examples", {
 
   # weighted bipartite network
   bip <- network(
-    bip,
+    bip[-4, ], # remove loop
     matrix.type = "bipartite",
     ignore.eval = FALSE,
-    names.eval = "weights"
+    # names.eval = "weights"
   )
 
   # test bipartite mode
@@ -256,7 +257,7 @@ test_that("examples", {
   expect_warning(ggnet2(network(matrix(1, nrow = 2, ncol = 2), loops = TRUE)), "self-loops")
 
   expect_error(ggnet2(1:2), "network object")
-  expect_error(ggnet2(network(data.frame(1:2, 3:4), hyper = TRUE)), "hyper graphs")
+  expect_error(ggnet2(network(data.frame(1:2, 3:4), hyper = TRUE)), "hyper")
   expect_error(ggnet2(network(data.frame(1:2, 3:4), multiple = TRUE)), "multiplex graphs")
 
   ### --- test igraph functionality

diff --git a/tests/testthat/test-ggnetworkmap.R b/tests/testthat/test-ggnetworkmap.R
@@ -20,7 +20,7 @@ skip_if_not_installed("geosphere")
 
 # first 500 rows of http://datasets.flowingdata.com/tuts/maparcs/airports.csv
 # avoids downloading the dataset to test the package
-airports <- read.csv("data/airports.csv", header = TRUE)
+airports <- read.csv(test_path("data/airports.csv"), header = TRUE)
 rownames(airports) <- airports$iata
 
 # select some random flights
@@ -31,7 +31,10 @@ flights <- data.frame(
 )
 
 # convert to network
-flights <- network(flights, directed = TRUE)
+flights <- network(
+  flights[-114,], # remove loop
+  directed = TRUE
+)
 
 # add geographic coordinates
 flights %v% "lat" <- airports[ network.vertex.names(flights), "lat" ] # nolint
@@ -205,7 +208,7 @@ test_that("network coercion", {
   )
 
   expect_error(ggnetworkmap(net = 1:2), "network object")
-  expect_error(ggnetworkmap(net = network(data.frame(1:2, 3:4), hyper = TRUE)), "hyper graphs")
+  expect_error(ggnetworkmap(net = network(data.frame(1:2, 3:4), hyper = TRUE)), "hyper")
   expect_error(
     ggnetworkmap(net = network(data.frame(1:2, 3:4), multiple = TRUE)),
     "multiplex graphs"

diff --git a/vignettes/ggsurv.Rmd b/vignettes/ggsurv.Rmd
@@ -25,7 +25,7 @@ library(GGally)
 
 
 This function produces Kaplan-Meier plots using `ggplot2`.
-As a first argument, `ggsurv()` needs a `survival::survfit()` object. 
+As a first argument, `ggsurv()` needs a `survival::survfit()` object.
 Default settings differ for single stratum and multiple strata objects.
 
 ## Single Stratum
@@ -57,7 +57,7 @@ Since a ggplot2 object is returned, plot objects may be altered after the origin
 
 ```{r ggsurv-legend}
 pl.sex +
-  ggplot2::guides(linetype = FALSE) +
+  ggplot2::guides(linetype = "none") +
   ggplot2::scale_colour_discrete(
     name   = 'Sex',
     breaks = c(1, 2),
@@ -94,5 +94,5 @@ pl.kid +
       direction = 1
     )(4)
   ) +
-  ggplot2::guides(color = FALSE, linetype = FALSE)
+  ggplot2::guides(color = "none", linetype = "none")
 ```