diff --git a/DESCRIPTION b/DESCRIPTION
index 349f905e59..093493c894 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: ggplot2
-Version: 3.4.4.9000
+Version: 3.5.0.9000
Title: Create Elegant Data Visualisations Using the Grammar of Graphics
Authors@R: c(
person("Hadley", "Wickham", , "hadley@posit.co", role = "aut",
@@ -79,7 +79,7 @@ Config/testthat/edition: 3
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
Collate:
'ggproto.R'
'ggplot-global.R'
diff --git a/LICENSE b/LICENSE
index cfa404d54a..f4515a155b 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,2 +1,2 @@
-YEAR: 2020
-COPYRIGHT HOLDER: ggplot2 authors
+YEAR: 2024
+COPYRIGHT HOLDER: ggplot2 core developer team
diff --git a/NAMESPACE b/NAMESPACE
index 967573b174..67c7a4941a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -112,7 +112,6 @@ S3method(print,ggproto_method)
S3method(print,rel)
S3method(print,theme)
S3method(print,uneval)
-S3method(scale_type,AsIs)
S3method(scale_type,Date)
S3method(scale_type,POSIXt)
S3method(scale_type,character)
@@ -719,7 +718,10 @@ import(scales)
import(vctrs)
importFrom(glue,glue)
importFrom(glue,glue_collapse)
+importFrom(grid,arrow)
+importFrom(grid,unit)
importFrom(lifecycle,deprecated)
+importFrom(scales,alpha)
importFrom(stats,setNames)
importFrom(tibble,tibble)
importFrom(utils,.DollarNames)
diff --git a/NEWS.md b/NEWS.md
index 60c7877119..e6f6dca449 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,7 @@
# ggplot2 (development version)
+# ggplot2 3.5.0
+
This is a minor release that turned out quite beefy. It is focused on
overhauling the guide system: the system responsible for displaying information
from scales in the guise of axes and legends. As part of that overhaul, new
@@ -53,8 +55,7 @@ vectors interact with the scale system, namely: not at all.
* The `trans` argument in scales and secondary axes has been renamed to
`transform`. The `trans` argument itself is deprecated. To access the
transformation from the scale, a new `get_transformation()` method is
- added to Scale-classes that retrieves the transformation object from the
- new `Scale$transformation` field (#5558).
+ added to Scale-classes (#5558).
* Providing a numeric vector to `theme(legend.position)` has been deprecated.
To set the default legend position inside the plot use
@@ -137,6 +138,9 @@ stats, facets and coords (#3329, @teunbrand)
`guides(x = guide_axis(position = "top"))` will display the title at the
top by default (#4650).
+* The default `vjust` for the `axis.title.y.right` element is now 1 instead of
+ 0.
+
* Unknown secondary axis guide positions are now inferred as the opposite
of the primary axis guide when the latter has a known `position` (#4650).
diff --git a/R/axis-secondary.R b/R/axis-secondary.R
index 673cc0ef5b..0c3fc4be6a 100644
--- a/R/axis-secondary.R
+++ b/R/axis-secondary.R
@@ -109,7 +109,7 @@ sec_axis <- function(transform = NULL,
transform <- as_function(transform)
ggproto(NULL, AxisSecondary,
- transform = transform,
+ trans = transform,
name = name,
breaks = breaks,
labels = labels,
@@ -119,8 +119,8 @@ sec_axis <- function(transform = NULL,
#' @rdname sec_axis
#'
#' @export
-dup_axis <- function(transform = ~., trans = deprecated(),
- name = derive(), breaks = derive(), labels = derive(), guide = derive()) {
+dup_axis <- function(transform = ~., name = derive(), breaks = derive(),
+ labels = derive(), guide = derive(), trans = deprecated()) {
sec_axis(transform, trans = trans, name, breaks, labels, guide)
}
@@ -153,7 +153,7 @@ is.derived <- function(x) {
#' @usage NULL
#' @export
AxisSecondary <- ggproto("AxisSecondary", NULL,
- transform = NULL,
+ trans = NULL,
axis = NULL,
name = waiver(),
breaks = waiver(),
@@ -165,7 +165,7 @@ AxisSecondary <- ggproto("AxisSecondary", NULL,
detail = 1000,
empty = function(self) {
- is.null(self$transform %||% self$trans)
+ is.null(self$trans)
},
# Inherit settings from the primary axis/scale
@@ -173,19 +173,19 @@ AxisSecondary <- ggproto("AxisSecondary", NULL,
if (self$empty()) {
return()
}
- transform <- self$transform %||% self$trans
+ transform <- self$trans
if (!is.function(transform)) {
cli::cli_abort("Transformation for secondary axes must be a function.")
}
if (is.derived(self$name) && !is.waive(scale$name)) self$name <- scale$name
if (is.derived(self$breaks)) self$breaks <- scale$breaks
- if (is.waive(self$breaks)) self$breaks <- scale$transformation$breaks
+ if (is.waive(self$breaks)) self$breaks <- scale$get_transformation()$breaks
if (is.derived(self$labels)) self$labels <- scale$labels
if (is.derived(self$guide)) self$guide <- scale$guide
},
transform_range = function(self, range) {
- self$transform(range)
+ self$trans(range)
},
mono_test = function(self, scale){
@@ -299,7 +299,7 @@ AxisSecondary <- ggproto("AxisSecondary", NULL,
labels = self$labels,
limits = range,
expand = c(0, 0),
- transformation = transformation
+ trans = transformation
)
scale$train(range)
scale
diff --git a/R/coord-munch.R b/R/coord-munch.R
index 6f2bbb2afb..9c314ffc59 100644
--- a/R/coord-munch.R
+++ b/R/coord-munch.R
@@ -61,7 +61,7 @@ munch_data <- function(data, dist = NULL, segment_length = 0.01) {
}
# How many endpoints for each old segment, not counting the last one
- extra <- pmax(floor(dist / segment_length), 1)
+ extra <- pmin(pmax(floor(dist / segment_length), 1), 1e4)
extra[is.na(extra)] <- 1
# Generate extra pieces for x and y values
# The final point must be manually inserted at the end
diff --git a/R/coord-radial.R b/R/coord-radial.R
index 70aa211898..d4aefc979f 100644
--- a/R/coord-radial.R
+++ b/R/coord-radial.R
@@ -15,7 +15,7 @@
#' in accordance with the computed `theta` position. If `FALSE` (default),
#' no such transformation is performed. Can be useful to rotate text geoms in
#' alignment with the coordinates.
-#' @param donut A `numeric` between 0 and 1 setting the size of a donut hole.
+#' @param inner.radius A `numeric` between 0 and 1 setting the size of a inner.radius hole.
#'
#' @note
#' In `coord_radial()`, position guides are can be defined by using
@@ -23,14 +23,14 @@
#' these guides require `r` and `theta` as available aesthetics. The classic
#' `guide_axis()` can be used for the `r` positions and `guide_axis_theta()` can
#' be used for the `theta` positions. Using the `theta.sec` position is only
-#' sensible when `donut > 0`.
+#' sensible when `inner.radius > 0`.
#'
#' @export
#' @examples
#' # A partial polar plot
#' ggplot(mtcars, aes(disp, mpg)) +
#' geom_point() +
-#' coord_radial(start = -0.4 * pi, end = 0.4 * pi, donut = 0.3)
+#' coord_radial(start = -0.4 * pi, end = 0.4 * pi, inner.radius = 0.3)
coord_radial <- function(theta = "x",
start = 0, end = NULL,
expand = TRUE,
@@ -38,7 +38,7 @@ coord_radial <- function(theta = "x",
clip = "off",
r_axis_inside = NULL,
rotate_angle = FALSE,
- donut = 0) {
+ inner.radius = 0) {
theta <- arg_match0(theta, c("x", "y"))
r <- if (theta == "x") "y" else "x"
@@ -47,7 +47,7 @@ coord_radial <- function(theta = "x",
check_bool(rotate_angle)
check_number_decimal(start, allow_infinite = FALSE)
check_number_decimal(end, allow_infinite = FALSE, allow_null = TRUE)
- check_number_decimal(donut, min = 0, max = 1, allow_infinite = FALSE)
+ check_number_decimal(inner.radius, min = 0, max = 1, allow_infinite = FALSE)
end <- end %||% (start + 2 * pi)
if (start > end) {
@@ -64,7 +64,7 @@ coord_radial <- function(theta = "x",
direction = sign(direction),
r_axis_inside = r_axis_inside,
rotate_angle = rotate_angle,
- donut = c(donut, 1) * 0.4,
+ inner_radius = c(inner.radius, 1) * 0.4,
clip = clip
)
}
@@ -84,13 +84,13 @@ CoordRadial <- ggproto("CoordRadial", Coord,
distance = function(self, x, y, details) {
arc <- details$arc %||% c(0, 2 * pi)
if (self$theta == "x") {
- r <- rescale(y, from = details$r.range, to = self$donut / 0.4)
+ r <- rescale(y, from = details$r.range, to = self$inner_radius / 0.4)
theta <- theta_rescale_no_clip(
x, details$theta.range,
arc, self$direction
)
} else {
- r <- rescale(x, from = details$r.range, to = self$donut / 0.4)
+ r <- rescale(x, from = details$r.range, to = self$inner_radius / 0.4)
theta <- theta_rescale_no_clip(
y, details$theta.range,
arc, self$direction
@@ -117,8 +117,8 @@ CoordRadial <- ggproto("CoordRadial", Coord,
c(
view_scales_polar(scale_x, self$theta, expand = self$expand),
view_scales_polar(scale_y, self$theta, expand = self$expand),
- list(bbox = polar_bbox(self$arc, donut = self$donut),
- arc = self$arc, donut = self$donut)
+ list(bbox = polar_bbox(self$arc, inner_radius = self$inner_radius),
+ arc = self$arc, inner_radius = self$inner_radius)
)
},
@@ -215,6 +215,12 @@ CoordRadial <- ggproto("CoordRadial", Coord,
gdefs[[r]] <- guides[[r]]$get_layer_key(gdefs[[r]], layers)
}
+ # Set theme suffixes
+ gdefs$theta$theme_suffix <- "theta"
+ gdefs$theta.sec$theme_suffix <- "theta"
+ gdefs$r$theme_suffix <- "r"
+ gdefs$r.sec$theme_suffix <- "r"
+
panel_params$guides$update_params(gdefs)
panel_params
},
@@ -224,7 +230,7 @@ CoordRadial <- ggproto("CoordRadial", Coord,
bbox <- panel_params$bbox %||% list(x = c(0, 1), y = c(0, 1))
arc <- panel_params$arc %||% c(0, 2 * pi)
- data$r <- r_rescale(data$r, panel_params$r.range, panel_params$donut)
+ data$r <- r_rescale(data$r, panel_params$r.range, panel_params$inner_radius)
data$theta <- theta_rescale(
data$theta, panel_params$theta.range,
arc, self$direction
@@ -233,7 +239,7 @@ CoordRadial <- ggproto("CoordRadial", Coord,
data$y <- rescale(data$r * cos(data$theta) + 0.5, from = bbox$y)
if (self$rotate_angle && "angle" %in% names(data)) {
- data$angle <- flip_text_angle(data$angle - rad2deg(data$theta))
+ data <- flip_data_text_angle(data)
}
data
@@ -258,7 +264,7 @@ CoordRadial <- ggproto("CoordRadial", Coord,
bbox <- panel_params$bbox %||% list(x = c(0, 1), y = c(0, 1))
arc <- panel_params$arc %||% c(0, 2 * pi)
dir <- self$direction
- donut <- panel_params$donut
+ inner_radius <- panel_params$inner_radius
theta_lim <- panel_params$theta.range
theta_maj <- panel_params$theta.major
@@ -273,7 +279,7 @@ CoordRadial <- ggproto("CoordRadial", Coord,
theta_fine <- seq(self$arc[1], self$arc[2], length.out = 100)
r_fine <- r_rescale(panel_params$r.major, panel_params$r.range,
- panel_params$donut)
+ panel_params$inner_radius)
# This gets the proper theme element for theta and r grid lines:
# panel.grid.major.x or .y
@@ -308,8 +314,8 @@ CoordRadial <- ggproto("CoordRadial", Coord,
ggname("grill", grobTree(
background,
- theta_grid(theta_maj, grid_elems[[1]], donut, bbox),
- theta_grid(theta_min, grid_elems[[2]], donut, bbox),
+ theta_grid(theta_maj, grid_elems[[1]], inner_radius, bbox),
+ theta_grid(theta_min, grid_elems[[2]], inner_radius, bbox),
element_render(
theme, majorr, name = "radius",
x = rescale(rep(r_fine, each = length(theta_fine)) *
@@ -453,7 +459,7 @@ view_scales_polar <- function(scale, theta = "x", expand = TRUE) {
#' @examples
#' polar_bbox(c(0, 1) * pi)
polar_bbox <- function(arc, margin = c(0.05, 0.05, 0.05, 0.05),
- donut = c(0, 0.4)) {
+ inner_radius = c(0, 0.4)) {
# Early exit if we have full circle or more
if (abs(diff(arc)) >= 2 * pi) {
@@ -463,8 +469,8 @@ polar_bbox <- function(arc, margin = c(0.05, 0.05, 0.05, 0.05),
# X and Y position of the sector arc ends
xmax <- 0.5 * sin(arc) + 0.5
ymax <- 0.5 * cos(arc) + 0.5
- xmin <- donut[1] * sin(arc) + 0.5
- ymin <- donut[1] * cos(arc) + 0.5
+ xmin <- inner_radius[1] * sin(arc) + 0.5
+ ymin <- inner_radius[1] * cos(arc) + 0.5
margin <- c(
max(ymin) + margin[1],
@@ -528,17 +534,34 @@ flip_text_angle <- function(angle) {
angle
}
+flip_data_text_angle <- function(data) {
+ if (!all(c("angle", "theta") %in% names(data))) {
+ return(data)
+ }
+ angle <- (data$angle - rad2deg(data$theta)) %% 360
+ flip <- angle > 90 & angle < 270
+ angle[flip] <- angle[flip] + 180
+ data$angle <- angle
+ if ("hjust" %in% names(data)) {
+ data$hjust[flip] <- 1 - data$hjust[flip]
+ }
+ if ("vjust" %in% names(data)) {
+ data$vjust[flip] <- 1 - data$vjust[flip]
+ }
+ data
+}
+
-theta_grid <- function(theta, element, donut = c(0, 0.4),
+theta_grid <- function(theta, element, inner_radius = c(0, 0.4),
bbox = list(x = c(0, 1), y = c(0, 1))) {
n <- length(theta)
if (n < 1) {
return(NULL)
}
- donut <- rep(donut, n)
- x <- rep(sin(theta), each = 2) * donut + 0.5
- y <- rep(cos(theta), each = 2) * donut + 0.5
+ inner_radius <- rep(inner_radius, n)
+ x <- rep(sin(theta), each = 2) * inner_radius + 0.5
+ y <- rep(cos(theta), each = 2) * inner_radius + 0.5
element_grob(
element,
diff --git a/R/facet-grid-.R b/R/facet-grid-.R
index 2d7977bccc..839c9ba839 100644
--- a/R/facet-grid-.R
+++ b/R/facet-grid-.R
@@ -338,6 +338,10 @@ FacetGrid <- ggproto("FacetGrid", Facet,
cli::cli_abort("{.fn {snake_class(coord)}} doesn't support free scales.")
}
+ # Fill missing parameters for backward compatibility
+ params$draw_axes <- params$draw_axes %||% list(x = FALSE, y = FALSE)
+ params$axis_labels <- params$axis_labels %||% list(x = TRUE, y = TRUE)
+
if (!params$axis_labels$x) {
cols <- seq_len(nrow(layout))
x_axis_order <- as.integer(layout$PANEL[order(layout$ROW, layout$COL)])
@@ -443,22 +447,26 @@ FacetGrid <- ggproto("FacetGrid", Facet,
panel_pos_col <- panel_cols(panel_table)
if (switch_x) {
if (!is.null(strips$x$bottom)) {
- if (inside_x || all(vapply(axes$x$bottom, is.zero, logical(1)))) {
+ if (inside_x) {
panel_table <- gtable_add_rows(panel_table, max_height(strips$x$bottom), -2)
panel_table <- gtable_add_grob(panel_table, strips$x$bottom, -2, panel_pos_col$l, clip = "on", name = paste0("strip-b-", seq_along(strips$x$bottom)), z = 2)
} else {
- panel_table <- gtable_add_rows(panel_table, strip_padding, -1)
+ if (!all(vapply(axes$x$bottom, is.zero, logical(1)))) {
+ panel_table <- gtable_add_rows(panel_table, strip_padding, -1)
+ }
panel_table <- gtable_add_rows(panel_table, max_height(strips$x$bottom), -1)
panel_table <- gtable_add_grob(panel_table, strips$x$bottom, -1, panel_pos_col$l, clip = "on", name = paste0("strip-b-", seq_along(strips$x$bottom)), z = 2)
}
}
} else {
if (!is.null(strips$x$top)) {
- if (inside_x || all(vapply(axes$x$top, is.zero, logical(1)))) {
+ if (inside_x) {
panel_table <- gtable_add_rows(panel_table, max_height(strips$x$top), 1)
panel_table <- gtable_add_grob(panel_table, strips$x$top, 2, panel_pos_col$l, clip = "on", name = paste0("strip-t-", seq_along(strips$x$top)), z = 2)
} else {
- panel_table <- gtable_add_rows(panel_table, strip_padding, 0)
+ if (!all(vapply(axes$x$top, is.zero, logical(1)))) {
+ panel_table <- gtable_add_rows(panel_table, strip_padding, 0)
+ }
panel_table <- gtable_add_rows(panel_table, max_height(strips$x$top), 0)
panel_table <- gtable_add_grob(panel_table, strips$x$top, 1, panel_pos_col$l, clip = "on", name = paste0("strip-t-", seq_along(strips$x$top)), z = 2)
}
@@ -467,22 +475,26 @@ FacetGrid <- ggproto("FacetGrid", Facet,
panel_pos_rows <- panel_rows(panel_table)
if (switch_y) {
if (!is.null(strips$y$left)) {
- if (inside_y || all(vapply(axes$y$left, is.zero, logical(1)))) {
+ if (inside_y) {
panel_table <- gtable_add_cols(panel_table, max_width(strips$y$left), 1)
panel_table <- gtable_add_grob(panel_table, strips$y$left, panel_pos_rows$t, 2, clip = "on", name = paste0("strip-l-", seq_along(strips$y$left)), z = 2)
} else {
- panel_table <- gtable_add_cols(panel_table, strip_padding, 0)
+ if (!all(vapply(axes$y$left, is.zero, logical(1)))) {
+ panel_table <- gtable_add_cols(panel_table, strip_padding, 0)
+ }
panel_table <- gtable_add_cols(panel_table, max_width(strips$y$left), 0)
panel_table <- gtable_add_grob(panel_table, strips$y$left, panel_pos_rows$t, 1, clip = "on", name = paste0("strip-l-", seq_along(strips$y$left)), z = 2)
}
}
} else {
if (!is.null(strips$y$right)) {
- if (inside_y || all(vapply(axes$y$right, is.zero, logical(1)))) {
+ if (inside_y) {
panel_table <- gtable_add_cols(panel_table, max_width(strips$y$right), -2)
panel_table <- gtable_add_grob(panel_table, strips$y$right, panel_pos_rows$t, -2, clip = "on", name = paste0("strip-r-", seq_along(strips$y$right)), z = 2)
} else {
- panel_table <- gtable_add_cols(panel_table, strip_padding, -1)
+ if (!all(vapply(axes$y$right, is.zero, logical(1)))) {
+ panel_table <- gtable_add_cols(panel_table, strip_padding, -1)
+ }
panel_table <- gtable_add_cols(panel_table, max_width(strips$y$right), -1)
panel_table <- gtable_add_grob(panel_table, strips$y$right, panel_pos_rows$t, -1, clip = "on", name = paste0("strip-r-", seq_along(strips$y$right)), z = 2)
}
diff --git a/R/facet-wrap.R b/R/facet-wrap.R
index c0588bdf1f..9aa488179f 100644
--- a/R/facet-wrap.R
+++ b/R/facet-wrap.R
@@ -275,6 +275,10 @@ FacetWrap <- ggproto("FacetWrap", Facet,
panels <- panels[panel_order]
panel_pos <- convertInd(layout$ROW, layout$COL, nrow)
+ # Fill missing parameters for backward compatibility
+ params$draw_axes <- params$draw_axes %||% list(x = FALSE, y = FALSE)
+ params$axis_labels <- params$axis_labels %||% list(x = TRUE, y = TRUE)
+
x_axis_order <- if (params$axis_labels$x) layout$SCALE_X else seq(n)
y_axis_order <- if (params$axis_labels$y) layout$SCALE_Y else seq(n)
diff --git a/R/geom-.R b/R/geom-.R
index 6d4ed6fc55..4b8952d4fa 100644
--- a/R/geom-.R
+++ b/R/geom-.R
@@ -126,9 +126,6 @@ Geom <- ggproto("Geom",
deprecate_soft0("3.4.0", I("Using the `size` aesthetic in this geom"), I("`linewidth` in the `default_aes` field and elsewhere"))
default_aes$linewidth <- default_aes$size
}
- if (is_pattern(params$fill)) {
- params$fill <- list(params$fill)
- }
# Fill in missing aesthetics with their defaults
missing_aes <- setdiff(names(default_aes), names(data))
@@ -175,8 +172,15 @@ Geom <- ggproto("Geom",
# Override mappings with params
aes_params <- intersect(self$aesthetics(), names(params))
- check_aesthetics(params[aes_params], nrow(data))
- data[aes_params] <- params[aes_params]
+ new_params <- params[aes_params]
+ check_aesthetics(new_params, nrow(data))
+ data[aes_params] <- new_params
+
+ # Restore any AsIs classes (#5656)
+ is_asis <- which(vapply(new_params, inherits, what = "AsIs", logical(1)))
+ for (i in aes_params[is_asis]) {
+ data[[i]] <- I(data[[i]])
+ }
data
},
diff --git a/R/geom-bar.R b/R/geom-bar.R
index a1007a3678..7a3618d50b 100644
--- a/R/geom-bar.R
+++ b/R/geom-bar.R
@@ -145,7 +145,7 @@ GeomBar <- ggproto("GeomBar", GeomRect,
data <- flip_data(data, params$flipped_aes)
data$width <- data$width %||%
params$width %||% (min(vapply(
- split(data$x, data$PANEL),
+ split(data$x, data$PANEL, drop = TRUE),
resolution, numeric(1), zero = FALSE
)) * 0.9)
data$just <- params$just %||% 0.5
diff --git a/R/geom-label.R b/R/geom-label.R
index d83434b386..c292fa1a66 100644
--- a/R/geom-label.R
+++ b/R/geom-label.R
@@ -73,12 +73,8 @@ GeomLabel <- ggproto("GeomLabel", Geom,
}
data <- coord$transform(data, panel_params)
- if (is.character(data$vjust)) {
- data$vjust <- compute_just(data$vjust, data$y, data$x, data$angle)
- }
- if (is.character(data$hjust)) {
- data$hjust <- compute_just(data$hjust, data$x, data$y, data$angle)
- }
+ data$vjust <- compute_just(data$vjust, data$y, data$x, data$angle)
+ data$hjust <- compute_just(data$hjust, data$x, data$y, data$angle)
if (!inherits(label.padding, "margin")) {
label.padding <- rep(label.padding, length.out = 4)
}
@@ -143,20 +139,27 @@ labelGrob <- function(label, x = unit(0.5, "npc"), y = unit(0.5, "npc"),
descent <- font_descent(
text.gp$fontfamily, text.gp$fontface, text.gp$fontsize, text.gp$cex
)
+ # To balance labels, we ensure the top includes at least the descent height
+ # and subtract the descent height from the bottom padding
+ padding[1] <- unit.pmax(padding[1], descent)
+ padding[3] <- unit.pmax(padding[3] - descent, unit(0, "pt"))
+
hjust <- resolveHJust(just, NULL)
vjust <- resolveVJust(just, NULL)
text <- titleGrob(
- label = label, hjust = hjust, vjust = vjust, x = x, y = y,
+ label = label, hjust = hjust, vjust = vjust, x = x,
+ y = y + (1 - vjust) * descent,
margin = padding, margin_x = TRUE, margin_y = TRUE,
gp = text.gp
)
+ height <- heightDetails(text)
box <- roundrectGrob(
- x = x, y = y - (1 - vjust) * descent,
+ x = x, y = y + (0.5 - vjust) * height,
width = widthDetails(text),
- height = heightDetails(text),
- just = c(hjust, vjust),
+ height = height,
+ just = c(hjust, 0.5),
r = r, gp = rect.gp, name = "box"
)
diff --git a/R/geom-raster.R b/R/geom-raster.R
index 2cd591d879..46e516d4aa 100644
--- a/R/geom-raster.R
+++ b/R/geom-raster.R
@@ -94,8 +94,8 @@ GeomRaster <- ggproto("GeomRaster", Geom,
}
# Convert vector of data to raster
- x_pos <- as.integer((data$x - min(data$x)) / resolution(data$x, FALSE))
- y_pos <- as.integer((data$y - min(data$y)) / resolution(data$y, FALSE))
+ x_pos <- as.integer((data$x - min(data$x)) / resolution(unclass(data$x), FALSE))
+ y_pos <- as.integer((data$y - min(data$y)) / resolution(unclass(data$y), FALSE))
data <- coord$transform(data, panel_params)
diff --git a/R/geom-text.R b/R/geom-text.R
index b8c98f7fba..c9ccb6595b 100644
--- a/R/geom-text.R
+++ b/R/geom-text.R
@@ -220,12 +220,8 @@ GeomText <- ggproto("GeomText", Geom,
data <- coord$transform(data, panel_params)
- if (is.character(data$vjust)) {
- data$vjust <- compute_just(data$vjust, data$y, data$x, data$angle)
- }
- if (is.character(data$hjust)) {
- data$hjust <- compute_just(data$hjust, data$x, data$y, data$angle)
- }
+ data$vjust <- compute_just(data$vjust, data$y, data$x, data$angle)
+ data$hjust <- compute_just(data$hjust, data$x, data$y, data$angle)
size.unit <- resolve_text_unit(size.unit)
@@ -248,7 +244,10 @@ GeomText <- ggproto("GeomText", Geom,
draw_key = draw_key_text
)
-compute_just <- function(just, a, b = a, angle = 0) {
+compute_just <- function(just, a = 0.5, b = a, angle = 0) {
+ if (!is.character(just)) {
+ return(just)
+ }
# As justification direction is relative to the text, not the plotting area
# we need to swap x and y if text direction is rotated so that hjust is
# applied along y and vjust along x.
diff --git a/R/guide-.R b/R/guide-.R
index e185ec67b0..0a334c4580 100644
--- a/R/guide-.R
+++ b/R/guide-.R
@@ -51,7 +51,7 @@ new_guide <- function(..., available_aes = "any", super) {
# Validate theme settings
if (!is.null(params$theme)) {
check_object(params$theme, is.theme, what = "a {.cls theme} object")
- validate_theme(params$theme)
+ validate_theme(params$theme, call = caller_env())
params$direction <- params$direction %||% params$theme$legend.direction
}
@@ -154,6 +154,9 @@ new_guide <- function(..., available_aes = "any", super) {
#' methods, the measurements from `measure_grobs()` and layout from
#' `arrange_layout()` to finalise the guide.
#'
+#' - `add_title` Adds the title to a gtable, taking into account the size
+#' of the title as well as the gtable size.
+#'
#' @rdname ggplot2-ggproto
#' @format NULL
#' @usage NULL
@@ -297,11 +300,12 @@ Guide <- ggproto(
draw = function(self, theme, position = NULL, direction = NULL,
params = self$params) {
- key <- params$key
-
- # Setup parameters and theme
+ # Setup parameters
params <- replace_null(params, position = position, direction = direction)
params <- self$setup_params(params)
+ key <- params$key
+
+ # Setup style options
elems <- self$setup_elements(params, self$elements, theme)
elems <- self$override_elements(params, elems, theme)
@@ -325,7 +329,7 @@ Guide <- ggproto(
# Arrange and assemble grobs
sizes <- self$measure_grobs(grobs, params, elems)
- layout <- self$arrange_layout(key, sizes, params)
+ layout <- self$arrange_layout(key, sizes, params, elems)
self$assemble_drawing(grobs, layout, sizes, params, elems)
},
@@ -336,7 +340,7 @@ Guide <- ggproto(
},
# Takes care of where grobs should be added to the output gtable.
- arrange_layout = function(key, sizes, params) {
+ arrange_layout = function(key, sizes, params, elements) {
return(invisible())
},
@@ -415,6 +419,69 @@ Guide <- ggproto(
draw_early_exit = function(self, params, elements) {
zeroGrob()
+ },
+
+ add_title = function(gtable, title, position, just) {
+ if (is.zero(title)) {
+ return(gtable)
+ }
+
+ title_width_cm <- width_cm(title)
+ title_height_cm <- height_cm(title)
+
+ # Add extra row/col for title
+ gtable <- switch(
+ position,
+ top = gtable_add_rows(gtable, unit(title_height_cm, "cm"), pos = 0),
+ right = gtable_add_cols(gtable, unit(title_width_cm, "cm"), pos = -1),
+ bottom = gtable_add_rows(gtable, unit(title_height_cm, "cm"), pos = -1),
+ left = gtable_add_cols(gtable, unit(title_width_cm, "cm"), pos = 0)
+ )
+
+ # Add title
+ args <- switch(
+ position,
+ top = list(t = 1, l = 1, r = -1, b = 1),
+ right = list(t = 1, l = -1, r = -1, b = -1),
+ bottom = list(t = -1, l = 1, r = -1, b = -1),
+ left = list(t = 1, l = 1, r = 1, b = -1),
+ )
+ gtable <- inject(gtable_add_grob(
+ x = gtable, grobs = title, !!!args, z = -Inf, name = "title", clip = "off"
+ ))
+
+ if (position %in% c("top", "bottom")) {
+
+ if (any(unitType(gtable$widths) == "null")) {
+ # Don't need to add extra title size for stretchy legends
+ return(gtable)
+ }
+ table_width <- sum(width_cm(gtable$widths))
+ extra_width <- max(0, title_width_cm - table_width)
+ if (extra_width == 0) {
+ return(gtable)
+ }
+ extra_width <- unit((c(1, -1) * just$hjust + c(0, 1)) * extra_width, "cm")
+ gtable <- gtable_add_cols(gtable, extra_width[1], pos = 0)
+ gtable <- gtable_add_cols(gtable, extra_width[2], pos = -1)
+
+ } else {
+
+ if (any(unitType(gtable$heights) == "null")) {
+ # Don't need to add extra title size for stretchy legends
+ return(gtable)
+ }
+ table_height <- sum(height_cm(gtable$heights))
+ extra_height <- max(0, title_height_cm - table_height)
+ if (extra_height == 0) {
+ return(gtable)
+ }
+ extra_height <- unit((c(-1, 1) * just$vjust + c(1, 0)) * extra_height, "cm")
+ gtable <- gtable_add_rows(gtable, extra_height[1], pos = 0)
+ gtable <- gtable_add_rows(gtable, extra_height[2], pos = -1)
+ }
+
+ gtable
}
)
diff --git a/R/guide-axis-logticks.R b/R/guide-axis-logticks.R
index a07e095de8..b30a493040 100644
--- a/R/guide-axis-logticks.R
+++ b/R/guide-axis-logticks.R
@@ -149,7 +149,7 @@ GuideAxisLogticks <- ggproto(
# Reconstruct a transformation if user has prescaled data
if (!is.null(params$prescale_base)) {
- trans_name <- scale$scale$transformation$name
+ trans_name <- scale$get_transformation()$name
if (trans_name != "identity") {
cli::cli_warn(paste0(
"The {.arg prescale_base} argument will override the scale's ",
diff --git a/R/guide-axis-stack.R b/R/guide-axis-stack.R
index 7c345dff20..c645c29d99 100644
--- a/R/guide-axis-stack.R
+++ b/R/guide-axis-stack.R
@@ -66,6 +66,7 @@ guide_axis_stack <- function(first = "axis", ..., title = waiver(), theme = NULL
theme = theme,
guides = axes,
guide_params = params,
+ spacing = spacing,
available_aes = c("x", "y", "theta", "r"),
order = order,
position = position,
@@ -86,6 +87,7 @@ GuideAxisStack <- ggproto(
guides = list(),
# List of parameters to each guide
guide_params = list(),
+ spacing = NULL,
# Standard guide stuff
name = "stacked_axis",
title = waiver(),
diff --git a/R/guide-axis-theta.R b/R/guide-axis-theta.R
index 79f5b2dea1..567cf08020 100644
--- a/R/guide-axis-theta.R
+++ b/R/guide-axis-theta.R
@@ -41,6 +41,7 @@ guide_axis_theta <- function(title = waiver(), theme = NULL, angle = waiver(),
angle = angle,
cap = cap,
minor.ticks = minor.ticks,
+ theme = theme,
# parameter
available_aes = c("x", "y", "theta"),
@@ -85,8 +86,6 @@ GuideAxisTheta <- ggproto(
key <- params$key
n <- nrow(key)
- params$theme_aes <- coord$theta %||% params$aesthetic
-
if (!("theta" %in% names(key))) {
# We likely have a linear coord, so we match the text angles to
# standard axes to be visually similar.
@@ -129,12 +128,13 @@ GuideAxisTheta <- ggproto(
},
setup_elements = function(params, elements, theme) {
+ theme <- add_theme(theme, params$theme)
axis_elem <- c("line", "text", "ticks", "minor", "major_length", "minor_length")
is_char <- vapply(elements[axis_elem], is.character, logical(1))
axis_elem <- axis_elem[is_char]
- aes <- switch(
+ aes <- params$theme_suffix %||% switch(
params$position,
theta = "x.bottom",
theta.sec = "x.top",
@@ -306,7 +306,7 @@ GuideAxisTheta <- ggproto(
list(offset = max(height))
},
- arrange_layout = function(key, sizes, params) {
+ arrange_layout = function(key, sizes, params, elements) {
NULL
},
@@ -327,7 +327,7 @@ GuideAxisTheta <- ggproto(
if (params$position %in% c("top", "bottom")) {
height <- sum(
elements$offset,
- unit(max(height_cm(grobs$labels$children)), "cm")
+ unit(max(height_cm(grobs$labels)), "cm")
)
vp <- viewport(
y = unit(as.numeric(params$position == "bottom"), "npc"),
@@ -337,7 +337,7 @@ GuideAxisTheta <- ggproto(
} else {
width <- sum(
elements$offset,
- unit(max(width_cm(grobs$labels$children)), "cm")
+ unit(max(width_cm(grobs$labels)), "cm")
)
vp <- viewport(
x = unit(as.numeric(params$position == "left"), "npc"),
diff --git a/R/guide-axis.R b/R/guide-axis.R
index ac59ef41b4..22cda82454 100644
--- a/R/guide-axis.R
+++ b/R/guide-axis.R
@@ -228,7 +228,8 @@ GuideAxis <- ggproto(
setup_elements = function(params, elements, theme) {
is_char <- vapply(elements, is.character, logical(1))
- suffix <- paste(params$aes, params$position, sep = ".")
+ suffix <- params$theme_suffix %||%
+ paste(params$aes, params$position, sep = ".")
elements[is_char] <- vapply(
elements[is_char],
function(x) paste(x, suffix, sep = "."),
@@ -386,7 +387,7 @@ GuideAxis <- ggproto(
sizes
},
- arrange_layout = function(key, sizes, params) {
+ arrange_layout = function(key, sizes, params, elements) {
layout <- seq_along(sizes)
diff --git a/R/guide-bins.R b/R/guide-bins.R
index c13447eb32..6f253aa0d6 100644
--- a/R/guide-bins.R
+++ b/R/guide-bins.R
@@ -114,7 +114,6 @@ GuideBins <- ggproto(
theme = NULL,
default_axis = element_line("black", linewidth = (0.5 / .pt)),
default_ticks = element_line(inherit.blank = TRUE),
- default_tick_length = unit(0.2, "npc"),
direction = NULL,
override.aes = list(),
@@ -228,7 +227,6 @@ GuideBins <- ggproto(
theme <- replace_null(
theme,
legend.text.position = valid_position[1],
- legend.ticks.length = params$default_tick_length,
legend.axis.line = params$default_axis,
legend.ticks = params$default_ticks
)
diff --git a/R/guide-colorbar.R b/R/guide-colorbar.R
index c0f2c15e7f..ad71d0bc82 100644
--- a/R/guide-colorbar.R
+++ b/R/guide-colorbar.R
@@ -179,7 +179,6 @@ GuideColourbar <- ggproto(
theme = NULL,
default_ticks = element_line(colour = "white", linewidth = 0.5 / .pt),
default_frame = element_blank(),
- default_tick_length = unit(0.2, "npc"),
# bar
nbin = 300,
@@ -224,7 +223,11 @@ GuideColourbar <- ggproto(
cli::cli_warn("{.fn guide_colourbar} needs continuous scales.")
return(NULL)
}
- Guide$extract_key(scale, aesthetic, ...)
+ key <- Guide$extract_key(scale, aesthetic, ...)
+ if (NROW(key) == 0) {
+ return(NULL)
+ }
+ key
},
extract_decor = function(scale, aesthetic, nbin = 300, reverse = FALSE, alpha = NA, ...) {
@@ -291,7 +294,6 @@ GuideColourbar <- ggproto(
theme <- replace_null(
theme,
legend.text.position = valid_position[1],
- legend.ticks.length = params$default_tick_length,
legend.ticks = params$default_ticks,
legend.frame = params$default_frame
)
diff --git a/R/guide-custom.R b/R/guide-custom.R
index 4a63942d4a..16a737d3fd 100644
--- a/R/guide-custom.R
+++ b/R/guide-custom.R
@@ -8,11 +8,6 @@
#' in [grid::unit()]s.
#' @param title A character string or expression indicating the title of guide.
#' If `NULL` (default), no title is shown.
-#' @param title.position A character string indicating the position of a title.
-#' One of `"top"` (default), `"bottom"`, `"left"` or `"right"`.
-#' @param margin Margins around the guide. See [margin()] for more details. If
-#' `NULL` (default), margins are taken from the `legend.margin` theme setting.
-#' @param position Currently not in use.
#' @inheritParams guide_legend
#'
#' @export
@@ -42,28 +37,25 @@
#' ))
guide_custom <- function(
grob, width = grobWidth(grob), height = grobHeight(grob),
- title = NULL, title.position = "top", margin = NULL,
+ title = NULL, theme = NULL,
position = NULL, order = 0
) {
check_object(grob, is.grob, "a {.cls grob} object")
check_object(width, is.unit, "a {.cls unit} object")
check_object(height, is.unit, "a {.cls unit} object")
- check_object(margin, is.margin, "a {.cls margin} object", allow_null = TRUE)
if (length(width) != 1) {
cli::cli_abort("{.arg width} must be a single {.cls unit}, not a unit vector.")
}
if (length(height) != 1) {
cli::cli_abort("{.arg height} must be a single {.cls unit}, not a unit vector.")
}
- title.position <- arg_match0(title.position, .trbl)
new_guide(
grob = grob,
width = width,
height = height,
title = title,
- title.position = title.position,
- margin = margin,
+ theme = theme,
hash = hash(list(title, grob)), # hash is already known
position = position,
order = order,
@@ -79,19 +71,15 @@ guide_custom <- function(
GuideCustom <- ggproto(
"GuideCustom", Guide,
- params = c(Guide$params, list(
- grob = NULL, width = NULL, height = NULL,
- margin = NULL,
- title = NULL,
- title.position = "top"
- )),
+ params = c(Guide$params, list(grob = NULL, width = NULL, height = NULL)),
hashables = exprs(title, grob),
elements = list(
- background = "legend.background",
- theme.margin = "legend.margin",
- theme.title = "legend.title"
+ background = "legend.background",
+ margin = "legend.margin",
+ title = "legend.title",
+ title_position = "legend.title.position"
),
train = function(...) {
@@ -102,72 +90,41 @@ GuideCustom <- ggproto(
params
},
- override_elements = function(params, elements, theme) {
- elements$title <- elements$theme.title
- elements$margin <- params$margin %||% elements$theme.margin
- elements
- },
-
draw = function(self, theme, position = NULL, direction = NULL,
params = self$params) {
# Render title
- elems <- self$setup_elements(params, self$elements, theme)
- elems <- self$override_elements(params, elems, theme)
+ params <- replace_null(params, position = position, direction = direction)
+ elems <- GuideLegend$setup_elements(params, self$elements, theme)
if (!is.waive(params$title) && !is.null(params$title)) {
title <- self$build_title(params$title, elems, params)
} else {
title <- zeroGrob()
}
- title.position <- params$title.position
- if (is.zero(title)) {
- title.position <- "none"
- }
+ title_position <- elems$title_position
+
+ # Start with putting the main grob in a gtable
width <- convertWidth(params$width, "cm", valueOnly = TRUE)
height <- convertHeight(params$height, "cm", valueOnly = TRUE)
gt <- gtable(widths = unit(width, "cm"), heights = unit(height, "cm"))
gt <- gtable_add_grob(gt, params$grob, t = 1, l = 1, clip = "off")
- extra_width <- max(0, width_cm(title) - width)
- extra_height <- max(0, height_cm(title) - height)
- just <- with(elems$title, rotate_just(angle, hjust, vjust))
- hjust <- just$hjust
- vjust <- just$vjust
-
- if (params$title.position == "top") {
- gt <- gtable_add_rows(gt, elems$margin[1], pos = 0)
- gt <- gtable_add_rows(gt, unit(height_cm(title), "cm"), pos = 0)
- gt <- gtable_add_grob(gt, title, t = 1, l = 1, name = "title", clip = "off")
- } else if (params$title.position == "bottom") {
- gt <- gtable_add_rows(gt, elems$margin[3], pos = -1)
- gt <- gtable_add_rows(gt, unit(height_cm(title), "cm"), pos = -1)
- gt <- gtable_add_grob(gt, title, t = -1, l = 1, name = "title", clip = "off")
- } else if (params$title.position == "left") {
- gt <- gtable_add_cols(gt, elems$margin[4], pos = 0)
- gt <- gtable_add_cols(gt, unit(width_cm(title), "cm"), pos = 0)
- gt <- gtable_add_grob(gt, title, t = 1, l = 1, name = "title", clip = "off")
- } else if (params$title.position == "right") {
- gt <- gtable_add_cols(gt, elems$margin[2], pos = -1)
- gt <- gtable_add_cols(gt, unit(width_cm(title), "cm"), pos = 0)
- gt <- gtable_add_grob(gt, title, t = 1, l = -1, name = "title", clip = "off")
- }
- if (params$title.position %in% c("top", "bottom")) {
- gt <- gtable_add_cols(gt, unit(extra_width * hjust, "cm"), pos = 0)
- gt <- gtable_add_cols(gt, unit(extra_width * (1 - hjust), "cm"), pos = -1)
- } else {
- gt <- gtable_add_rows(gt, unit(extra_height * (1 - vjust), "cm"), pos = 0)
- gt <- gtable_add_rows(gt, unit(extra_height * vjust, "cm"), pos = -1)
- }
+ gt <- self$add_title(
+ gt, title, title_position,
+ with(elems$title, rotate_just(angle, hjust, vjust))
+ )
+
+ # Add padding and background
gt <- gtable_add_padding(gt, elems$margin)
- background <- element_grob(elems$background)
gt <- gtable_add_grob(
- gt, background,
+ gt, element_grob(elems$background),
t = 1, l = 1, r = -1, b = -1,
z = -Inf, clip = "off"
)
+
gt
}
)
diff --git a/R/guide-legend.R b/R/guide-legend.R
index 26a0b401b0..885e24b3ce 100644
--- a/R/guide-legend.R
+++ b/R/guide-legend.R
@@ -471,147 +471,53 @@ GuideLegend <- ggproto(
)
heights <- head(vec_interleave(!!!heights), -1)
- has_title <- !is.zero(grobs$title)
-
- if (has_title) {
- # Measure title
- title_width <- width_cm(grobs$title)
- title_height <- height_cm(grobs$title)
-
- # Titles are assumed to have sufficient size when keys are null units
- extra_width <-
- if (isTRUE(elements$stretch_x)) 0 else max(0, title_width - sum(widths))
- extra_height <-
- if (isTRUE(elements$stretch_y)) 0 else max(0, title_height - sum(heights))
-
- just <- with(elements$title, rotate_just(angle, hjust, vjust))
-
- # Combine title with rest of the sizes based on its position
- widths <- switch(
- elements$title_position,
- "left" = c(title_width, widths),
- "right" = c(widths, title_width),
- c(extra_width * just$hjust, widths, extra_width * (1 - just$hjust))
- )
- heights <- switch(
- elements$title_position,
- "top" = c(title_height, heights),
- "bottom" = c(heights, title_height),
- c(extra_height * (1 - just$vjust), heights, extra_height * just$vjust)
- )
- }
-
- list(
- widths = widths,
- heights = heights,
- padding = elements$padding,
- has_title = has_title,
- label_position = elements$text_position,
- title_position = elements$title_position
- )
+ list(widths = widths, heights = heights)
},
- arrange_layout = function(key, sizes, params) {
+ arrange_layout = function(key, sizes, params, elements) {
break_seq <- seq_len(params$n_breaks %||% 1L)
dim <- c(params$nrow %||% 1L, params$ncol %||% 1L)
# Find rows / columns of legend items
- if (params$byrow %||% FALSE) {
+ if (elements$byrow %||% FALSE) {
row <- ceiling(break_seq / dim[2L])
col <- (break_seq - 1L) %% dim[2L] + 1L
} else {
- df <- mat_2_df(arrayInd(break_seq, dim), c("R", "C"))
- row <- df$R
- col <- df$C
+ row <- (break_seq - 1L) %% dim[1L] + 1L
+ col <- ceiling(break_seq / dim[1L])
}
- # Make spacing for padding / gaps. For example: because first gtable cell
- # will be padding, first item will be at [2, 2] position. Then the
- # second item-row will be [4, 2] because [3, 2] will be a gap cell.
- key_row <- label_row <- row * 2
- key_col <- label_col <- col * 2
+ # Account for spacing in between keys
+ key_row <- row * 2 - 1
+ key_col <- col * 2 - 1
# Make gaps for key-label spacing depending on label position
- switch(
- sizes$label_position,
- "top" = {
- key_row <- key_row + row
- label_row <- key_row - 1
- },
- "bottom" = {
- key_row <- key_row + row - 1
- label_row <- key_row + 1
- },
- "left" = {
- key_col <- key_col + col
- label_col <- key_col - 1
- },
- "right" = {
- key_col <- key_col + col - 1
- label_col <- key_col + 1
- }
+ position <- elements$text_position
+ key_row <- key_row + switch(position, top = row, bottom = row - 1, 0)
+ lab_row <- key_row + switch(position, top = -1, bottom = 1, 0)
+ key_col <- key_col + switch(position, left = col, right = col - 1, 0)
+ lab_col <- key_col + switch(position, left = -1, right = 1, 0)
+
+ data_frame0(
+ key_row = key_row, key_col = key_col,
+ label_row = lab_row, label_col = lab_col
)
-
- # Offset layout based on title position
- if (sizes$has_title) {
- position <- sizes$title_position
- if (position != "right") {
- key_col <- key_col + 1
- label_col <- label_col + 1
- }
- if (position != "bottom") {
- key_row <- key_row + 1
- label_row <- label_row + 1
- }
- nrow <- length(sizes$heights)
- ncol <- length(sizes$widths)
- title_row <- switch(position, top = 1, bottom = nrow, seq_len(nrow)) + 1
- title_col <- switch(position, left = 1, right = ncol, seq_len(ncol)) + 1
- } else {
- title_row <- NA
- title_col <- NA
- }
-
- df <- cbind(df, key_row, key_col, label_row, label_col)
-
- list(layout = df, title_row = title_row, title_col = title_col)
},
- assemble_drawing = function(grobs, layout, sizes, params, elements) {
- widths <- unit(c(sizes$padding[4], sizes$widths, sizes$padding[2]), "cm")
+ assemble_drawing = function(self, grobs, layout, sizes, params, elements) {
+
+ widths <- unit(sizes$widths, "cm")
if (isTRUE(elements$stretch_x)) {
- widths[unique(layout$layout$key_col)] <- elements$key_width
+ widths[unique0(layout$key_col)] <- elements$key_width
}
- heights <- unit(c(sizes$padding[1], sizes$heights, sizes$padding[3]), "cm")
+ heights <- unit(sizes$heights, "cm")
if (isTRUE(elements$stretch_y)) {
- heights[unique(layout$layout$key_row)] <- elements$key_height
+ heights[unique0(layout$key_row)] <- elements$key_height
}
gt <- gtable(widths = widths, heights = heights)
- # Add background
- if (!is.zero(elements$background)) {
- gt <- gtable_add_grob(
- gt, elements$background,
- name = "background", clip = "off",
- t = 1, r = -1, b = -1, l =1
- )
- }
-
- # Add title
- if (!is.zero(grobs$title)) {
- gt <- gtable_add_grob(
- gt, grobs$title,
- name = "title", clip = "off",
- t = min(layout$title_row), r = max(layout$title_col),
- b = max(layout$title_row), l = min(layout$title_col)
- )
- }
-
- # Extract appropriate part of layout
- layout <- layout$layout
-
# Add keys
if (!is.zero(grobs$decor)) {
n_key_layers <- params$n_key_layers %||% 1L
@@ -640,6 +546,21 @@ GuideLegend <- ggproto(
)
}
+ gt <- self$add_title(
+ gt, grobs$title, elements$title_position,
+ with(elements$title, rotate_just(angle, hjust, vjust))
+ )
+
+ gt <- gtable_add_padding(gt, unit(elements$padding, "cm"))
+
+ # Add background
+ if (!is.zero(elements$background)) {
+ gt <- gtable_add_grob(
+ gt, elements$background,
+ name = "background", clip = "off",
+ t = 1, r = -1, b = -1, l =1, z = -Inf
+ )
+ }
gt
}
)
@@ -724,7 +645,7 @@ keep_key_data <- function(key, data, aes, show) {
}
keep <- rep(FALSE, nrow(key))
for (column in match) {
- keep <- keep | vec_in(key$.value, data[[column]])
+ keep <- keep | key$.value %in% data[[column]]
}
keep
}
@@ -781,7 +702,7 @@ deprecated_guide_args <- function(
unit(x, default.unit)
}
- theme <- theme %||% list()
+ theme <- theme %||% theme()
# Resolve straightforward arguments
theme <- replace_null(
diff --git a/R/guides-.R b/R/guides-.R
index 1742d07df0..2280c40def 100644
--- a/R/guides-.R
+++ b/R/guides-.R
@@ -547,7 +547,8 @@ Guides <- ggproto(
direction = directions[i], params = params[[i]]
)
}
- split(grobs, positions)
+ keep <- !vapply(grobs, is.zero, logical(1))
+ split(grobs[keep], positions[keep])
},
package_box = function(grobs, position, theme) {
diff --git a/R/layer.R b/R/layer.R
index eb590f8dea..02649348ac 100644
--- a/R/layer.R
+++ b/R/layer.R
@@ -124,6 +124,12 @@ layer <- function(geom = NULL, stat = NULL,
all <- c(geom$parameters(TRUE), stat$parameters(TRUE), geom$aesthetics())
+ # Take care of plain patterns provided as aesthetic
+ pattern <- vapply(aes_params, is_pattern, logical(1))
+ if (any(pattern)) {
+ aes_params[pattern] <- lapply(aes_params[pattern], list)
+ }
+
# Warn about extra params and aesthetics
extra_param <- setdiff(names(params), all)
# Take care of size->linewidth renaming in layer params
diff --git a/R/legend-draw.R b/R/legend-draw.R
index 12ec69ed0d..f1de0b80e5 100644
--- a/R/legend-draw.R
+++ b/R/legend-draw.R
@@ -258,17 +258,16 @@ draw_key_smooth <- function(data, params, size) {
#' @export
#' @rdname draw_key
draw_key_text <- function(data, params, size) {
- data <- replace_null(
- unclass(data),
- label = "a", hjust = 0.5, vjust = 0.5, angle = 0
- )
- just <- rotate_just(data$angle, data$hjust, data$vjust)
- grob <- titleGrob(
+ data <- replace_null(unclass(data), label = "a", angle = 0)
+ hjust <- compute_just(data$hjust %||% 0.5)
+ vjust <- compute_just(data$vjust %||% 0.5)
+ just <- rotate_just(data$angle, hjust, vjust)
+ grob <- titleGrob(
data$label,
x = unit(just$hjust, "npc"), y = unit(just$vjust, "npc"),
angle = data$angle,
- hjust = data$hjust,
- vjust = data$vjust,
+ hjust = hjust,
+ vjust = vjust,
gp = gpar(
col = alpha(data$colour %||% data$fill %||% "black", data$alpha),
fontfamily = data$family %||% "",
@@ -286,12 +285,11 @@ draw_key_text <- function(data, params, size) {
#' @export
#' @rdname draw_key
draw_key_label <- function(data, params, size) {
- data <- replace_null(
- unclass(data),
- label = "a", hjust = 0.5, vjust = 0.5, angle = 0
- )
+ data <- replace_null(unclass(data), label = "a", angle = 0)
params$label.size <- params$label.size %||% 0.25
- just <- rotate_just(data$angle, data$hjust, data$vjust)
+ hjust <- compute_just(data$hjust %||% 0.5)
+ vjust <- compute_just(data$vjust %||% 0.5)
+ just <- rotate_just(data$angle, hjust, vjust)
padding <- rep(params$label.padding %||% unit(0.25, "lines"), length.out = 4)
descent <- font_descent(
family = data$family %||% "",
@@ -303,7 +301,7 @@ draw_key_label <- function(data, params, size) {
x = unit(just$hjust, "npc"),
y = unit(just$vjust, "npc") + descent,
angle = data$angle,
- just = c(data$hjust, data$vjust),
+ just = c(hjust, vjust),
padding = padding,
r = params$label.r %||% unit(0.15, "lines"),
text.gp = gpar(
diff --git a/R/margins.R b/R/margins.R
index 674d05bd46..b563331002 100644
--- a/R/margins.R
+++ b/R/margins.R
@@ -253,6 +253,15 @@ rotate_just <- function(angle, hjust, vjust) {
angle <- (angle %||% 0) %% 360
+ if (is.character(hjust)) {
+ hjust <- match(hjust, c("left", "right")) - 1
+ hjust[is.na(hjust)] <- 0.5
+ }
+ if (is.character(vjust)) {
+ vjust <- match(vjust, c("bottom", "top")) - 1
+ vjust[is.na(vjust)] <- 0.5
+ }
+
# Apply recycle rules
size <- vec_size_common(angle, hjust, vjust)
angle <- vec_recycle(angle, size)
diff --git a/R/scale-.R b/R/scale-.R
index d4776ca5ea..036e0052a9 100644
--- a/R/scale-.R
+++ b/R/scale-.R
@@ -143,7 +143,7 @@ continuous_scale <- function(aesthetics, scale_name = deprecated(), palette, nam
range = ContinuousRange$new(),
limits = limits,
- transformation = transform,
+ trans = transform,
na.value = na.value,
expand = expand,
rescaler = rescaler,
@@ -313,7 +313,7 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name =
range = ContinuousRange$new(),
limits = limits,
- transformation = transform,
+ trans = transform,
na.value = na.value,
expand = expand,
rescaler = rescaler,
@@ -356,7 +356,7 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name =
#' - `clone()` Returns a copy of the scale that can be trained
#' independently without affecting the original scale.
#'
-#' - `transform()` Transforms a vector of values using `self$transformation`.
+#' - `transform()` Transforms a vector of values using `self$trans`.
#' This occurs before the `Stat` is calculated.
#'
#' - `train()` Update the `self$range` of observed (transformed) data values with
@@ -386,7 +386,7 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name =
#' (`self$range`).
#'
#' - `get_breaks()` Calculates the final scale breaks in transformed data space
-#' based on on the combination of `self$breaks`, `self$transformation$breaks()` (for
+#' based on on the combination of `self$breaks`, `self$trans$breaks()` (for
#' continuous scales), and `limits`. Breaks outside of `limits` are assigned
#' a value of `NA` (continuous scales) or dropped (discrete scales).
#'
@@ -395,7 +395,7 @@ binned_scale <- function(aesthetics, scale_name = deprecated(), palette, name =
#'
#' - `get_breaks_minor()` For continuous scales, calculates the final scale minor breaks
#' in transformed data space based on the rescaled `breaks`, the value of `self$minor_breaks`,
-#' and the value of `self$transformation$minor_breaks()`. Discrete scales always return `NULL`.
+#' and the value of `self$trans$minor_breaks()`. Discrete scales always return `NULL`.
#'
#' - `get_transformation()` Returns the scale's transformation object.
#'
@@ -554,11 +554,7 @@ Scale <- ggproto("Scale", NULL,
},
get_transformation = function(self) {
- if (!is.null(self$trans)) {
- deprecate_soft0("3.5.0", I("Scale$trans"), I("Scale$transformation"))
- return(self$trans)
- }
- self$transformation
+ self$trans
},
clone = function(self) {
@@ -609,7 +605,7 @@ check_breaks_labels <- function(breaks, labels, call = NULL) {
default_transform <- function(self, x) {
transformation <- self$get_transformation()
new_x <- transformation$transform(x)
- check_transformation(x, new_x, self$transformation$name, call = self$call)
+ check_transformation(x, new_x, transformation$name, call = self$call)
new_x
}
@@ -629,7 +625,7 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale,
oob = censor,
minor_breaks = waiver(),
n.breaks = NULL,
- transformation = transform_identity(),
+ trans = transform_identity(),
is_discrete = function() FALSE,
@@ -639,11 +635,15 @@ ScaleContinuous <- ggproto("ScaleContinuous", Scale,
}
# Intercept error here to give examples and mention scale in call
if (is.factor(x) || !typeof(x) %in% c("integer", "double")) {
- cli::cli_abort(
- c("Discrete values supplied to continuous scale.",
- i = "Example values: {.and {.val {head(x, 5)}}}"),
- call = self$call
- )
+ # These assumptions only hold for standard ContinuousRange class, so
+ # we skip the error if another range class is used
+ if (inherits(self$range, "ContinuousRange")) {
+ cli::cli_abort(
+ c("Discrete values supplied to continuous scale.",
+ i = "Example values: {.and {.val {head(x, 5)}}}"),
+ call = self$call
+ )
+ }
}
self$range$train(x)
},
@@ -913,11 +913,15 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale,
}
# Intercept error here to give examples and mention scale in call
if (!is.discrete(x)) {
- cli::cli_abort(
- c("Continuous values supplied to discrete scale.",
- i = "Example values: {.and {.val {head(x, 5)}}}"),
- call = self$call
- )
+ # These assumptions only hold for standard DiscreteRange class, so
+ # we skip the error if another range class is used
+ if (inherits(self$range, "DiscreteRange")) {
+ cli::cli_abort(
+ c("Continuous values supplied to discrete scale.",
+ i = "Example values: {.and {.val {head(x, 5)}}}"),
+ call = self$call
+ )
+ }
}
self$range$train(x, drop = self$drop, na.rm = !self$na.translate)
},
diff --git a/R/scale-continuous.R b/R/scale-continuous.R
index 19b3e9cb44..53657c7817 100644
--- a/R/scale-continuous.R
+++ b/R/scale-continuous.R
@@ -86,7 +86,7 @@ scale_x_continuous <- function(name = waiver(), breaks = waiver(),
guide = waiver(), position = "bottom",
sec.axis = waiver()) {
call <- caller_call()
- if (is.null(call) || !any(startsWith(as.character(call[[1]]), "scale_"))) {
+ if (scale_override_call(call)) {
call <- current_call()
}
sc <- continuous_scale(
@@ -113,7 +113,7 @@ scale_y_continuous <- function(name = waiver(), breaks = waiver(),
guide = waiver(), position = "left",
sec.axis = waiver()) {
call <- caller_call()
- if (is.null(call) || !any(startsWith(as.character(call[[1]]), "scale_"))) {
+ if (scale_override_call(call)) {
call <- current_call()
}
sc <- continuous_scale(
@@ -198,3 +198,13 @@ scale_x_sqrt <- function(...) {
scale_y_sqrt <- function(...) {
scale_y_continuous(..., transform = transform_sqrt())
}
+
+# Helpers -----------------------------------------------------------------
+
+scale_override_call <- function(call = NULL) {
+ if (is.null(call) || is.function(call[[1]])) {
+ return(TRUE)
+ }
+ !any(startsWith(as.character(call[[1]]), "scale_"))
+}
+
diff --git a/R/scale-date.R b/R/scale-date.R
index f607b78847..a4adacdb2d 100644
--- a/R/scale-date.R
+++ b/R/scale-date.R
@@ -358,7 +358,7 @@ ScaleContinuousDatetime <- ggproto("ScaleContinuousDatetime", ScaleContinuous,
tz <- attr(x, "tzone")
if (is.null(self$timezone) && !is.null(tz)) {
self$timezone <- tz
- self$transformation <- transform_time(self$timezone)
+ self$trans <- transform_time(self$timezone)
}
ggproto_parent(ScaleContinuous, self)$transform(x)
},
@@ -405,7 +405,6 @@ ScaleContinuousDate <- ggproto("ScaleContinuousDate", ScaleContinuous,
return(NULL)
}
breaks <- floor(breaks)
- breaks[breaks >= limits[1] & breaks <= limits[2]]
},
break_info = function(self, range = NULL) {
breaks <- ggproto_parent(ScaleContinuous, self)$break_info(range)
diff --git a/R/scale-type.R b/R/scale-type.R
index 2feaa69c82..e9f3b8cc9b 100644
--- a/R/scale-type.R
+++ b/R/scale-type.R
@@ -2,7 +2,7 @@ find_scale <- function(aes, x, env = parent.frame()) {
# Inf is ambiguous; it can be used either with continuous scales or with
# discrete scales, so just skip in the hope that we will have a better guess
# with the other layers
- if (is.null(x) || (is_atomic(x) && all(is.infinite(x)))) {
+ if (is.null(x) || (is_atomic(x) && all(is.infinite(x))) || inherits(x, "AsIs")) {
return(NULL)
}
@@ -70,9 +70,6 @@ scale_type.default <- function(x) {
#' @export
scale_type.list <- function(x) "identity"
-#' @export
-scale_type.AsIs <- function(x) "identity"
-
#' @export
scale_type.logical <- function(x) "discrete"
diff --git a/R/scales-.R b/R/scales-.R
index 5e1fd3208a..e62eb0e8cb 100644
--- a/R/scales-.R
+++ b/R/scales-.R
@@ -89,8 +89,9 @@ ScalesList <- ggproto("ScalesList", NULL,
# If the scale contains to trans or trans is identity, there is no need
# to transform anything
idx_skip <- vapply(self$scales, function(x) {
+ transformation <- x$get_transformation()
has_default_transform(x) &&
- (is.null(x$transformation) || identical(x$transformation$transform, identity))
+ (is.null(transformation) || identical(transformation$transform, identity))
}, logical(1L))
scales <- self$scales[!idx_skip]
@@ -113,8 +114,9 @@ ScalesList <- ggproto("ScalesList", NULL,
# If the scale contains to trans or trans is identity, there is no need
# to transform anything
idx_skip <- vapply(self$scales, function(x) {
+ transformation <- x$get_transformation()
has_default_transform(x) &&
- (is.null(x$transformation) || identical(x$transformation$transform, identity))
+ (is.null(transformation) || identical(transformation$transform, identity))
}, logical(1))
scales <- self$scales[!idx_skip]
@@ -129,7 +131,11 @@ ScalesList <- ggproto("ScalesList", NULL,
if (length(aesthetics) == 0) {
return()
}
- lapply(df[aesthetics], scale$transformation$inverse)
+ inverse <- scale$get_transformation()$inverse
+ if (is.null(inverse)) {
+ return()
+ }
+ lapply(df[aesthetics], inverse)
}
), recursive = FALSE)
diff --git a/R/stat-function.R b/R/stat-function.R
index b43af4fb5a..8f31b8daba 100644
--- a/R/stat-function.R
+++ b/R/stat-function.R
@@ -66,7 +66,7 @@ StatFunction <- ggproto("StatFunction", Stat,
} else {
# For continuous scales, need to back transform from transformed range
# to original values
- x_trans <- scales$x$transformation$inverse(xseq)
+ x_trans <- scales$x$get_transformation()$inverse(xseq)
}
}
@@ -75,7 +75,7 @@ StatFunction <- ggproto("StatFunction", Stat,
y_out <- inject(fun(x_trans, !!!args))
if (!is.null(scales$y) && !scales$y$is_discrete()) {
# For continuous scales, need to apply transform
- y_out <- scales$y$transformation$transform(y_out)
+ y_out <- scales$y$get_transformation()$transform(y_out)
}
data_frame0(x = xseq, y = y_out)
diff --git a/R/theme-defaults.R b/R/theme-defaults.R
index e9436acfb9..00983d54ee 100644
--- a/R/theme-defaults.R
+++ b/R/theme-defaults.R
@@ -139,6 +139,8 @@ theme_grey <- function(base_size = 11, base_family = "",
axis.text.x.top = element_text(margin = margin(b = 0.8 * half_line / 2), vjust = 0),
axis.text.y = element_text(margin = margin(r = 0.8 * half_line / 2), hjust = 1),
axis.text.y.right = element_text(margin = margin(l = 0.8 * half_line / 2), hjust = 0),
+ axis.text.r = element_text(margin = margin(l = 0.8 * half_line / 2, r = 0.8 * half_line / 2),
+ hjust = 0.5),
axis.ticks = element_line(colour = "grey20"),
axis.ticks.length = unit(half_line / 2, "pt"),
axis.ticks.length.x = NULL,
@@ -164,7 +166,7 @@ theme_grey <- function(base_size = 11, base_family = "",
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
- vjust = 0
+ vjust = 1
),
legend.background = element_rect(colour = NA),
@@ -179,6 +181,7 @@ theme_grey <- function(base_size = 11, base_family = "",
legend.key.spacing = unit(half_line, "pt"),
legend.text = element_text(size = rel(0.8)),
legend.title = element_text(hjust = 0),
+ legend.ticks.length = rel(0.2),
legend.position = "right",
legend.direction = NULL,
legend.justification = "center",
@@ -476,6 +479,7 @@ theme_void <- function(base_size = 11, base_family = "",
legend.text = element_text(size = rel(0.8)),
legend.title = element_text(hjust = 0),
legend.key.spacing = unit(half_line, "pt"),
+ legend.ticks.length = rel(0.2),
strip.clip = "inherit",
strip.text = element_text(size = rel(0.8)),
strip.switch.pad.grid = unit(half_line / 2, "pt"),
@@ -569,7 +573,7 @@ theme_test <- function(base_size = 11, base_family = "",
axis.title.y.right = element_text(
angle = -90,
margin = margin(l = half_line / 2),
- vjust = 0
+ vjust = 1
),
legend.background = element_rect(colour = NA),
@@ -586,6 +590,7 @@ theme_test <- function(base_size = 11, base_family = "",
legend.key.spacing.y = NULL,
legend.text = element_text(size = rel(0.8)),
legend.title = element_text(hjust = 0),
+ legend.ticks.length = rel(0.2),
legend.position = "right",
legend.direction = NULL,
legend.justification = "center",
diff --git a/R/theme-elements.R b/R/theme-elements.R
index d90d11ae11..2d0a969c91 100644
--- a/R/theme-elements.R
+++ b/R/theme-elements.R
@@ -441,6 +441,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
axis.line.y = el_def("element_line", "axis.line"),
axis.line.y.left = el_def("element_line", "axis.line.y"),
axis.line.y.right = el_def("element_line", "axis.line.y"),
+ axis.line.theta = el_def("element_line", "axis.line.x"),
+ axis.line.r = el_def("element_line", "axis.line.y"),
axis.text.x = el_def("element_text", "axis.text"),
axis.text.x.top = el_def("element_text", "axis.text.x"),
@@ -448,6 +450,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
axis.text.y = el_def("element_text", "axis.text"),
axis.text.y.left = el_def("element_text", "axis.text.y"),
axis.text.y.right = el_def("element_text", "axis.text.y"),
+ axis.text.theta = el_def("element_text", "axis.text.x"),
+ axis.text.r = el_def("element_text", "axis.text.y"),
axis.ticks.length = el_def("unit"),
axis.ticks.length.x = el_def(c("unit", "rel"), "axis.ticks.length"),
@@ -456,6 +460,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
axis.ticks.length.y = el_def(c("unit", "rel"), "axis.ticks.length"),
axis.ticks.length.y.left = el_def(c("unit", "rel"), "axis.ticks.length.y"),
axis.ticks.length.y.right = el_def(c("unit", "rel"), "axis.ticks.length.y"),
+ axis.ticks.length.theta = el_def(c("unit", "rel"), "axis.ticks.length.x"),
+ axis.ticks.length.r = el_def(c("unit", "rel"), "axis.ticks.length.y"),
axis.ticks.x = el_def("element_line", "axis.ticks"),
axis.ticks.x.top = el_def("element_line", "axis.ticks.x"),
@@ -463,6 +469,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
axis.ticks.y = el_def("element_line", "axis.ticks"),
axis.ticks.y.left = el_def("element_line", "axis.ticks.y"),
axis.ticks.y.right = el_def("element_line", "axis.ticks.y"),
+ axis.ticks.theta = el_def("element_line", "axis.ticks.x"),
+ axis.ticks.r = el_def("element_line", "axis.ticks.y"),
axis.title.x = el_def("element_text", "axis.title"),
axis.title.x.top = el_def("element_text", "axis.title.x"),
@@ -475,6 +483,8 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
axis.minor.ticks.x.bottom = el_def("element_line", "axis.ticks.x.bottom"),
axis.minor.ticks.y.left = el_def("element_line", "axis.ticks.y.left"),
axis.minor.ticks.y.right = el_def("element_line", "axis.ticks.y.right"),
+ axis.minor.ticks.theta = el_def("element_line", "axis.ticks.theta"),
+ axis.minor.ticks.r = el_def("element_line", "axis.ticks.r"),
axis.minor.ticks.length = el_def(c("unit", "rel")),
axis.minor.ticks.length.x = el_def(c("unit", "rel"), "axis.minor.ticks.length"),
@@ -491,6 +501,12 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
axis.minor.ticks.length.y.right = el_def(
c("unit", "rel"), c("axis.minor.ticks.length.y", "axis.ticks.length.y.right")
),
+ axis.minor.ticks.length.theta = el_def(
+ c("unit", "rel"), c("axis.minor.ticks.length.x", "axis.ticks.length.theta"),
+ ),
+ axis.minor.ticks.length.r = el_def(
+ c("unit", "rel"), c("axis.minor.ticks.length.y", "axis.ticks.length.r")
+ ),
legend.background = el_def("element_rect", "rect"),
legend.margin = el_def("margin"),
@@ -506,7 +522,7 @@ el_def <- function(class = NULL, inherit = NULL, description = NULL) {
legend.frame = el_def("element_rect", "rect"),
legend.axis.line = el_def("element_line", "line"),
legend.ticks = el_def("element_line", "legend.axis.line"),
- legend.ticks.length = el_def("unit"),
+ legend.ticks.length = el_def(c("rel", "unit"), "legend.key.size"),
legend.text = el_def("element_text", "text"),
legend.text.position = el_def("character"),
legend.title = el_def("element_text", "title"),
diff --git a/R/theme.R b/R/theme.R
index 1e012d13ad..86bf893225 100644
--- a/R/theme.R
+++ b/R/theme.R
@@ -34,28 +34,28 @@
#' `axis.title.y.left`, `axis.title.y.right`). `axis.title.*.*` inherits from
#' `axis.title.*` which inherits from `axis.title`, which in turn inherits
#' from `text`
-#' @param axis.text,axis.text.x,axis.text.y,axis.text.x.top,axis.text.x.bottom,axis.text.y.left,axis.text.y.right
+#' @param axis.text,axis.text.x,axis.text.y,axis.text.x.top,axis.text.x.bottom,axis.text.y.left,axis.text.y.right,axis.text.theta,axis.text.r
#' tick labels along axes ([element_text()]). Specify all axis tick labels (`axis.text`),
#' tick labels by plane (using `axis.text.x` or `axis.text.y`), or individually
#' for each axis (using `axis.text.x.bottom`, `axis.text.x.top`,
#' `axis.text.y.left`, `axis.text.y.right`). `axis.text.*.*` inherits from
#' `axis.text.*` which inherits from `axis.text`, which in turn inherits
#' from `text`
-#' @param axis.ticks,axis.ticks.x,axis.ticks.x.top,axis.ticks.x.bottom,axis.ticks.y,axis.ticks.y.left,axis.ticks.y.right
+#' @param axis.ticks,axis.ticks.x,axis.ticks.x.top,axis.ticks.x.bottom,axis.ticks.y,axis.ticks.y.left,axis.ticks.y.right,axis.ticks.theta,axis.ticks.r
#' tick marks along axes ([element_line()]). Specify all tick marks (`axis.ticks`),
#' ticks by plane (using `axis.ticks.x` or `axis.ticks.y`), or individually
#' for each axis (using `axis.ticks.x.bottom`, `axis.ticks.x.top`,
#' `axis.ticks.y.left`, `axis.ticks.y.right`). `axis.ticks.*.*` inherits from
#' `axis.ticks.*` which inherits from `axis.ticks`, which in turn inherits
#' from `line`
-#' @param axis.minor.ticks.x.top,axis.minor.ticks.x.bottom,axis.minor.ticks.y.left,axis.minor.ticks.y.right,
+#' @param axis.minor.ticks.x.top,axis.minor.ticks.x.bottom,axis.minor.ticks.y.left,axis.minor.ticks.y.right,axis.minor.ticks.theta,axis.minor.ticks.r,
#' minor tick marks along axes ([element_line()]). `axis.minor.ticks.*.*`
#' inherit from the corresponding major ticks `axis.ticks.*.*`.
-#' @param axis.ticks.length,axis.ticks.length.x,axis.ticks.length.x.top,axis.ticks.length.x.bottom,axis.ticks.length.y,axis.ticks.length.y.left,axis.ticks.length.y.right
+#' @param axis.ticks.length,axis.ticks.length.x,axis.ticks.length.x.top,axis.ticks.length.x.bottom,axis.ticks.length.y,axis.ticks.length.y.left,axis.ticks.length.y.right,axis.ticks.length.theta,axis.ticks.length.r
#' length of tick marks (`unit`)
-#' @param axis.minor.ticks.length,axis.minor.ticks.length.x,axis.minor.ticks.length.x.top,axis.minor.ticks.length.x.bottom,axis.minor.ticks.length.y,axis.minor.ticks.length.y.left,axis.minor.ticks.length.y.right
+#' @param axis.minor.ticks.length,axis.minor.ticks.length.x,axis.minor.ticks.length.x.top,axis.minor.ticks.length.x.bottom,axis.minor.ticks.length.y,axis.minor.ticks.length.y.left,axis.minor.ticks.length.y.right,axis.minor.ticks.length.theta,axis.minor.ticks.length.r
#' length of minor tick marks (`unit`), or relative to `axis.ticks.length` when provided with `rel()`.
-#' @param axis.line,axis.line.x,axis.line.x.top,axis.line.x.bottom,axis.line.y,axis.line.y.left,axis.line.y.right
+#' @param axis.line,axis.line.x,axis.line.x.top,axis.line.x.bottom,axis.line.y,axis.line.y.left,axis.line.y.right,axis.line.theta,axis.line.r
#' lines along axes ([element_line()]). Specify lines along all axes (`axis.line`),
#' lines for each plane (using `axis.line.x` or `axis.line.y`), or individually
#' for each axis (using `axis.line.x.bottom`, `axis.line.x.top`,
@@ -323,6 +323,8 @@ theme <- function(...,
axis.text.y,
axis.text.y.left,
axis.text.y.right,
+ axis.text.theta,
+ axis.text.r,
axis.ticks,
axis.ticks.x,
axis.ticks.x.top,
@@ -330,10 +332,14 @@ theme <- function(...,
axis.ticks.y,
axis.ticks.y.left,
axis.ticks.y.right,
+ axis.ticks.theta,
+ axis.ticks.r,
axis.minor.ticks.x.top,
axis.minor.ticks.x.bottom,
axis.minor.ticks.y.left,
axis.minor.ticks.y.right,
+ axis.minor.ticks.theta,
+ axis.minor.ticks.r,
axis.ticks.length,
axis.ticks.length.x,
axis.ticks.length.x.top,
@@ -341,6 +347,8 @@ theme <- function(...,
axis.ticks.length.y,
axis.ticks.length.y.left,
axis.ticks.length.y.right,
+ axis.ticks.length.theta,
+ axis.ticks.length.r,
axis.minor.ticks.length,
axis.minor.ticks.length.x,
axis.minor.ticks.length.x.top,
@@ -348,6 +356,8 @@ theme <- function(...,
axis.minor.ticks.length.y,
axis.minor.ticks.length.y.left,
axis.minor.ticks.length.y.right,
+ axis.minor.ticks.length.theta,
+ axis.minor.ticks.length.r,
axis.line,
axis.line.x,
axis.line.x.top,
@@ -355,6 +365,8 @@ theme <- function(...,
axis.line.y,
axis.line.y.left,
axis.line.y.right,
+ axis.line.theta,
+ axis.line.r,
legend.background,
legend.margin,
legend.spacing,
@@ -529,13 +541,13 @@ is_theme_validate <- function(x) {
isTRUE(validate %||% TRUE)
}
-validate_theme <- function(theme, tree = get_element_tree()) {
+validate_theme <- function(theme, tree = get_element_tree(), call = caller_env()) {
if (!is_theme_validate(theme)) {
return()
}
mapply(
validate_element, theme, names(theme),
- MoreArgs = list(element_tree = tree)
+ MoreArgs = list(element_tree = tree, call = call)
)
}
diff --git a/R/utilities.R b/R/utilities.R
index 127765dafb..83037d475c 100644
--- a/R/utilities.R
+++ b/R/utilities.R
@@ -320,7 +320,7 @@ find_args <- function(...) {
vals <- mget(args, envir = env)
vals <- vals[!vapply(vals, is_missing_arg, logical(1))]
- modify_list(vals, list2(..., `...` = NULL))
+ modify_list(vals, dots_list(..., `...` = NULL, .ignore_empty = "all"))
}
# Used in annotations to ensure printed even when no
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 1bf6161b79..699e2df919 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -268,6 +268,8 @@ articles:
news:
releases:
+ - text: "Version 3.5.0"
+ href: https://www.tidyverse.org/blog/2024/02/ggplot2-3-5-0/
- text: "Version 3.4.0"
href: https://www.tidyverse.org/blog/2022/11/ggplot2-3-4-0/
- text: "Version 3.3.0"
diff --git a/cran-comments.md b/cran-comments.md
index 78f461ac54..63d8a4bc4c 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,66 +1,220 @@
-This is a patch release responding to changes in R-devel concerning the behavior
-of `is.atomic()`. Further, it contains the removal of maptools and rgeos which
-is set for archival soon
+This is a large minor release with both a lot of new features and a complete
+rewrite of part of the internals. As a result, this release does break a range
+of reverse dependencies. All of them has been informed very well in advance (4
+weeks) and have been provided with patches to fix their issues. The remaining
+problematic reverse dependencies were further notified 2 weeks ago to remind
+them to submit a fix, so we believe we have been very lenient towards them.
## revdepcheck results
-We checked 4771 reverse dependencies (4716 from CRAN + 55 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 4935 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
- * We saw 2 new problems
- * We failed to check 42 packages
+ * We saw 56 new problems
+ * We failed to check 13 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
-* jfa
- checking re-building of vignette outputs ... WARNING
+* AcademicThemes
+ checking tests ... ERROR
+
+* afex
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* archeoViz
+ checking tests ... ERROR
+
+* assignPOP
+ checking tests ... ERROR
+
+* bioassays
+ checking tests ... ERROR
+
+* BOSO
+ checking re-building of vignette outputs ... ERROR
+
+* breakDown
+ checking tests ... ERROR
+
+* canadianmaps
+ checking tests ... ERROR
+
+* CAST
+ checking installed package size ... NOTE
+
+* CEDA
+ checking re-building of vignette outputs ... ERROR
+
+* cobalt
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* constructive
+ checking tests ... ERROR
+
+* docxtools
+ checking tests ... ERROR
+
+* dynamAedes
+ checking re-building of vignette outputs ... ERROR
+
+* EcoDiet
+ checking re-building of vignette outputs ... ERROR
+
+* epos
+ checking tests ... ERROR
+
+* feasts
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* fitODBODRshiny
+ checking examples ... ERROR
+
+* fmeffects
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* genekitr
+ checking examples ... ERROR
+
+* geomtextpath
+ checking tests ... ERROR
+
+* ggedit
+ checking examples ... ERROR
+
+* gghdr
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggiraph
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* ggiraphExtra
+ checking examples ... ERROR
+
+* ggparallel
+ checking tests ... ERROR
+
+* ggprism
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggraph
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggside
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggstance
+ checking tests ... ERROR
+
+* ggstatsplot
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* ghibli
+ checking tests ... ERROR
+
+* glancedata
+ checking tests ... ERROR
+
+* grafify
+ checking tests ... ERROR
+
+* inTextSummaryTable
+ checking tests ... ERROR
+
+* LMoFit
+ checking re-building of vignette outputs ... ERROR
+
+* manydata
+ checking tests ... ERROR
+
+* MiscMetabar
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* miWQS
+ checking re-building of vignette outputs ... ERROR
+
+* NAIR
+ checking tests ... ERROR
+
+* OpenLand
+ checking tests ... ERROR
+
+* platetools
+ checking tests ... ERROR
+
+* plot3logit
+ checking re-building of vignette outputs ... ERROR
+
+* PTXQC
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* rabhit
+ checking re-building of vignette outputs ... ERROR
+
+* santaR
+ checking tests ... ERROR
+
+* saros
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* scCustomize
+ checking examples ... ERROR
+
+* scdhlm
+ checking tests ... ERROR
+
+* see
+ checking examples ... ERROR
+
+* spqdep
+ checking re-building of vignette outputs ... ERROR
+
+* TCIU
+ checking re-building of vignette outputs ... ERROR
+
+* tmt
+ checking tests ... ERROR
+
+* tvthemes
+ checking tests ... ERROR
+
+* ufs
+ checking examples ... ERROR
-* SCORPIUS
+* visR
+ checking examples ... ERROR
checking tests ... ERROR
### Failed to check
-* ale (NA)
-* aPEAR (NA)
-* bayesdfa (NA)
-* BrailleR (NA)
-* CausalImpact (NA)
-* CensMFM (NA)
-* cinaR (NA)
-* fdacluster (NA)
-* genekitr (NA)
-* ggPMX (NA)
-* grandR (NA)
-* HeckmanEM (NA)
-* immcp (NA)
-* loon.ggplot (NA)
-* MACP (NA)
-* MarketMatching (NA)
-* MARVEL (NA)
-* MSclassifR (NA)
-* nlmixr2 (NA)
-* nlmixr2extra (NA)
-* nlmixr2plot (NA)
-* nlmixr2rpt (NA)
-* numbat (NA)
-* oHMMed (NA)
-* OlinkAnalyze (NA)
-* OpenMx (NA)
-* phylosem (NA)
-* PsychWordVec (NA)
-* RcppCensSpatial (NA)
-* rmsb (NA)
-* rstanarm (NA)
-* RVA (NA)
-* SCpubr (NA)
-* SSVS (NA)
-* streamDAG (NA)
-* TestAnaAPP (NA)
-* tidySEM (NA)
-* tinyarray (NA)
-* TOmicsVis (NA)
-* valse (NA)
-* vivid (NA)
-* xpose.nlmixr2 (NA)
+* bayesdfa (NA)
+* ctsem (NA)
+* geostan (NA)
+* ggtern (NA)
+* grandR (NA)
+* rmsb (NA)
+* rstanarm (NA)
+* Seurat (NA)
+* streamDAG (NA)
+* treestats (NA)
+* TriDimRegression (NA)
+* triptych (NA)
+* valse (NA)
diff --git a/man/coord_polar.Rd b/man/coord_polar.Rd
index da54c854fa..b4b3ac18bd 100644
--- a/man/coord_polar.Rd
+++ b/man/coord_polar.Rd
@@ -16,7 +16,7 @@ coord_radial(
clip = "off",
r_axis_inside = NULL,
rotate_angle = FALSE,
- donut = 0
+ inner.radius = 0
)
}
\arguments{
@@ -49,7 +49,7 @@ in accordance with the computed \code{theta} position. If \code{FALSE} (default)
no such transformation is performed. Can be useful to rotate text geoms in
alignment with the coordinates.}
-\item{donut}{A \code{numeric} between 0 and 1 setting the size of a donut hole.}
+\item{inner.radius}{A \code{numeric} between 0 and 1 setting the size of a inner.radius hole.}
}
\description{
The polar coordinate system is most commonly used for pie charts, which
@@ -62,7 +62,7 @@ In \code{coord_radial()}, position guides are can be defined by using
these guides require \code{r} and \code{theta} as available aesthetics. The classic
\code{guide_axis()} can be used for the \code{r} positions and \code{guide_axis_theta()} can
be used for the \code{theta} positions. Using the \code{theta.sec} position is only
-sensible when \code{donut > 0}.
+sensible when \code{inner.radius > 0}.
}
\examples{
# NOTE: Use these plots with caution - polar coordinates has
@@ -114,5 +114,5 @@ doh + geom_bar(width = 0.9, position = "fill") + coord_polar(theta = "y")
# A partial polar plot
ggplot(mtcars, aes(disp, mpg)) +
geom_point() +
- coord_radial(start = -0.4 * pi, end = 0.4 * pi, donut = 0.3)
+ coord_radial(start = -0.4 * pi, end = 0.4 * pi, inner.radius = 0.3)
}
diff --git a/man/ggplot2-ggproto.Rd b/man/ggplot2-ggproto.Rd
index 282ab4e5ce..1531fe7994 100644
--- a/man/ggplot2-ggproto.Rd
+++ b/man/ggplot2-ggproto.Rd
@@ -450,6 +450,8 @@ the \verb{build_*()} methods should be arranged.
\item \code{assemble_drawing()} Take the graphical objects produced by the \verb{build_*()}
methods, the measurements from \code{measure_grobs()} and layout from
\code{arrange_layout()} to finalise the guide.
+\item \code{add_title} Adds the title to a gtable, taking into account the size
+of the title as well as the gtable size.
}
}
@@ -517,7 +519,7 @@ Methods:
it has no information with which to calculate its \code{limits}).
\item \code{clone()} Returns a copy of the scale that can be trained
independently without affecting the original scale.
-\item \code{transform()} Transforms a vector of values using \code{self$transformation}.
+\item \code{transform()} Transforms a vector of values using \code{self$trans}.
This occurs before the \code{Stat} is calculated.
\item \code{train()} Update the \code{self$range} of observed (transformed) data values with
a vector of (possibly) new values.
@@ -540,14 +542,14 @@ accept a data frame, and apply the \code{transform}, \code{train}, and \code{map
based on the combination of \code{self$limits} and/or the range of observed values
(\code{self$range}).
\item \code{get_breaks()} Calculates the final scale breaks in transformed data space
-based on on the combination of \code{self$breaks}, \code{self$transformation$breaks()} (for
+based on on the combination of \code{self$breaks}, \code{self$trans$breaks()} (for
continuous scales), and \code{limits}. Breaks outside of \code{limits} are assigned
a value of \code{NA} (continuous scales) or dropped (discrete scales).
\item \code{get_labels()} Calculates labels for a given set of (transformed) \code{breaks}
based on the combination of \code{self$labels} and \code{breaks}.
\item \code{get_breaks_minor()} For continuous scales, calculates the final scale minor breaks
in transformed data space based on the rescaled \code{breaks}, the value of \code{self$minor_breaks},
-and the value of \code{self$transformation$minor_breaks()}. Discrete scales always return \code{NULL}.
+and the value of \code{self$trans$minor_breaks()}. Discrete scales always return \code{NULL}.
\item \code{get_transformation()} Returns the scale's transformation object.
\item \code{make_title()} Hook to modify the title that is calculated during guide construction
(for non-position scales) or when the \code{Layout} calculates the x and y labels
diff --git a/man/guide_custom.Rd b/man/guide_custom.Rd
index ad8a77b80b..74c8a9f00a 100644
--- a/man/guide_custom.Rd
+++ b/man/guide_custom.Rd
@@ -9,8 +9,7 @@ guide_custom(
width = grobWidth(grob),
height = grobHeight(grob),
title = NULL,
- title.position = "top",
- margin = NULL,
+ theme = NULL,
position = NULL,
order = 0
)
@@ -24,13 +23,12 @@ in \code{\link[grid:unit]{grid::unit()}}s.}
\item{title}{A character string or expression indicating the title of guide.
If \code{NULL} (default), no title is shown.}
-\item{title.position}{A character string indicating the position of a title.
-One of \code{"top"} (default), \code{"bottom"}, \code{"left"} or \code{"right"}.}
+\item{theme}{A \code{\link[=theme]{theme}} object to style the guide individually or
+differently from the plot's theme settings. The \code{theme} argument in the
+guide overrides, and is combined with, the plot's theme.}
-\item{margin}{Margins around the guide. See \code{\link[=margin]{margin()}} for more details. If
-\code{NULL} (default), margins are taken from the \code{legend.margin} theme setting.}
-
-\item{position}{Currently not in use.}
+\item{position}{A character string indicating where the legend should be
+placed relative to the plot panels.}
\item{order}{positive integer less than 99 that specifies the order of
this guide among multiple guides. This controls the order in which
diff --git a/man/sec_axis.Rd b/man/sec_axis.Rd
index bca906a079..c8435fe28f 100644
--- a/man/sec_axis.Rd
+++ b/man/sec_axis.Rd
@@ -17,11 +17,11 @@ sec_axis(
dup_axis(
transform = ~.,
- trans = deprecated(),
name = derive(),
breaks = derive(),
labels = derive(),
- guide = derive()
+ guide = derive(),
+ trans = deprecated()
)
derive()
diff --git a/man/theme.Rd b/man/theme.Rd
index 8f4ea20015..3b93db359d 100644
--- a/man/theme.Rd
+++ b/man/theme.Rd
@@ -25,6 +25,8 @@ theme(
axis.text.y,
axis.text.y.left,
axis.text.y.right,
+ axis.text.theta,
+ axis.text.r,
axis.ticks,
axis.ticks.x,
axis.ticks.x.top,
@@ -32,10 +34,14 @@ theme(
axis.ticks.y,
axis.ticks.y.left,
axis.ticks.y.right,
+ axis.ticks.theta,
+ axis.ticks.r,
axis.minor.ticks.x.top,
axis.minor.ticks.x.bottom,
axis.minor.ticks.y.left,
axis.minor.ticks.y.right,
+ axis.minor.ticks.theta,
+ axis.minor.ticks.r,
axis.ticks.length,
axis.ticks.length.x,
axis.ticks.length.x.top,
@@ -43,6 +49,8 @@ theme(
axis.ticks.length.y,
axis.ticks.length.y.left,
axis.ticks.length.y.right,
+ axis.ticks.length.theta,
+ axis.ticks.length.r,
axis.minor.ticks.length,
axis.minor.ticks.length.x,
axis.minor.ticks.length.x.top,
@@ -50,6 +58,8 @@ theme(
axis.minor.ticks.length.y,
axis.minor.ticks.length.y.left,
axis.minor.ticks.length.y.right,
+ axis.minor.ticks.length.theta,
+ axis.minor.ticks.length.r,
axis.line,
axis.line.x,
axis.line.x.top,
@@ -57,6 +67,8 @@ theme(
axis.line.y,
axis.line.y.left,
axis.line.y.right,
+ axis.line.theta,
+ axis.line.r,
legend.background,
legend.margin,
legend.spacing,
@@ -156,28 +168,28 @@ for each axis (using \code{axis.title.x.bottom}, \code{axis.title.x.top},
\verb{axis.title.*} which inherits from \code{axis.title}, which in turn inherits
from \code{text}}
-\item{axis.text, axis.text.x, axis.text.y, axis.text.x.top, axis.text.x.bottom, axis.text.y.left, axis.text.y.right}{tick labels along axes (\code{\link[=element_text]{element_text()}}). Specify all axis tick labels (\code{axis.text}),
+\item{axis.text, axis.text.x, axis.text.y, axis.text.x.top, axis.text.x.bottom, axis.text.y.left, axis.text.y.right, axis.text.theta, axis.text.r}{tick labels along axes (\code{\link[=element_text]{element_text()}}). Specify all axis tick labels (\code{axis.text}),
tick labels by plane (using \code{axis.text.x} or \code{axis.text.y}), or individually
for each axis (using \code{axis.text.x.bottom}, \code{axis.text.x.top},
\code{axis.text.y.left}, \code{axis.text.y.right}). \verb{axis.text.*.*} inherits from
\verb{axis.text.*} which inherits from \code{axis.text}, which in turn inherits
from \code{text}}
-\item{axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right}{tick marks along axes (\code{\link[=element_line]{element_line()}}). Specify all tick marks (\code{axis.ticks}),
+\item{axis.ticks, axis.ticks.x, axis.ticks.x.top, axis.ticks.x.bottom, axis.ticks.y, axis.ticks.y.left, axis.ticks.y.right, axis.ticks.theta, axis.ticks.r}{tick marks along axes (\code{\link[=element_line]{element_line()}}). Specify all tick marks (\code{axis.ticks}),
ticks by plane (using \code{axis.ticks.x} or \code{axis.ticks.y}), or individually
for each axis (using \code{axis.ticks.x.bottom}, \code{axis.ticks.x.top},
\code{axis.ticks.y.left}, \code{axis.ticks.y.right}). \verb{axis.ticks.*.*} inherits from
\verb{axis.ticks.*} which inherits from \code{axis.ticks}, which in turn inherits
from \code{line}}
-\item{axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, }{minor tick marks along axes (\code{\link[=element_line]{element_line()}}). \verb{axis.minor.ticks.*.*}
+\item{axis.minor.ticks.x.top, axis.minor.ticks.x.bottom, axis.minor.ticks.y.left, axis.minor.ticks.y.right, axis.minor.ticks.theta, axis.minor.ticks.r, }{minor tick marks along axes (\code{\link[=element_line]{element_line()}}). \verb{axis.minor.ticks.*.*}
inherit from the corresponding major ticks \verb{axis.ticks.*.*}.}
-\item{axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right}{length of tick marks (\code{unit})}
+\item{axis.ticks.length, axis.ticks.length.x, axis.ticks.length.x.top, axis.ticks.length.x.bottom, axis.ticks.length.y, axis.ticks.length.y.left, axis.ticks.length.y.right, axis.ticks.length.theta, axis.ticks.length.r}{length of tick marks (\code{unit})}
-\item{axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right}{length of minor tick marks (\code{unit}), or relative to \code{axis.ticks.length} when provided with \code{rel()}.}
+\item{axis.minor.ticks.length, axis.minor.ticks.length.x, axis.minor.ticks.length.x.top, axis.minor.ticks.length.x.bottom, axis.minor.ticks.length.y, axis.minor.ticks.length.y.left, axis.minor.ticks.length.y.right, axis.minor.ticks.length.theta, axis.minor.ticks.length.r}{length of minor tick marks (\code{unit}), or relative to \code{axis.ticks.length} when provided with \code{rel()}.}
-\item{axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right}{lines along axes (\code{\link[=element_line]{element_line()}}). Specify lines along all axes (\code{axis.line}),
+\item{axis.line, axis.line.x, axis.line.x.top, axis.line.x.bottom, axis.line.y, axis.line.y.left, axis.line.y.right, axis.line.theta, axis.line.r}{lines along axes (\code{\link[=element_line]{element_line()}}). Specify lines along all axes (\code{axis.line}),
lines for each plane (using \code{axis.line.x} or \code{axis.line.y}), or individually
for each axis (using \code{axis.line.x.bottom}, \code{axis.line.x.top},
\code{axis.line.y.left}, \code{axis.line.y.right}). \verb{axis.line.*.*} inherits from
diff --git a/revdep/README.md b/revdep/README.md
index f33e525c66..1b349fca91 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,111 +1,81 @@
# Revdeps
-## Failed to check (97)
+## Failed to check (13)
-|package |version |error |warning |note |
-|:---------------|:-------|:-----|:-------|:----|
-|NA |? | | | |
-|NA |? | | | |
-|ale |0.1.0 |1 | | |
-|aPEAR |? | | | |
-|NA |? | | | |
-|bayesdfa |1.2.0 |1 | | |
-|NA |? | | | |
-|BrailleR |1.0.2 |1 | | |
-|NA |? | | | |
-|CausalImpact |? | | | |
-|CensMFM |? | | | |
-|cinaR |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|fdacluster |0.3.0 |1 | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|genekitr |? | | | |
-|NA |? | | | |
-|ggPMX |? | | | |
-|NA |? | | | |
-|grandR |? | | | |
-|HeckmanEM |? | | | |
-|immcp |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|loon.ggplot |? | | | |
-|MACP |? | | | |
-|NA |? | | | |
-|MarketMatching |? | | | |
-|MARVEL |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|MSclassifR |? | | | |
-|nlmixr2 |? | | | |
-|nlmixr2extra |? | | | |
-|nlmixr2plot |? | | | |
-|nlmixr2rpt |? | | | |
-|NA |? | | | |
-|numbat |? | | | |
-|NA |? | | | |
-|oHMMed |? | | | |
-|OlinkAnalyze |? | | | |
-|OpenMx |? | | | |
-|phylosem |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|PsychWordVec |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|RcppCensSpatial |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|rmsb |1.0-0 |1 | | |
-|rstanarm |2.26.1 |1 | | |
-|NA |? | | | |
-|RVA |? | | | |
-|NA |? | | | |
-|SCpubr |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|SSVS |? | | | |
-|streamDAG |? | | | |
-|TestAnaAPP |? | | | |
-|tidySEM |? | | | |
-|NA |? | | | |
-|tinyarray |? | | | |
-|TOmicsVis |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|valse |0.1-0 |1 | | |
-|NA |? | | | |
-|NA |? | | | |
-|vivid |? | | | |
-|NA |? | | | |
-|NA |? | | | |
-|xpose.nlmixr2 |? | | | |
-|NA |? | | | |
+|package |version |error |warning |note |
+|:----------------|:-------|:------|:-------|:----|
+|bayesdfa |1.3.2 |1 | | |
+|ctsem |3.9.1 |1 | | |
+|geostan |0.5.3 |1 | | |
+|[ggtern](failures.md#ggtern)|3.4.2 |__+1__ | |1 -1 |
+|grandR |? | | | |
+|rmsb |1.0-0 |1 | | |
+|rstanarm |2.32.1 |1 | | |
+|Seurat |? | | | |
+|streamDAG |? | | | |
+|treestats |1.0.5 |1 | | |
+|TriDimRegression |1.0.2 |1 | | |
+|triptych |0.1.2 |1 | | |
+|valse |0.1-0 |1 | | |
-## New problems (2)
+## New problems (56)
-|package |version |error |warning |note |
-|:--------------------------------|:-------|:------|:-------|:----|
-|[jfa](problems.md#jfa) |0.7.0 | |__+1__ |3 |
-|[SCORPIUS](problems.md#scorpius) |1.0.9 |__+1__ | | |
+|package |version |error |warning |note |
+|:------------------|:-------|:------|:-------|:------|
+|[AcademicThemes](problems.md#academicthemes)|0.0.1 |__+1__ | | |
+|[afex](problems.md#afex)|1.3-0 |__+2__ | | |
+|[archeoViz](problems.md#archeoviz)|1.3.4 |__+1__ | | |
+|[assignPOP](problems.md#assignpop)|1.2.4 |__+1__ | | |
+|[bioassays](problems.md#bioassays)|1.0.1 |__+1__ | | |
+|[BOSO](problems.md#boso)|1.0.3 |__+1__ | |1 |
+|[breakDown](problems.md#breakdown)|0.2.1 |__+1__ | | |
+|[canadianmaps](problems.md#canadianmaps)|1.3.0 |__+1__ | |2 |
+|[CAST](problems.md#cast)|0.9.0 | | |__+1__ |
+|[CEDA](problems.md#ceda)|1.1.0 |__+1__ | | |
+|[cobalt](problems.md#cobalt)|4.5.3 |__+2__ | | |
+|[constructive](problems.md#constructive)|0.2.0 |__+1__ | | |
+|[docxtools](problems.md#docxtools)|0.3.0 |__+1__ | | |
+|[dynamAedes](problems.md#dynamaedes)|2.2.8 |__+1__ | | |
+|[EcoDiet](problems.md#ecodiet)|2.0.0 |__+1__ | | |
+|[epos](problems.md#epos)|1.0 |__+1__ | |2 |
+|[feasts](problems.md#feasts)|0.3.1 |__+3__ | | |
+|[fitODBODRshiny](problems.md#fitodbodrshiny)|1.0.0 |__+1__ | |1 |
+|[fmeffects](problems.md#fmeffects)|0.1.1 |__+2__ | | |
+|[genekitr](problems.md#genekitr)|1.2.5 |__+1__ | | |
+|[geomtextpath](problems.md#geomtextpath)|0.1.1 |__+1__ | | |
+|[ggedit](problems.md#ggedit)|0.3.1 |__+1__ | |1 |
+|[gghdr](problems.md#gghdr)|0.2.0 |__+3__ | | |
+|[ggiraph](problems.md#ggiraph)|0.8.8 |__+2__ | |1 |
+|[ggiraphExtra](problems.md#ggiraphextra)|0.3.0 |__+1__ | | |
+|[ggparallel](problems.md#ggparallel)|0.3.0 |__+1__ | | |
+|[ggprism](problems.md#ggprism)|1.0.4 |__+3__ | | |
+|[ggraph](problems.md#ggraph)|2.1.0 |__+2__ | |2 |
+|[ggside](problems.md#ggside)|0.2.3 |__+3__ | | |
+|[ggstance](problems.md#ggstance)|0.3.6 |__+1__ | | |
+|[ggstatsplot](problems.md#ggstatsplot)|0.12.2 |__+2__ | | |
+|[ghibli](problems.md#ghibli)|0.3.3 |__+1__ | | |
+|[glancedata](problems.md#glancedata)|1.0.1 |__+1__ | |1 |
+|[grafify](problems.md#grafify)|4.0 |__+1__ | |2 |
+|[inTextSummaryTable](problems.md#intextsummarytable)|3.3.1 |__+1__ | |1 |
+|[LMoFit](problems.md#lmofit)|0.1.6 |__+1__ | | |
+|[manydata](problems.md#manydata)|0.8.3 |__+1__ | |1 |
+|[MiscMetabar](problems.md#miscmetabar)|0.7.9 |__+2__ | | |
+|[miWQS](problems.md#miwqs)|0.4.4 |__+1__ |-1 | |
+|[NAIR](problems.md#nair)|1.0.3 |__+1__ | |1 |
+|[OpenLand](problems.md#openland)|1.0.2 |__+1__ | | |
+|[platetools](problems.md#platetools)|0.1.5 |__+1__ | | |
+|[plot3logit](problems.md#plot3logit)|3.1.4 |__+1__ | | |
+|[PTXQC](problems.md#ptxqc)|1.1.0 |__+2__ | |1 |
+|[rabhit](problems.md#rabhit)|0.2.5 |__+1__ |-1 | |
+|[santaR](problems.md#santar)|1.2.3 |__+1__ | |1 |
+|[saros](problems.md#saros)|1.0.1 |__+2__ | | |
+|[scCustomize](problems.md#sccustomize)|2.0.1 |__+1__ | | |
+|[scdhlm](problems.md#scdhlm)|0.7.2 |__+1__ | | |
+|[see](problems.md#see)|0.8.2 |__+1__ | | |
+|[spqdep](problems.md#spqdep)|0.1.3.2 |__+1__ | |2 |
+|[TCIU](problems.md#tciu)|1.2.4 |__+1__ | |1 |
+|[tmt](problems.md#tmt)|0.3.1-2 |__+1__ | | |
+|[tvthemes](problems.md#tvthemes)|1.3.2 |__+1__ | | |
+|[ufs](problems.md#ufs)|0.5.10 |__+1__ | | |
+|[visR](problems.md#visr)|0.4.0 |__+2__ | | |
diff --git a/revdep/cran.md b/revdep/cran.md
index ca9d093bbe..25098e5f12 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,62 +1,213 @@
## revdepcheck results
-We checked 4771 reverse dependencies (4716 from CRAN + 55 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 4935 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
- * We saw 2 new problems
- * We failed to check 42 packages
+ * We saw 56 new problems
+ * We failed to check 13 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
-* jfa
- checking re-building of vignette outputs ... WARNING
+* AcademicThemes
+ checking tests ... ERROR
+
+* afex
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* archeoViz
+ checking tests ... ERROR
+
+* assignPOP
+ checking tests ... ERROR
+
+* bioassays
+ checking tests ... ERROR
+
+* BOSO
+ checking re-building of vignette outputs ... ERROR
+
+* breakDown
+ checking tests ... ERROR
+
+* canadianmaps
+ checking tests ... ERROR
+
+* CAST
+ checking installed package size ... NOTE
+
+* CEDA
+ checking re-building of vignette outputs ... ERROR
+
+* cobalt
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* constructive
+ checking tests ... ERROR
+
+* docxtools
+ checking tests ... ERROR
+
+* dynamAedes
+ checking re-building of vignette outputs ... ERROR
+
+* EcoDiet
+ checking re-building of vignette outputs ... ERROR
+
+* epos
+ checking tests ... ERROR
+
+* feasts
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* fitODBODRshiny
+ checking examples ... ERROR
+
+* fmeffects
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* genekitr
+ checking examples ... ERROR
+
+* geomtextpath
+ checking tests ... ERROR
+
+* ggedit
+ checking examples ... ERROR
+
+* gghdr
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggiraph
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* ggiraphExtra
+ checking examples ... ERROR
+
+* ggparallel
+ checking tests ... ERROR
+
+* ggprism
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggraph
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggside
+ checking examples ... ERROR
+ checking tests ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* ggstance
+ checking tests ... ERROR
+
+* ggstatsplot
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* ghibli
+ checking tests ... ERROR
+
+* glancedata
+ checking tests ... ERROR
+
+* grafify
+ checking tests ... ERROR
+
+* inTextSummaryTable
+ checking tests ... ERROR
+
+* LMoFit
+ checking re-building of vignette outputs ... ERROR
+
+* manydata
+ checking tests ... ERROR
+
+* MiscMetabar
+ checking examples ... ERROR
+ checking re-building of vignette outputs ... ERROR
+
+* miWQS
+ checking re-building of vignette outputs ... ERROR
+
+* NAIR
+ checking tests ... ERROR
+
+* OpenLand
+ checking tests ... ERROR
+
+* platetools
+ checking tests ... ERROR
+
+* plot3logit
+ checking re-building of vignette outputs ... ERROR
+
+* PTXQC
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* rabhit
+ checking re-building of vignette outputs ... ERROR
+
+* santaR
+ checking tests ... ERROR
+
+* saros
+ checking examples ... ERROR
+ checking tests ... ERROR
+
+* scCustomize
+ checking examples ... ERROR
+
+* scdhlm
+ checking tests ... ERROR
+
+* see
+ checking examples ... ERROR
+
+* spqdep
+ checking re-building of vignette outputs ... ERROR
+
+* TCIU
+ checking re-building of vignette outputs ... ERROR
+
+* tmt
+ checking tests ... ERROR
+
+* tvthemes
+ checking tests ... ERROR
+
+* ufs
+ checking examples ... ERROR
-* SCORPIUS
+* visR
+ checking examples ... ERROR
checking tests ... ERROR
### Failed to check
-* ale (NA)
-* aPEAR (NA)
-* bayesdfa (NA)
-* BrailleR (NA)
-* CausalImpact (NA)
-* CensMFM (NA)
-* cinaR (NA)
-* fdacluster (NA)
-* genekitr (NA)
-* ggPMX (NA)
-* grandR (NA)
-* HeckmanEM (NA)
-* immcp (NA)
-* loon.ggplot (NA)
-* MACP (NA)
-* MarketMatching (NA)
-* MARVEL (NA)
-* MSclassifR (NA)
-* nlmixr2 (NA)
-* nlmixr2extra (NA)
-* nlmixr2plot (NA)
-* nlmixr2rpt (NA)
-* numbat (NA)
-* oHMMed (NA)
-* OlinkAnalyze (NA)
-* OpenMx (NA)
-* phylosem (NA)
-* PsychWordVec (NA)
-* RcppCensSpatial (NA)
-* rmsb (NA)
-* rstanarm (NA)
-* RVA (NA)
-* SCpubr (NA)
-* SSVS (NA)
-* streamDAG (NA)
-* TestAnaAPP (NA)
-* tidySEM (NA)
-* tinyarray (NA)
-* TOmicsVis (NA)
-* valse (NA)
-* vivid (NA)
-* xpose.nlmixr2 (NA)
+* bayesdfa (NA)
+* ctsem (NA)
+* geostan (NA)
+* ggtern (NA)
+* grandR (NA)
+* rmsb (NA)
+* rstanarm (NA)
+* Seurat (NA)
+* streamDAG (NA)
+* treestats (NA)
+* TriDimRegression (NA)
+* triptych (NA)
+* valse (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 74fbd69701..fe7d82c244 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1,93 +1,271 @@
-# NA
+# bayesdfa
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Version: 1.3.2
+* GitHub: https://github.com/fate-ewi/bayesdfa
+* Source code: https://github.com/cran/bayesdfa
+* Date/Publication: 2024-01-12 15:50:02 UTC
+* Number of recursive dependencies: 85
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "bayesdfa")` for more info
-## Error before installation
+## In both
-### Devel
+* checking whether package ‘bayesdfa’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details.
+ ```
-```
+## Installation
+### Devel
+```
+* installing *source* package ‘bayesdfa’ ...
+** package ‘bayesdfa’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
+...
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+g++: fatal error: Killed signal terminated program cc1plus
+compilation terminated.
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1
+ERROR: compilation failed for package ‘bayesdfa’
+* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’
```
### CRAN
```
+* installing *source* package ‘bayesdfa’ ...
+** package ‘bayesdfa’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
-
-
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
+...
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+g++: fatal error: Killed signal terminated program cc1plus
+compilation terminated.
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_dfa.o] Error 1
+ERROR: compilation failed for package ‘bayesdfa’
+* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’
```
-# NA
+# ctsem
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Version: 3.9.1
+* GitHub: https://github.com/cdriveraus/ctsem
+* Source code: https://github.com/cran/ctsem
+* Date/Publication: 2023-10-30 14:20:02 UTC
+* Number of recursive dependencies: 138
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "ctsem")` for more info
-## Error before installation
+## In both
+
+* checking whether package ‘ctsem’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
### Devel
```
+* installing *source* package ‘ctsem’ ...
+** package ‘ctsem’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
+...
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+g++: fatal error: Killed signal terminated program cc1plus
+compilation terminated.
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1
+ERROR: compilation failed for package ‘ctsem’
+* removing ‘/tmp/workdir/ctsem/new/ctsem.Rcheck/ctsem’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘ctsem’ ...
+** package ‘ctsem’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
+...
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_ctsm_namespace::model_ctsm; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+g++: fatal error: Killed signal terminated program cc1plus
+compilation terminated.
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_ctsm.o] Error 1
+ERROR: compilation failed for package ‘ctsem’
+* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’
```
-### CRAN
+# geostan
+
+
+
+* Version: 0.5.3
+* GitHub: https://github.com/ConnorDonegan/geostan
+* Source code: https://github.com/cran/geostan
+* Date/Publication: 2023-11-24 22:30:02 UTC
+* Number of recursive dependencies: 109
+
+Run `revdepcheck::cloud_details(, "geostan")` for more info
+
+
+
+## In both
+
+* checking whether package ‘geostan’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/geostan/new/geostan.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
```
+* installing *source* package ‘geostan’ ...
+** package ‘geostan’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+
+
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
+...
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_foundation_namespace::model_foundation; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+g++: fatal error: Killed signal terminated program cc1plus
+compilation terminated.
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1
+ERROR: compilation failed for package ‘geostan’
+* removing ‘/tmp/workdir/geostan/new/geostan.Rcheck/geostan’
+```
+### CRAN
+
+```
+* installing *source* package ‘geostan’ ...
+** package ‘geostan’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+g++ -std=gnu++17 -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.3.1/lib/R/site-library/BH/include' -I'/opt/R/4.3.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.3.1/lib/R/site-library/rstan/include' -I'/opt/R/4.3.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.3.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
+In file included from /opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
+...
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_foundation_namespace::model_foundation; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
+/opt/R/4.3.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
+/opt/R/4.3.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+g++: fatal error: Killed signal terminated program cc1plus
+compilation terminated.
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stanExports_foundation.o] Error 1
+ERROR: compilation failed for package ‘geostan’
+* removing ‘/tmp/workdir/geostan/old/geostan.Rcheck/geostan’
```
-# ale
+# ggtern
-* Version: 0.1.0
-* GitHub: https://github.com/Tripartio/ale
-* Source code: https://github.com/cran/ale
-* Date/Publication: 2023-08-29 16:30:15 UTC
-* Number of recursive dependencies: 76
+* Version: 3.4.2
+* GitHub: NA
+* Source code: https://github.com/cran/ggtern
+* Date/Publication: 2023-06-06 11:10:02 UTC
+* Number of recursive dependencies: 42
-Run `cloud_details(, "ale")` for more info
+Run `revdepcheck::cloud_details(, "ggtern")` for more info
-## In both
+## Newly broken
-* checking whether package ‘ale’ can be installed ... ERROR
+* checking whether package ‘ggtern’ can be installed ... ERROR
```
Installation failed.
- See ‘/tmp/workdir/ale/new/ale.Rcheck/00install.out’ for details.
+ See ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/00install.out’ for details.
+ ```
+
+## Newly fixed
+
+* checking Rd cross-references ... NOTE
+ ```
+ Package unavailable to check Rd xrefs: ‘chemometrics’
+ ```
+
+## In both
+
+* checking package dependencies ... NOTE
+ ```
+ Package which this enhances but not available for checking: ‘sp’
```
## Installation
@@ -95,48 +273,55 @@ Run `cloud_details(, "ale")` for more info
### Devel
```
-* installing *source* package ‘ale’ ...
-** package ‘ale’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘ggtern’ ...
+** package ‘ggtern’ successfully unpacked and MD5 sums checked
** using staged installation
** R
-Error in parse(outFile) :
- /tmp/workdir/ale/new/ale.Rcheck/00_pkg_src/ale/R/ale_core.R:720:22: unexpected input
-719: }) |>
-720: c(0, y = _
- ^
-ERROR: unable to collate and parse R files for package ‘ale’
-* removing ‘/tmp/workdir/ale/new/ale.Rcheck/ale’
+** data
+** demo
+** inst
+** byte-compile and prepare package for lazy loading
+Error in get(x, envir = ns, inherits = FALSE) :
+ object 'build_guides' not found
+Error: unable to load R code in package ‘ggtern’
+Execution halted
+ERROR: lazy loading failed for package ‘ggtern’
+* removing ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/ggtern’
```
### CRAN
```
-* installing *source* package ‘ale’ ...
-** package ‘ale’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘ggtern’ ...
+** package ‘ggtern’ successfully unpacked and MD5 sums checked
** using staged installation
** R
-Error in parse(outFile) :
- /tmp/workdir/ale/old/ale.Rcheck/00_pkg_src/ale/R/ale_core.R:720:22: unexpected input
-719: }) |>
-720: c(0, y = _
- ^
-ERROR: unable to collate and parse R files for package ‘ale’
-* removing ‘/tmp/workdir/ale/old/ale.Rcheck/ale’
+** data
+** demo
+** inst
+** byte-compile and prepare package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded from temporary location
+** testing if installed package can be loaded from final location
+** testing if installed package keeps a record of temporary installation path
+* DONE (ggtern)
```
-# aPEAR
+# grandR
-* Version: 1.0.0
-* GitHub: NA
-* Source code: https://github.com/cran/aPEAR
-* Date/Publication: 2023-06-12 18:10:13 UTC
-* Number of recursive dependencies: 169
+* Version: 0.2.5
+* GitHub: https://github.com/erhard-lab/grandR
+* Source code: https://github.com/cran/grandR
+* Date/Publication: 2024-02-15 15:30:02 UTC
+* Number of recursive dependencies: 267
-Run `cloud_details(, "aPEAR")` for more info
+Run `revdepcheck::cloud_details(, "grandR")` for more info
@@ -145,27 +330,27 @@ Run `cloud_details(, "aPEAR")` for more info
### Devel
```
-* using log directory ‘/tmp/workdir/aPEAR/new/aPEAR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
+* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’
+* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+ GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
-* checking for file ‘aPEAR/DESCRIPTION’ ... OK
-* this is package ‘aPEAR’ version ‘1.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
+* checking for file ‘grandR/DESCRIPTION’ ... OK
...
---- failed re-building ‘aPEAR-vignette.Rmd’
-
-SUMMARY: processing the following file failed:
- ‘aPEAR-vignette.Rmd’
-
-Error: Vignette re-building failed.
-Execution halted
-
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+ ‘getting-started.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
* DONE
-Status: 1 WARNING, 1 NOTE
+Status: 2 NOTEs
@@ -175,88 +360,105 @@ Status: 1 WARNING, 1 NOTE
### CRAN
```
-* using log directory ‘/tmp/workdir/aPEAR/old/aPEAR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
+* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’
+* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+ GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
-* checking for file ‘aPEAR/DESCRIPTION’ ... OK
-* this is package ‘aPEAR’ version ‘1.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
+* checking for file ‘grandR/DESCRIPTION’ ... OK
...
---- failed re-building ‘aPEAR-vignette.Rmd’
-
-SUMMARY: processing the following file failed:
- ‘aPEAR-vignette.Rmd’
-
-Error: Vignette re-building failed.
-Execution halted
-
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ... NONE
+ ‘getting-started.Rmd’ using ‘UTF-8’... OK
+* checking re-building of vignette outputs ... OK
* DONE
-Status: 1 WARNING, 1 NOTE
+Status: 2 NOTEs
```
-# NA
+# rmsb
-* Version: NA
+* Version: 1.0-0
* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Source code: https://github.com/cran/rmsb
+* Date/Publication: 2023-09-26 13:10:02 UTC
+* Number of recursive dependencies: 144
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "rmsb")` for more info
-## Error before installation
-
-### Devel
-
-```
+## In both
+* checking whether package ‘rmsb’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details.
+ ```
+## Installation
+### Devel
+```
+* installing *source* package ‘rmsb’ ...
+** package ‘rmsb’ successfully unpacked and MD5 sums checked
+** using staged installation
+Error in loadNamespace(x) : there is no package called ‘rstantools’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: configuration failed for package ‘rmsb’
+* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’
```
### CRAN
```
-
-
-
-
+* installing *source* package ‘rmsb’ ...
+** package ‘rmsb’ successfully unpacked and MD5 sums checked
+** using staged installation
+Error in loadNamespace(x) : there is no package called ‘rstantools’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: configuration failed for package ‘rmsb’
+* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’
```
-# bayesdfa
+# rstanarm
-* Version: 1.2.0
-* GitHub: https://github.com/fate-ewi/bayesdfa
-* Source code: https://github.com/cran/bayesdfa
-* Date/Publication: 2021-09-28 13:20:02 UTC
-* Number of recursive dependencies: 86
+* Version: 2.32.1
+* GitHub: https://github.com/stan-dev/rstanarm
+* Source code: https://github.com/cran/rstanarm
+* Date/Publication: 2024-01-18 23:00:03 UTC
+* Number of recursive dependencies: 139
-Run `cloud_details(, "bayesdfa")` for more info
+Run `revdepcheck::cloud_details(, "rstanarm")` for more info
## In both
-* checking whether package ‘bayesdfa’ can be installed ... ERROR
+* checking whether package ‘rstanarm’ can be installed ... ERROR
```
Installation failed.
- See ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/00install.out’ for details.
+ See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details.
```
## Installation
@@ -264,67 +466,68 @@ Run `cloud_details(, "bayesdfa")` for more info
### Devel
```
-* installing *source* package ‘bayesdfa’ ...
-** package ‘bayesdfa’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘rstanarm’ ...
+** package ‘rstanarm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan
+Wrote C++ file "stan_files/lm.cc"
-g++ -std=gnu++17 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.1.1/lib/R/site-library/BH/include' -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.1.1/lib/R/site-library/rstan/include' -I'/opt/R/4.1.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-In file included from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
- from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
- from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
...
-/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
-/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
-/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
-/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
-/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+stan_files/mvmer.hpp: In constructor ‘model_mvmer_namespace::model_mvmer::model_mvmer(stan::io::var_context&, unsigned int, std::ostream*)’:
+stan_files/mvmer.hpp:5240:3: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
+ 5240 | model_mvmer(stan::io::var_context& context__, unsigned int
+ | ^~~~~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
-make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stanExports_dfa.o] Error 1
-ERROR: compilation failed for package ‘bayesdfa’
-* removing ‘/tmp/workdir/bayesdfa/new/bayesdfa.Rcheck/bayesdfa’
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/mvmer.o] Error 1
+rm stan_files/lm.cc stan_files/mvmer.cc
+ERROR: compilation failed for package ‘rstanarm’
+* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’
```
### CRAN
```
-* installing *source* package ‘bayesdfa’ ...
-** package ‘bayesdfa’ successfully unpacked and MD5 sums checked
+* installing *source* package ‘rstanarm’ ...
+** package ‘rstanarm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
+using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+using C++17
+"/opt/R/4.3.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan
+Wrote C++ file "stan_files/lm.cc"
-g++ -std=gnu++17 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.1.1/lib/R/site-library/BH/include' -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -I'/opt/R/4.1.1/lib/R/site-library/rstan/include' -I'/opt/R/4.1.1/lib/R/site-library/StanHeaders/include' -I/usr/local/include -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-In file included from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
- from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Dense:1,
- from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/RcppEigenForward.h:30,
...
-/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h:35:90: required from ‘Eigen::internal::evaluator >::evaluator(const XprType&) [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Options = 0; Eigen::internal::evaluator >::XprType = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>, Eigen::Matrix, 0>]’
-/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/Product.h:132:22: required from ‘Eigen::internal::dense_product_base::operator const Scalar() const [with Lhs = Eigen::Product, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose > >, Eigen::Matrix, 0>; Rhs = Eigen::Matrix; int Option = 0; Eigen::internal::dense_product_base::Scalar = double]’
-/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:22:56: required from ‘double stan::mcmc::dense_e_metric::T(stan::mcmc::dense_e_point&) [with Model = model_dfa_namespace::model_dfa; BaseRNG = boost::random::additive_combine_engine, boost::random::linear_congruential_engine >]’
-/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp:21:10: required from here
-/opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:55:30: warning: ignoring attributes on template argument ‘Eigen::internal::packet_traits::type’ {aka ‘__vector(2) double’} [-Wignored-attributes]
+stan_files/mvmer.hpp: In constructor ‘model_mvmer_namespace::model_mvmer::model_mvmer(stan::io::var_context&, unsigned int, std::ostream*)’:
+stan_files/mvmer.hpp:5240:3: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
+ 5240 | model_mvmer(stan::io::var_context& context__, unsigned int
+ | ^~~~~~~~~~~
g++: fatal error: Killed signal terminated program cc1plus
compilation terminated.
-make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stanExports_dfa.o] Error 1
-ERROR: compilation failed for package ‘bayesdfa’
-* removing ‘/tmp/workdir/bayesdfa/old/bayesdfa.Rcheck/bayesdfa’
+make: *** [/opt/R/4.3.1/lib/R/etc/Makeconf:198: stan_files/mvmer.o] Error 1
+rm stan_files/lm.cc stan_files/mvmer.cc
+ERROR: compilation failed for package ‘rstanarm’
+* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’
```
-# NA
+# Seurat
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Version: 5.0.1
+* GitHub: https://github.com/satijalab/seurat
+* Source code: https://github.com/cran/Seurat
+* Date/Publication: 2023-11-17 23:10:06 UTC
+* Number of recursive dependencies: 264
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "Seurat")` for more info
@@ -333,7 +536,27 @@ Run `cloud_details(, "NA")` for more info
### Devel
```
-
+* using log directory ‘/tmp/workdir/Seurat/new/Seurat.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+ GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+* running under: Ubuntu 20.04.6 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘Seurat/DESCRIPTION’ ... OK
+...
+* checking for GNU extensions in Makefiles ... OK
+* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
+* checking use of PKG_*FLAGS in Makefiles ... OK
+* checking compiled code ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 3 NOTEs
@@ -343,135 +566,66 @@ Run `cloud_details(, "NA")` for more info
### CRAN
```
-
+* using log directory ‘/tmp/workdir/Seurat/old/Seurat.Rcheck’
+* using R version 4.3.1 (2023-06-16)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+ GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+* running under: Ubuntu 20.04.6 LTS
+* using session charset: UTF-8
+* using option ‘--no-manual’
+* checking for file ‘Seurat/DESCRIPTION’ ... OK
+...
+* checking for GNU extensions in Makefiles ... OK
+* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
+* checking use of PKG_*FLAGS in Makefiles ... OK
+* checking compiled code ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+ Running ‘testthat.R’
+* DONE
+Status: 3 NOTEs
```
-# BrailleR
+# streamDAG
-* Version: 1.0.2
-* GitHub: https://github.com/ajrgodfrey/BrailleR
-* Source code: https://github.com/cran/BrailleR
-* Date/Publication: 2023-07-10 19:10:12 UTC
-* Number of recursive dependencies: 196
+* Version: 1.5
+* GitHub: NA
+* Source code: https://github.com/cran/streamDAG
+* Date/Publication: 2023-10-06 18:50:02 UTC
+* Number of recursive dependencies: 133
-Run `cloud_details(, "BrailleR")` for more info
+Run `revdepcheck::cloud_details(, "streamDAG")` for more info
-## In both
+## Error before installation
-* checking whether package ‘BrailleR’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/BrailleR/new/BrailleR.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘BrailleR’ ...
-** package ‘BrailleR’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-Error in parse(outFile) :
- /tmp/workdir/BrailleR/new/BrailleR.Rcheck/00_pkg_src/BrailleR/R/AddXMLInternal.R:398:48: unexpected input
-397: group_split() |>
-398: Filter(function(x) nrow(x) >= 2, x = _
- ^
-ERROR: unable to collate and parse R files for package ‘BrailleR’
-* removing ‘/tmp/workdir/BrailleR/new/BrailleR.Rcheck/BrailleR’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘BrailleR’ ...
-** package ‘BrailleR’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-Error in parse(outFile) :
- /tmp/workdir/BrailleR/old/BrailleR.Rcheck/00_pkg_src/BrailleR/R/AddXMLInternal.R:398:48: unexpected input
-397: group_split() |>
-398: Filter(function(x) nrow(x) >= 2, x = _
- ^
-ERROR: unable to collate and parse R files for package ‘BrailleR’
-* removing ‘/tmp/workdir/BrailleR/old/BrailleR.Rcheck/BrailleR’
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# CausalImpact
-
-
-
-* Version: 1.3.0
-* GitHub: NA
-* Source code: https://github.com/cran/CausalImpact
-* Date/Publication: 2022-11-09 08:40:40 UTC
-* Number of recursive dependencies: 81
-
-Run `cloud_details(, "CausalImpact")` for more info
-
-
-
-## Error before installation
-
-### Devel
+### Devel
```
-* using log directory ‘/tmp/workdir/CausalImpact/new/CausalImpact.Rcheck’
-* using R version 4.1.1 (2021-08-10)
+* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’
+* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+ GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
-* checking for file ‘CausalImpact/DESCRIPTION’ ... OK
-* this is package ‘CausalImpact’ version ‘1.3.0’
+* checking for file ‘streamDAG/DESCRIPTION’ ... OK
+* this is package ‘streamDAG’ version ‘1.5’
* checking package namespace information ... OK
* checking package dependencies ... ERROR
-Packages required but not available: 'bsts', 'Boom'
+Package required but not available: ‘asbio’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
@@ -486,16 +640,20 @@ Status: 1 ERROR
### CRAN
```
-* using log directory ‘/tmp/workdir/CausalImpact/old/CausalImpact.Rcheck’
-* using R version 4.1.1 (2021-08-10)
+* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’
+* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
+* R was compiled by
+ gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+ GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0
+* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
-* checking for file ‘CausalImpact/DESCRIPTION’ ... OK
-* this is package ‘CausalImpact’ version ‘1.3.0’
+* checking for file ‘streamDAG/DESCRIPTION’ ... OK
+* this is package ‘streamDAG’ version ‘1.5’
* checking package namespace information ... OK
* checking package dependencies ... ERROR
-Packages required but not available: 'bsts', 'Boom'
+Package required but not available: ‘asbio’
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
@@ -507,4011 +665,218 @@ Status: 1 ERROR
```
-# CensMFM
+# treestats
-* Version: 3.0
-* GitHub: NA
-* Source code: https://github.com/cran/CensMFM
-* Date/Publication: 2023-01-30 14:00:10 UTC
-* Number of recursive dependencies: 41
+* Version: 1.0.5
+* GitHub: https://github.com/thijsjanzen/treestats
+* Source code: https://github.com/cran/treestats
+* Date/Publication: 2024-01-30 15:50:02 UTC
+* Number of recursive dependencies: 229
-Run `cloud_details(, "CensMFM")` for more info
+Run `revdepcheck::cloud_details(, "treestats")` for more info
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/CensMFM/new/CensMFM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘CensMFM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘CensMFM’ version ‘3.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'MomTrunc', 'tlrmvnmvt'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/CensMFM/old/CensMFM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘CensMFM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘CensMFM’ version ‘3.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'MomTrunc', 'tlrmvnmvt'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# cinaR
-
-
-
-* Version: 0.2.3
-* GitHub: https://github.com/eonurk/cinaR
-* Source code: https://github.com/cran/cinaR
-* Date/Publication: 2022-05-18 14:00:09 UTC
-* Number of recursive dependencies: 179
-
-Run `cloud_details(, "cinaR")` for more info
+## In both
-
+* checking whether package ‘treestats’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/treestats/new/treestats.Rcheck/00install.out’ for details.
+ ```
-## Error before installation
+## Installation
### Devel
```
-* using log directory ‘/tmp/workdir/cinaR/new/cinaR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘cinaR/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘cinaR’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘ChIPseeker’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
+* installing *source* package ‘treestats’ ...
+** package ‘treestats’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+Error: C++20 standard requested but CXX20 is not defined
+* removing ‘/tmp/workdir/treestats/new/treestats.Rcheck/treestats’
```
### CRAN
```
-* using log directory ‘/tmp/workdir/cinaR/old/cinaR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘cinaR/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘cinaR’ version ‘0.2.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘ChIPseeker’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
+* installing *source* package ‘treestats’ ...
+** package ‘treestats’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+Error: C++20 standard requested but CXX20 is not defined
+* removing ‘/tmp/workdir/treestats/old/treestats.Rcheck/treestats’
```
-# NA
+# TriDimRegression
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Version: 1.0.2
+* GitHub: https://github.com/alexander-pastukhov/tridim-regression
+* Source code: https://github.com/cran/TriDimRegression
+* Date/Publication: 2023-09-13 14:10:03 UTC
+* Number of recursive dependencies: 100
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "TriDimRegression")` for more info
-## Error before installation
-
-### Devel
-
-```
+## In both
+* checking whether package ‘TriDimRegression’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details.
+ ```
+## Installation
+### Devel
+```
+* installing *source* package ‘TriDimRegression’ ...
+** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
+** using staged installation
+Error in loadNamespace(x) : there is no package called ‘rstantools’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: configuration failed for package ‘TriDimRegression’
+* removing ‘/tmp/workdir/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’
```
### CRAN
```
-
-
-
-
+* installing *source* package ‘TriDimRegression’ ...
+** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
+** using staged installation
+Error in loadNamespace(x) : there is no package called ‘rstantools’
+Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
+Execution halted
+ERROR: configuration failed for package ‘TriDimRegression’
+* removing ‘/tmp/workdir/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’
```
-# NA
+# triptych
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Version: 0.1.2
+* GitHub: https://github.com/aijordan/triptych
+* Source code: https://github.com/cran/triptych
+* Date/Publication: 2023-10-03 16:30:02 UTC
+* Number of recursive dependencies: 64
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "triptych")` for more info
-## Error before installation
-
-### Devel
-
-```
+## In both
+* checking whether package ‘triptych’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/triptych/new/triptych.Rcheck/00install.out’ for details.
+ ```
+## Installation
+### Devel
+```
+* installing *source* package ‘triptych’ ...
+** package ‘triptych’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+Error: C++20 standard requested but CXX20 is not defined
+* removing ‘/tmp/workdir/triptych/new/triptych.Rcheck/triptych’
```
### CRAN
```
-
-
-
-
+* installing *source* package ‘triptych’ ...
+** package ‘triptych’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+Error: C++20 standard requested but CXX20 is not defined
+* removing ‘/tmp/workdir/triptych/old/triptych.Rcheck/triptych’
```
-# NA
+# valse
-* Version: NA
+* Version: 0.1-0
* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
+* Source code: https://github.com/cran/valse
+* Date/Publication: 2021-05-31 08:00:02 UTC
+* Number of recursive dependencies: 55
-Run `cloud_details(, "NA")` for more info
+Run `revdepcheck::cloud_details(, "valse")` for more info
-## Error before installation
-
-### Devel
-
-```
-
-
-
+## In both
+* checking whether package ‘valse’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/valse/new/valse.Rcheck/00install.out’ for details.
+ ```
+## Installation
-```
-### CRAN
+### Devel
```
-
-
-
-
+* installing *source* package ‘valse’ ...
+** package ‘valse’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o
+...
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded from temporary location
+Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...):
+ unable to load shared object '/tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so':
+ /tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_vector_free
+Error: loading failed
+Execution halted
+ERROR: loading failed
+* removing ‘/tmp/workdir/valse/new/valse.Rcheck/valse’
```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# fdacluster
-
-
-
-* Version: 0.3.0
-* GitHub: https://github.com/astamm/fdacluster
-* Source code: https://github.com/cran/fdacluster
-* Date/Publication: 2023-07-04 15:53:04 UTC
-* Number of recursive dependencies: 121
-
-Run `cloud_details(, "fdacluster")` for more info
-
-
-
-## In both
-
-* checking whether package ‘fdacluster’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/fdacluster/new/fdacluster.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘fdacluster’ ...
-** package ‘fdacluster’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c affineWarpingClass.cpp -o affineWarpingClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseDissimilarityClass.cpp -o baseDissimilarityClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseOptimizerClass.cpp -o baseOptimizerClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseWarpingClass.cpp -o baseWarpingClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c bobyqaOptimizerClass.cpp -o bobyqaOptimizerClass.o
-...
-g++ -std=gnu++14 -shared -L/opt/R/4.1.1/lib/R/lib -L/usr/local/lib -o fdacluster.so RcppExports.o affineWarpingClass.o baseDissimilarityClass.o baseOptimizerClass.o baseWarpingClass.o bobyqaOptimizerClass.o dilationWarpingClass.o kmaModelClass.o kmap.o kumaraswamyWarpingClass.o l2DissimilarityClass.o lowessCenterClass.o meanCenterClass.o medianCenterClass.o medoidCenterClass.o noWarpingClass.o pearsonDissimilarityClass.o polyCenterClass.o shiftWarpingClass.o utilityFunctions.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.1.1/lib/R/lib -lR
-installing to /tmp/workdir/fdacluster/new/fdacluster.Rcheck/00LOCK-fdacluster/00new/fdacluster/libs
-** R
-Error in parse(outFile) :
- /tmp/workdir/fdacluster/new/fdacluster.Rcheck/00_pkg_src/fdacluster/R/utils.R:132:31: unexpected input
-131: purrr::imap(\(values, id) stats::approx(x@argvals[[id]], values, n = M)$y) |>
-132: do.call(rbind, args = _
- ^
-ERROR: unable to collate and parse R files for package ‘fdacluster’
-* removing ‘/tmp/workdir/fdacluster/new/fdacluster.Rcheck/fdacluster’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘fdacluster’ ...
-** package ‘fdacluster’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c affineWarpingClass.cpp -o affineWarpingClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseDissimilarityClass.cpp -o baseDissimilarityClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseOptimizerClass.cpp -o baseOptimizerClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c baseWarpingClass.cpp -o baseWarpingClass.o
-g++ -std=gnu++14 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I../inst/include -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppArmadillo/include' -I'/opt/R/4.1.1/lib/R/site-library/nloptr/include' -I/usr/local/include -fopenmp -fpic -g -O2 -c bobyqaOptimizerClass.cpp -o bobyqaOptimizerClass.o
-...
-g++ -std=gnu++14 -shared -L/opt/R/4.1.1/lib/R/lib -L/usr/local/lib -o fdacluster.so RcppExports.o affineWarpingClass.o baseDissimilarityClass.o baseOptimizerClass.o baseWarpingClass.o bobyqaOptimizerClass.o dilationWarpingClass.o kmaModelClass.o kmap.o kumaraswamyWarpingClass.o l2DissimilarityClass.o lowessCenterClass.o meanCenterClass.o medianCenterClass.o medoidCenterClass.o noWarpingClass.o pearsonDissimilarityClass.o polyCenterClass.o shiftWarpingClass.o utilityFunctions.o -fopenmp -llapack -lblas -lgfortran -lm -lquadmath -L/opt/R/4.1.1/lib/R/lib -lR
-installing to /tmp/workdir/fdacluster/old/fdacluster.Rcheck/00LOCK-fdacluster/00new/fdacluster/libs
-** R
-Error in parse(outFile) :
- /tmp/workdir/fdacluster/old/fdacluster.Rcheck/00_pkg_src/fdacluster/R/utils.R:132:31: unexpected input
-131: purrr::imap(\(values, id) stats::approx(x@argvals[[id]], values, n = M)$y) |>
-132: do.call(rbind, args = _
- ^
-ERROR: unable to collate and parse R files for package ‘fdacluster’
-* removing ‘/tmp/workdir/fdacluster/old/fdacluster.Rcheck/fdacluster’
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# genekitr
-
-
-
-* Version: 1.2.5
-* GitHub: https://github.com/GangLiLab/genekitr
-* Source code: https://github.com/cran/genekitr
-* Date/Publication: 2023-09-07 08:50:09 UTC
-* Number of recursive dependencies: 211
-
-Run `cloud_details(, "genekitr")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/genekitr/new/genekitr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘genekitr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.2.5’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/genekitr/old/genekitr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘genekitr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.2.5’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# ggPMX
-
-
-
-* Version: 1.2.10
-* GitHub: https://github.com/ggPMXdevelopment/ggPMX
-* Source code: https://github.com/cran/ggPMX
-* Date/Publication: 2023-06-16 23:20:07 UTC
-* Number of recursive dependencies: 177
-
-Run `cloud_details(, "ggPMX")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/ggPMX/new/ggPMX.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘ggPMX/DESCRIPTION’ ... OK
-* this is package ‘ggPMX’ version ‘1.2.10’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking for unstated dependencies in ‘tests’ ... OK
-* checking tests ... OK
- Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘ggPMX-guide.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/ggPMX/old/ggPMX.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘ggPMX/DESCRIPTION’ ... OK
-* this is package ‘ggPMX’ version ‘1.2.10’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking for unstated dependencies in ‘tests’ ... OK
-* checking tests ... OK
- Running ‘testthat.R’
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘ggPMX-guide.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# grandR
-
-
-
-* Version: 0.2.2
-* GitHub: https://github.com/erhard-lab/grandR
-* Source code: https://github.com/cran/grandR
-* Date/Publication: 2023-04-20 21:22:30 UTC
-* Number of recursive dependencies: 261
-
-Run `cloud_details(, "grandR")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/grandR/new/grandR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘grandR/DESCRIPTION’ ... OK
-* this is package ‘grandR’ version ‘0.2.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘getting-started.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/grandR/old/grandR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘grandR/DESCRIPTION’ ... OK
-* this is package ‘grandR’ version ‘0.2.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘getting-started.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-# HeckmanEM
-
-
-
-* Version: 0.2-0
-* GitHub: NA
-* Source code: https://github.com/cran/HeckmanEM
-* Date/Publication: 2023-06-11 15:00:03 UTC
-* Number of recursive dependencies: 95
-
-Run `cloud_details(, "HeckmanEM")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/HeckmanEM/new/HeckmanEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘HeckmanEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘HeckmanEM’ version ‘0.2-0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘MomTrunc’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/HeckmanEM/old/HeckmanEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘HeckmanEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘HeckmanEM’ version ‘0.2-0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘MomTrunc’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# immcp
-
-
-
-* Version: 1.0.3
-* GitHub: https://github.com/YuanlongHu/immcp
-* Source code: https://github.com/cran/immcp
-* Date/Publication: 2022-05-12 05:50:02 UTC
-* Number of recursive dependencies: 198
-
-Run `cloud_details(, "immcp")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/immcp/new/immcp.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘immcp/DESCRIPTION’ ... OK
-* this is package ‘immcp’ version ‘1.0.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/immcp/old/immcp.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘immcp/DESCRIPTION’ ... OK
-* this is package ‘immcp’ version ‘1.0.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# loon.ggplot
-
-
-
-* Version: 1.3.3
-* GitHub: https://github.com/great-northern-diver/loon.ggplot
-* Source code: https://github.com/cran/loon.ggplot
-* Date/Publication: 2022-11-12 22:30:02 UTC
-* Number of recursive dependencies: 106
-
-Run `cloud_details(, "loon.ggplot")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/loon.ggplot/new/loon.ggplot.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘loon.ggplot/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘loon.ggplot’ version ‘1.3.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘loon’
-
-Package suggested but not available for checking: ‘zenplots’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/loon.ggplot/old/loon.ggplot.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘loon.ggplot/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘loon.ggplot’ version ‘1.3.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘loon’
-
-Package suggested but not available for checking: ‘zenplots’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# MACP
-
-
-
-* Version: 0.1.0
-* GitHub: https://github.com/mrbakhsh/MACP
-* Source code: https://github.com/cran/MACP
-* Date/Publication: 2023-02-28 17:32:30 UTC
-* Number of recursive dependencies: 235
-
-Run `cloud_details(, "MACP")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/MACP/new/MACP.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MACP/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘MACP’ version ‘0.1.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘MACP_tutorial.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 3 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/MACP/old/MACP.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MACP/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘MACP’ version ‘0.1.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘MACP_tutorial.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 3 NOTEs
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# MarketMatching
-
-
-
-* Version: 1.2.0
-* GitHub: NA
-* Source code: https://github.com/cran/MarketMatching
-* Date/Publication: 2021-01-08 20:10:02 UTC
-* Number of recursive dependencies: 74
-
-Run `cloud_details(, "MarketMatching")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/MarketMatching/new/MarketMatching.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MarketMatching/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘MarketMatching’ version ‘1.2.0’
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'CausalImpact', 'bsts', 'Boom'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/MarketMatching/old/MarketMatching.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MarketMatching/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘MarketMatching’ version ‘1.2.0’
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'CausalImpact', 'bsts', 'Boom'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# MARVEL
-
-
-
-* Version: 1.4.0
-* GitHub: NA
-* Source code: https://github.com/cran/MARVEL
-* Date/Publication: 2022-10-31 10:22:50 UTC
-* Number of recursive dependencies: 238
-
-Run `cloud_details(, "MARVEL")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/MARVEL/new/MARVEL.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MARVEL/DESCRIPTION’ ... OK
-* this is package ‘MARVEL’ version ‘1.4.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘MARVEL.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/MARVEL/old/MARVEL.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MARVEL/DESCRIPTION’ ... OK
-* this is package ‘MARVEL’ version ‘1.4.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘MARVEL.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 2 NOTEs
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# MSclassifR
-
-
-
-* Version: 0.3.3
-* GitHub: https://github.com/agodmer/MSclassifR_examples
-* Source code: https://github.com/cran/MSclassifR
-* Date/Publication: 2023-08-09 09:00:06 UTC
-* Number of recursive dependencies: 230
-
-Run `cloud_details(, "MSclassifR")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/MSclassifR/new/MSclassifR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MSclassifR/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘MSclassifR’ version ‘0.3.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'MALDIquantForeign', 'VSURF'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/MSclassifR/old/MSclassifR.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘MSclassifR/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘MSclassifR’ version ‘0.3.3’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'MALDIquantForeign', 'VSURF'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# nlmixr2
-
-
-
-* Version: 2.0.9
-* GitHub: https://github.com/nlmixr2/nlmixr2
-* Source code: https://github.com/cran/nlmixr2
-* Date/Publication: 2023-02-21 04:00:02 UTC
-* Number of recursive dependencies: 194
-
-Run `cloud_details(, "nlmixr2")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2/new/nlmixr2.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2’ version ‘2.0.9’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available:
- 'nlmixr2est', 'nlmixr2extra', 'nlmixr2plot'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2/old/nlmixr2.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2’ version ‘2.0.9’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available:
- 'nlmixr2est', 'nlmixr2extra', 'nlmixr2plot'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# nlmixr2extra
-
-
-
-* Version: 2.0.8
-* GitHub: https://github.com/nlmixr2/nlmixr2extra
-* Source code: https://github.com/cran/nlmixr2extra
-* Date/Publication: 2022-10-22 22:32:34 UTC
-* Number of recursive dependencies: 186
-
-Run `cloud_details(, "nlmixr2extra")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2extra/new/nlmixr2extra.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2extra/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2extra’ version ‘2.0.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'nlmixr2est', 'symengine'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2extra/old/nlmixr2extra.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2extra/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2extra’ version ‘2.0.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'nlmixr2est', 'symengine'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# nlmixr2plot
-
-
-
-* Version: 2.0.7
-* GitHub: https://github.com/nlmixr2/nlmixr2plot
-* Source code: https://github.com/cran/nlmixr2plot
-* Date/Publication: 2022-10-20 03:12:36 UTC
-* Number of recursive dependencies: 162
-
-Run `cloud_details(, "nlmixr2plot")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2plot/new/nlmixr2plot.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2plot/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2plot’ version ‘2.0.7’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'nlmixr2est', 'nlmixr2extra'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2plot/old/nlmixr2plot.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2plot/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2plot’ version ‘2.0.7’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'nlmixr2est', 'nlmixr2extra'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# nlmixr2rpt
-
-
-
-* Version: 0.2.0
-* GitHub: https://github.com/nlmixr2/nlmixr2rpt
-* Source code: https://github.com/cran/nlmixr2rpt
-* Date/Publication: 2023-06-06 13:10:05 UTC
-* Number of recursive dependencies: 216
-
-Run `cloud_details(, "nlmixr2rpt")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2rpt/new/nlmixr2rpt.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2rpt/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2rpt’ version ‘0.2.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available:
- 'nlmixr2', 'nlmixr2extra', 'xpose.nlmixr2'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/nlmixr2rpt/old/nlmixr2rpt.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘nlmixr2rpt/DESCRIPTION’ ... OK
-* this is package ‘nlmixr2rpt’ version ‘0.2.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available:
- 'nlmixr2', 'nlmixr2extra', 'xpose.nlmixr2'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# numbat
-
-
-
-* Version: 1.3.2-1
-* GitHub: https://github.com/kharchenkolab/numbat
-* Source code: https://github.com/cran/numbat
-* Date/Publication: 2023-06-17 18:50:02 UTC
-* Number of recursive dependencies: 136
-
-Run `cloud_details(, "numbat")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/numbat/new/numbat.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.3.2-1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'ggtree', 'scistreer'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/numbat/old/numbat.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘numbat/DESCRIPTION’ ... OK
-* this is package ‘numbat’ version ‘1.3.2-1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'ggtree', 'scistreer'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# oHMMed
-
-
-
-* Version: 1.0.0
-* GitHub: https://github.com/LynetteCaitlin/oHMMed
-* Source code: https://github.com/cran/oHMMed
-* Date/Publication: 2023-07-05 14:30:02 UTC
-* Number of recursive dependencies: 117
-
-Run `cloud_details(, "oHMMed")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/oHMMed/new/oHMMed.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘oHMMed/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘oHMMed’ version ‘1.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘cvms’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/oHMMed/old/oHMMed.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘oHMMed/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘oHMMed’ version ‘1.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘cvms’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# OlinkAnalyze
-
-
-
-* Version: 3.5.1
-* GitHub: NA
-* Source code: https://github.com/cran/OlinkAnalyze
-* Date/Publication: 2023-08-08 21:00:02 UTC
-* Number of recursive dependencies: 212
-
-Run `cloud_details(, "OlinkAnalyze")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/OlinkAnalyze/new/OlinkAnalyze.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘OlinkAnalyze’ version ‘3.5.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘OutlierExclusion.Rmd’ using ‘UTF-8’... OK
- ‘Vignett.Rmd’ using ‘UTF-8’... OK
- ‘bridging_introduction.Rmd’ using ‘UTF-8’... OK
- ‘plate_randomizer.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/OlinkAnalyze/old/OlinkAnalyze.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘OlinkAnalyze’ version ‘3.5.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘OutlierExclusion.Rmd’ using ‘UTF-8’... OK
- ‘Vignett.Rmd’ using ‘UTF-8’... OK
- ‘bridging_introduction.Rmd’ using ‘UTF-8’... OK
- ‘plate_randomizer.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-# OpenMx
-
-
-
-* Version: 2.21.8
-* GitHub: https://github.com/OpenMx/OpenMx
-* Source code: https://github.com/cran/OpenMx
-* Date/Publication: 2023-04-05 20:43:20 UTC
-* Number of recursive dependencies: 147
-
-Run `cloud_details(, "OpenMx")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/OpenMx/new/OpenMx.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘OpenMx/DESCRIPTION’ ... OK
-* this is package ‘OpenMx’ version ‘2.21.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘deriv.Rmd’ using ‘UTF-8’... OK
- ‘reg_mimic.Rmd’ using ‘UTF-8’... OK
- ‘factor_analysis.Rmd’ using ‘UTF-8’... OK
- ‘regularization.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 4 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/OpenMx/old/OpenMx.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘OpenMx/DESCRIPTION’ ... OK
-* this is package ‘OpenMx’ version ‘2.21.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘deriv.Rmd’ using ‘UTF-8’... OK
- ‘reg_mimic.Rmd’ using ‘UTF-8’... OK
- ‘factor_analysis.Rmd’ using ‘UTF-8’... OK
- ‘regularization.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 4 NOTEs
-
-
-
-
-
-```
-# phylosem
-
-
-
-* Version: 1.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/phylosem
-* Date/Publication: 2023-10-06 20:30:02 UTC
-* Number of recursive dependencies: 206
-
-Run `cloud_details(, "phylosem")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/phylosem/new/phylosem.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘phylosem/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘phylosem’ version ‘1.1.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘phylopath’
-
-Package which this enhances but not available for checking: ‘DiagrammeR’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/phylosem/old/phylosem.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘phylosem/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘phylosem’ version ‘1.1.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘phylopath’
-
-Package which this enhances but not available for checking: ‘DiagrammeR’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# PsychWordVec
-
-
-
-* Version: 2023.9
-* GitHub: https://github.com/psychbruce/PsychWordVec
-* Source code: https://github.com/cran/PsychWordVec
-* Date/Publication: 2023-09-27 14:20:02 UTC
-* Number of recursive dependencies: 234
-
-Run `cloud_details(, "PsychWordVec")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/PsychWordVec/new/PsychWordVec.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘PsychWordVec/DESCRIPTION’ ... OK
-* this is package ‘PsychWordVec’ version ‘2023.9’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘bruceR’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/PsychWordVec/old/PsychWordVec.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘PsychWordVec/DESCRIPTION’ ... OK
-* this is package ‘PsychWordVec’ version ‘2023.9’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘bruceR’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# RcppCensSpatial
-
-
-
-* Version: 0.3.0
-* GitHub: NA
-* Source code: https://github.com/cran/RcppCensSpatial
-* Date/Publication: 2022-06-27 23:00:02 UTC
-* Number of recursive dependencies: 64
-
-Run `cloud_details(, "RcppCensSpatial")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/RcppCensSpatial/new/RcppCensSpatial.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘RcppCensSpatial/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘RcppCensSpatial’ version ‘0.3.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘MomTrunc’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/RcppCensSpatial/old/RcppCensSpatial.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘RcppCensSpatial/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘RcppCensSpatial’ version ‘0.3.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘MomTrunc’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# rmsb
-
-
-
-* Version: 1.0-0
-* GitHub: NA
-* Source code: https://github.com/cran/rmsb
-* Date/Publication: 2023-09-26 13:10:02 UTC
-* Number of recursive dependencies: 144
-
-Run `cloud_details(, "rmsb")` for more info
-
-
-
-## In both
-
-* checking whether package ‘rmsb’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘rmsb’ ...
-** package ‘rmsb’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘rmsb’
-* removing ‘/tmp/workdir/rmsb/new/rmsb.Rcheck/rmsb’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘rmsb’ ...
-** package ‘rmsb’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘rmsb’
-* removing ‘/tmp/workdir/rmsb/old/rmsb.Rcheck/rmsb’
-
-
-```
-# rstanarm
-
-
-
-* Version: 2.26.1
-* GitHub: https://github.com/stan-dev/rstanarm
-* Source code: https://github.com/cran/rstanarm
-* Date/Publication: 2023-09-13 22:50:03 UTC
-* Number of recursive dependencies: 138
-
-Run `cloud_details(, "rstanarm")` for more info
-
-
-
-## In both
-
-* checking whether package ‘rstanarm’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘rstanarm’ ...
-** package ‘rstanarm’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-"/opt/R/4.1.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan
-Wrote C++ file "stan_files/lm.cc"
-
-
-g++ -std=gnu++17 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.1.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.1.1/lib/R/site-library/rstan/include' -I'/opt/R/4.1.1/lib/R/site-library/BH/include' -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c stan_files/lm.cc -o stan_files/lm.o
-In file included from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
-...
-stan_files/mvmer.hpp: In constructor ‘model_mvmer_namespace::model_mvmer::model_mvmer(stan::io::var_context&, unsigned int, std::ostream*)’:
-stan_files/mvmer.hpp:5105:3: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
- 5105 | model_mvmer(stan::io::var_context& context__,
- | ^~~~~~~~~~~
-g++: fatal error: Killed signal terminated program cc1plus
-compilation terminated.
-make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stan_files/mvmer.o] Error 1
-rm stan_files/lm.cc stan_files/mvmer.cc
-ERROR: compilation failed for package ‘rstanarm’
-* removing ‘/tmp/workdir/rstanarm/new/rstanarm.Rcheck/rstanarm’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘rstanarm’ ...
-** package ‘rstanarm’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-"/opt/R/4.1.1/lib/R/bin/Rscript" -e "source(file.path('..', 'tools', 'make_cc.R')); make_cc(commandArgs(TRUE))" stan_files/lm.stan
-Wrote C++ file "stan_files/lm.cc"
-
-
-g++ -std=gnu++17 -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I"../inst/include" -I"/opt/R/4.1.1/lib/R/site-library/StanHeaders/include/src" -DBOOST_DISABLE_ASSERTS -DEIGEN_NO_DEBUG -DBOOST_MATH_OVERFLOW_ERROR_POLICY=errno_on_error -DUSE_STANC3 -D_HAS_AUTO_PTR_ETC=0 -I'/opt/R/4.1.1/lib/R/site-library/StanHeaders/include' -I'/opt/R/4.1.1/lib/R/site-library/rstan/include' -I'/opt/R/4.1.1/lib/R/site-library/BH/include' -I'/opt/R/4.1.1/lib/R/site-library/Rcpp/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppEigen/include' -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -I/usr/local/include -I'/opt/R/4.1.1/lib/R/site-library/RcppParallel/include' -D_REENTRANT -DSTAN_THREADS -fpic -g -O2 -c stan_files/lm.cc -o stan_files/lm.o
-In file included from /opt/R/4.1.1/lib/R/site-library/RcppEigen/include/Eigen/Core:397,
-...
-stan_files/mvmer.hpp: In constructor ‘model_mvmer_namespace::model_mvmer::model_mvmer(stan::io::var_context&, unsigned int, std::ostream*)’:
-stan_files/mvmer.hpp:5105:3: note: variable tracking size limit exceeded with ‘-fvar-tracking-assignments’, retrying without
- 5105 | model_mvmer(stan::io::var_context& context__,
- | ^~~~~~~~~~~
-g++: fatal error: Killed signal terminated program cc1plus
-compilation terminated.
-make: *** [/opt/R/4.1.1/lib/R/etc/Makeconf:175: stan_files/mvmer.o] Error 1
-rm stan_files/lm.cc stan_files/mvmer.cc
-ERROR: compilation failed for package ‘rstanarm’
-* removing ‘/tmp/workdir/rstanarm/old/rstanarm.Rcheck/rstanarm’
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# RVA
-
-
-
-* Version: 0.0.5
-* GitHub: https://github.com/THERMOSTATS/RVA
-* Source code: https://github.com/cran/RVA
-* Date/Publication: 2021-11-01 21:40:02 UTC
-* Number of recursive dependencies: 210
-
-Run `cloud_details(, "RVA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/RVA/new/RVA.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘RVA/DESCRIPTION’ ... OK
-* this is package ‘RVA’ version ‘0.0.5’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/RVA/old/RVA.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘RVA/DESCRIPTION’ ... OK
-* this is package ‘RVA’ version ‘0.0.5’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# SCpubr
-
-
-
-* Version: 2.0.1
-* GitHub: https://github.com/enblacar/SCpubr
-* Source code: https://github.com/cran/SCpubr
-* Date/Publication: 2023-08-13 12:40:15 UTC
-* Number of recursive dependencies: 295
-
-Run `cloud_details(, "SCpubr")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/SCpubr/new/SCpubr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘SCpubr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘SCpubr’ version ‘2.0.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
- [ FAIL 10 | WARN 0 | SKIP 381 | PASS 72 ]
- Error: Test failures
- Execution halted
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘reference_manual.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 ERROR, 1 WARNING, 2 NOTEs
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/SCpubr/old/SCpubr.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘SCpubr/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘SCpubr’ version ‘2.0.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
- [ FAIL 10 | WARN 0 | SKIP 381 | PASS 72 ]
- Error: Test failures
- Execution halted
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘reference_manual.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 ERROR, 1 WARNING, 2 NOTEs
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# SSVS
-
-
-
-* Version: 2.0.0
-* GitHub: https://github.com/sabainter/SSVS
-* Source code: https://github.com/cran/SSVS
-* Date/Publication: 2022-05-29 05:40:09 UTC
-* Number of recursive dependencies: 124
-
-Run `cloud_details(, "SSVS")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/SSVS/new/SSVS.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘SSVS/DESCRIPTION’ ... OK
-* this is package ‘SSVS’ version ‘2.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘BoomSpikeSlab’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/SSVS/old/SSVS.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘SSVS/DESCRIPTION’ ... OK
-* this is package ‘SSVS’ version ‘2.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘BoomSpikeSlab’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# streamDAG
-
-
-
-* Version: 1.5
-* GitHub: NA
-* Source code: https://github.com/cran/streamDAG
-* Date/Publication: 2023-10-06 18:50:02 UTC
-* Number of recursive dependencies: 133
-
-Run `cloud_details(, "streamDAG")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/streamDAG/new/streamDAG.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘streamDAG/DESCRIPTION’ ... OK
-* this is package ‘streamDAG’ version ‘1.5’
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘asbio’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/streamDAG/old/streamDAG.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘streamDAG/DESCRIPTION’ ... OK
-* this is package ‘streamDAG’ version ‘1.5’
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘asbio’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# TestAnaAPP
-
-
-
-* Version: 0.1.2
-* GitHub: https://github.com/jiangyouxiang/TestAnaAPP
-* Source code: https://github.com/cran/TestAnaAPP
-* Date/Publication: 2023-09-11 08:40:05 UTC
-* Number of recursive dependencies: 240
-
-Run `cloud_details(, "TestAnaAPP")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/TestAnaAPP/new/TestAnaAPP.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘TestAnaAPP/DESCRIPTION’ ... OK
-* this is package ‘TestAnaAPP’ version ‘0.1.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘bruceR’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/TestAnaAPP/old/TestAnaAPP.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘TestAnaAPP/DESCRIPTION’ ... OK
-* this is package ‘TestAnaAPP’ version ‘0.1.2’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘bruceR’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# tidySEM
-
-
-
-* Version: 0.2.4
-* GitHub: https://github.com/cjvanlissa/tidySEM
-* Source code: https://github.com/cran/tidySEM
-* Date/Publication: 2023-05-01 20:00:06 UTC
-* Number of recursive dependencies: 191
-
-Run `cloud_details(, "tidySEM")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/tidySEM/new/tidySEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tidySEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tidySEM’ version ‘0.2.4’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
- ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK
- ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK
- ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK
- ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK
- ‘lca_lcga.Rmd’ using ‘UTF-8’... OK
- ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK
- ‘sem_graph.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/tidySEM/old/tidySEM.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tidySEM/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tidySEM’ version ‘0.2.4’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-...
- ‘Plotting_graphs.Rmd’ using ‘UTF-8’... OK
- ‘Tabulating_results.Rmd’ using ‘UTF-8’... OK
- ‘lca_confirmatory.Rmd’ using ‘UTF-8’... OK
- ‘lca_exploratory.Rmd’ using ‘UTF-8’... OK
- ‘lca_lcga.Rmd’ using ‘UTF-8’... OK
- ‘lca_ordinal.Rmd’ using ‘UTF-8’... OK
- ‘sem_graph.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# tinyarray
-
-
-
-* Version: 2.3.1
-* GitHub: https://github.com/xjsun1221/tinyarray
-* Source code: https://github.com/cran/tinyarray
-* Date/Publication: 2023-08-18 08:20:02 UTC
-* Number of recursive dependencies: 233
-
-Run `cloud_details(, "tinyarray")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/tinyarray/new/tinyarray.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tinyarray/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tinyarray’ version ‘2.3.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/tinyarray/old/tinyarray.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘tinyarray/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘tinyarray’ version ‘2.3.1’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘clusterProfiler’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# TOmicsVis
-
-
-
-* Version: 2.0.0
-* GitHub: https://github.com/benben-miao/TOmicsVis
-* Source code: https://github.com/cran/TOmicsVis
-* Date/Publication: 2023-08-28 18:30:02 UTC
-* Number of recursive dependencies: 258
-
-Run `cloud_details(, "TOmicsVis")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/TOmicsVis/new/TOmicsVis.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘TOmicsVis/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘TOmicsVis’ version ‘2.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'clusterProfiler', 'enrichplot'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/TOmicsVis/old/TOmicsVis.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘TOmicsVis/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘TOmicsVis’ version ‘2.0.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Packages required but not available: 'clusterProfiler', 'enrichplot'
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# valse
-
-
-
-* Version: 0.1-0
-* GitHub: NA
-* Source code: https://github.com/cran/valse
-* Date/Publication: 2021-05-31 08:00:02 UTC
-* Number of recursive dependencies: 56
-
-Run `cloud_details(, "valse")` for more info
-
-
-
-## In both
-
-* checking whether package ‘valse’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/valse/new/valse.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘valse’ ...
-** package ‘valse’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o
-Error in loadNamespace(x) : there is no package called ‘RcppGSL’
-...
-*** installing help indices
-** building package indices
-** testing if installed package can be loaded from temporary location
-Error: package or namespace load failed for ‘valse’ in dyn.load(file, DLLpath = DLLpath, ...):
- unable to load shared object '/tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so':
- /tmp/workdir/valse/new/valse.Rcheck/00LOCK-valse/00new/valse/libs/valse.so: undefined symbol: gsl_vector_free
-Error: loading failed
-Execution halted
-ERROR: loading failed
-* removing ‘/tmp/workdir/valse/new/valse.Rcheck/valse’
-
-
-```
-### CRAN
+### CRAN
```
* installing *source* package ‘valse’ ...
** package ‘valse’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o
-gcc -I"/opt/R/4.1.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o
-Error in loadNamespace(x) : there is no package called ‘RcppGSL’
+using C compiler: ‘gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0’
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGLLF.c -o EMGLLF.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c EMGrank.c -o EMGrank.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGLLF.c -o a.EMGLLF.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c a.EMGrank.c -o a.EMGrank.o
+gcc -I"/opt/R/4.3.1/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -c valse_init.c -o valse_init.o
...
*** installing help indices
** building package indices
@@ -4525,327 +890,4 @@ ERROR: loading failed
* removing ‘/tmp/workdir/valse/old/valse.Rcheck/valse’
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# vivid
-
-
-
-* Version: 0.2.8
-* GitHub: NA
-* Source code: https://github.com/cran/vivid
-* Date/Publication: 2023-07-10 22:20:02 UTC
-* Number of recursive dependencies: 212
-
-Run `cloud_details(, "vivid")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/vivid/new/vivid.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘vivid/DESCRIPTION’ ... OK
-* this is package ‘vivid’ version ‘0.2.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘vividVignette.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/vivid/old/vivid.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘vivid/DESCRIPTION’ ... OK
-* this is package ‘vivid’ version ‘0.2.8’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... NOTE
-...
-* checking installed files from ‘inst/doc’ ... OK
-* checking files in ‘vignettes’ ... OK
-* checking examples ... OK
-* checking for unstated dependencies in vignettes ... OK
-* checking package vignettes in ‘inst/doc’ ... OK
-* checking running R code from vignettes ... NONE
- ‘vividVignette.Rmd’ using ‘UTF-8’... OK
-* checking re-building of vignette outputs ... OK
-* DONE
-Status: 1 NOTE
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
-```
-# xpose.nlmixr2
-
-
-
-* Version: 0.4.0
-* GitHub: NA
-* Source code: https://github.com/cran/xpose.nlmixr2
-* Date/Publication: 2022-06-08 09:10:02 UTC
-* Number of recursive dependencies: 156
-
-Run `cloud_details(, "xpose.nlmixr2")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-* using log directory ‘/tmp/workdir/xpose.nlmixr2/new/xpose.nlmixr2.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘xpose.nlmixr2/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘xpose.nlmixr2’ version ‘0.4.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘nlmixr2est’
-
-Package suggested but not available for checking: ‘nlmixr2’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-### CRAN
-
-```
-* using log directory ‘/tmp/workdir/xpose.nlmixr2/old/xpose.nlmixr2.Rcheck’
-* using R version 4.1.1 (2021-08-10)
-* using platform: x86_64-pc-linux-gnu (64-bit)
-* using session charset: UTF-8
-* using option ‘--no-manual’
-* checking for file ‘xpose.nlmixr2/DESCRIPTION’ ... OK
-* checking extension type ... Package
-* this is package ‘xpose.nlmixr2’ version ‘0.4.0’
-* package encoding: UTF-8
-* checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Package required but not available: ‘nlmixr2est’
-
-Package suggested but not available for checking: ‘nlmixr2’
-
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
-* DONE
-Status: 1 ERROR
-
-
-
-
-
-```
-# NA
-
-
-
-* Version: NA
-* GitHub: NA
-* Source code: https://github.com/cran/NA
-* Number of recursive dependencies: 0
-
-Run `cloud_details(, "NA")` for more info
-
-
-
-## Error before installation
-
-### Devel
-
-```
-
-
-
-
-
-
-```
-### CRAN
-
-```
-
-
-
-
-
-
```
diff --git a/revdep/problems.md b/revdep/problems.md
index 70d42f0dd7..af2178c0fb 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,77 +1,2773 @@
-# jfa
+# AcademicThemes
-* Version: 0.7.0
-* GitHub: https://github.com/koenderks/jfa
-* Source code: https://github.com/cran/jfa
-* Date/Publication: 2023-10-04 14:50:02 UTC
-* Number of recursive dependencies: 187
+* Version: 0.0.1
+* GitHub: https://github.com/hwarden162/AcademicThemes
+* Source code: https://github.com/cran/AcademicThemes
+* Date/Publication: 2023-03-27 12:40:02 UTC
+* Number of recursive dependencies: 119
-Run `cloud_details(, "jfa")` for more info
+Run `revdepcheck::cloud_details(, "AcademicThemes")` for more info
## Newly broken
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > # This file is part of the standard setup for testthat.
+ > # It is recommended that you do not modify it.
+ > #
+ > # Where should you do additional test configuration?
+ > # Learn more about the roles of various files in:
+ > # * https://r-pkgs.org/tests.html
+ > # * https://testthat.r-lib.org/reference/test_package.html#special-files
+ ...
+ `environment(actual$super)$env$call`: `scale_fill_academic_d(palette_name)`
+ `environment(expected$super)$env$call`: `eval(code, test_env)`
+
+ environment(actual$super)$members$call vs environment(expected$super)$members$call
+ - `scale_fill_academic_d(palette_name)`
+ + `eval(code, test_env)`
+
+ [ FAIL 124 | WARN 124 | SKIP 0 | PASS 133 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# afex
+
+
+
+* Version: 1.3-0
+* GitHub: https://github.com/singmann/afex
+* Source code: https://github.com/cran/afex
+* Date/Publication: 2023-04-17 22:00:02 UTC
+* Number of recursive dependencies: 226
+
+Run `revdepcheck::cloud_details(, "afex")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(afex)
+ Loading required package: lme4
+ Loading required package: Matrix
+ ************
+ Welcome to afex. For support visit: http://afex.singmann.science/
+ - Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
+ ...
+ • afex_plot-default-support/afex-plots-nlme-3.svg
+ • afex_plot-default-support/afex-plots-nlme-4.svg
+ • afex_plot-default-support/afex-plots-nlme-5.svg
+ • afex_plot-default-support/afex-plots-poisson-glm-1.svg
+ • afex_plot-default-support/afex-plots-poisson-glm-2.svg
+ • afex_plot-vignette/afex-plot-glmmtmb-1.svg
+ • afex_plot-vignette/afex-plot-glmmtmb-2.svg
+ • afex_plot-vignette/afex-plot-glmmtmb-3.svg
+ Error: Test failures
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘afex_analysing_accuracy_data.Rmd’ using rmarkdown
+ --- finished re-building ‘afex_analysing_accuracy_data.Rmd’
+
+ --- re-building ‘afex_anova_example.Rmd’ using rmarkdown
+ --- finished re-building ‘afex_anova_example.Rmd’
+
+ --- re-building ‘afex_mixed_example.Rmd’ using rmarkdown
+ --- finished re-building ‘afex_mixed_example.Rmd’
+
+ ...
+ --- finished re-building ‘assumptions_of_ANOVAs.Rmd’
+
+ --- re-building ‘introduction-mixed-models.pdf.asis’ using asis
+ --- finished re-building ‘introduction-mixed-models.pdf.asis’
+
+ SUMMARY: processing the following file failed:
+ ‘afex_plot_supported_models.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# archeoViz
+
+
+
+* Version: 1.3.4
+* GitHub: https://github.com/sebastien-plutniak/archeoviz
+* Source code: https://github.com/cran/archeoViz
+* Date/Publication: 2024-01-31 18:00:13 UTC
+* Number of recursive dependencies: 120
+
+Run `revdepcheck::cloud_details(, "archeoViz")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(archeoViz)
+ >
+ > test_check("archeoViz")
+ 10 X squares, but 9 labels provided: 1, 2, 3, 4, 5, 6, 7, 8, 9.
+
+ 100 X squares, but 10 labels provided: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10.
+ ...
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 82 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure ('test.do_section_plot.R:105:3'): .do_section_plot: Altitude values ──
+ fig.y$x$layoutAttrs[[1]]$yaxis$range[2] is not strictly less than 200. Difference: 3
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 82 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# assignPOP
+
+
+
+* Version: 1.2.4
+* GitHub: https://github.com/alexkychen/assignPOP
+* Source code: https://github.com/cran/assignPOP
+* Date/Publication: 2021-10-27 19:30:02 UTC
+* Number of recursive dependencies: 142
+
+Run `revdepcheck::cloud_details(, "assignPOP")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(assignPOP)
+ >
+ > test_check("assignPOP")
+
+ Correct assignment rates were estimated!!
+ A total of 3 assignment tests for 3 pops.
+ ...
+ Actual value: "List of 11\\n \$ data :'data\.frame':\\t72 obs\. of 6 variables:\\n \.\.\$ Ind\.ID : Factor w/ 24 levels "A10","A12","AA9",\.\.: 3 1 2 5 6 4 7 8 11 9 \.\.\.\\n \.\.\$ origin\.pop: Factor w/ 3 levels "pop\.1","pop\.2",\.\.: 1 1 1 2 2 2 3 3 1 1 \.\.\.\\n \.\.\$ pred\.pop : Factor w/ 3 levels "pop\.1","pop\.3",\.\.: 1 2 2 1 1 1 1 1 2 2 \.\.\.\\n \.\.\$ fold_n : chr \[1:72\] "fold_1" "fold_1" "fold_1" "fold_1" \.\.\.\\n \.\.\$ variable : Factor w/ 3 levels "pop\.1","pop\.2",\.\.: 1 1 1 1 1 1 1 1 1 1 \.\.\.\\n \.\.\$ value : num \[1:72\] 0\.4 0\.326 0\.26 0\.383 0\.44 \.\.\.\\n \$ layers :List of 1\\n \.\.\$ :Classes 'LayerInstance', 'Layer', 'ggproto', 'gg' \\n aes_params: list\\n compute_aesthetics: function\\n compute_geom_1: function\\n compute_geom_2: function\\n compute_position: function\\n compute_statistic: function\\n computed_geom_params: NULL\\n computed_mapping: NULL\\n computed_stat_params: NULL\\n constructor: call\\n data: waiver\\n draw_geom: function\\n finish_statistics: function\\n geom: \\n aesthetics: function\\n default_aes: uneval\\n draw_group: function\\n draw_key: function\\n draw_layer: function\\n draw_panel: function\\n extra_params: just na\.rm orientation\\n handle_na: function\\n non_missing_aes: xmin xmax ymin ymax\\n optional_aes: \\n parameters: function\\n rename_size: TRUE\\n required_aes: x y\\n setup_data: function\\n setup_params: function\\n use_defaults: function\\n super: \\n geom_params: list\\n inherit\.aes: TRUE\\n layer_data: function\\n map_statistic: function\\n mapping: NULL\\n position: \\n compute_layer: function\\n compute_panel: function\\n fill: FALSE\\n required_aes: \\n reverse: FALSE\\n setup_data: function\\n setup_params: function\\n type: NULL\\n vjust: 1\\n super: \\n print: function\\n setup_layer: function\\n show\.legend: NA\\n stat: \\n aesthetics: function\\n compute_group: function\\n compute_layer: function\\n compute_panel: function\\n default_aes: uneval\\n dropped_aes: \\n extra_params: na\.rm\\n finish_layer: function\\n non_missing_aes: \\n optional_aes: \\n parameters: function\\n required_aes: \\n retransform: TRUE\\n setup_data: function\\n setup_params: function\\n super: \\n stat_params: list\\n super: \\n \$ scales :Classes 'ScalesList', 'ggproto', 'gg' \\n add: function\\n add_defaults: function\\n add_missing: function\\n backtransform_df: function\\n clone: function\\n find: function\\n get_scales: function\\n has_scale: function\\n input: function\\n map_df: function\\n n: function\\n non_position_scales: function\\n scales: list\\n train_df: function\\n transform_df: function\\n super: \\n \$ guides :Classes 'Guides', 'ggproto', 'gg' \\n add: function\\n assemble: function\\n build: function\\n draw: function\\n get_custom: function\\n get_guide: function\\n get_params: function\\n get_position: function\\n guides: list\\n merge: function\\n missing: \\n add_title: function\\n arrange_layout: function\\n assemble_drawing: function\\n available_aes: any\\n build_decor: function\\n build_labels: function\\n build_ticks: function\\n build_title: function\\n draw: function\\n draw_early_exit: function\\n elements: list\\n extract_decor: function\\n extract_key: function\\n extract_params: function\\n get_layer_key: function\\n hashables: list\\n measure_grobs: function\\n merge: function\\n override_elements: function\\n params: list\\n process_layers: function\\n setup_elements: function\\n setup_params: function\\n train: function\\n transform: function\\n super: \\n package_box: function\\n print: function\\n process_layers: function\\n setup: function\\n subset_guides: function\\n train: function\\n update_params: function\\n super: \\n \$ mapping :List of 3\\n \.\.\$ x : language ~Ind\.ID\\n \.\. \.\.- attr\(\*, "\.Environment"\)= \\n \.\.\$ y : language ~value\\n \.\. \.\.- attr\(\*, "\.Environment"\)= \\n \.\.\$ fill: language ~variable\\n \.\. \.\.- attr\(\*, "\.Environment"\)= \\n \.\.- attr\(\*, "class"\)= chr "uneval"\\n \$ theme :List of 136\\n \.\.\$ line :List of 6\\n \.\. \.\.\$ colour : chr "black"\\n \.\. \.\.\$ linewidth : num 0\.5\\n \.\. \.\.\$ linetype : num 1\\n \.\. \.\.\$ lineend : chr "butt"\\n \.\. \.\.\$ arrow : logi FALSE\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_line" "element"\\n \.\.\$ rect :List of 5\\n \.\. \.\.\$ fill : chr "white"\\n \.\. \.\.\$ colour : chr "black"\\n \.\. \.\.\$ linewidth : num 0\.5\\n \.\. \.\.\$ linetype : num 1\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_rect" "element"\\n \.\.\$ text :List of 11\\n \.\. \.\.\$ family : chr ""\\n \.\. \.\.\$ face : chr "plain"\\n \.\. \.\.\$ colour : chr "black"\\n \.\. \.\.\$ size : num 11\\n \.\. \.\.\$ hjust : num 0\.5\\n \.\. \.\.\$ vjust : num 0\.5\\n \.\. \.\.\$ angle : num 0\\n \.\. \.\.\$ lineheight : num 0\.9\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 0points 0points 0points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : logi FALSE\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ title : NULL\\n \.\.\$ aspect\.ratio : NULL\\n \.\.\$ axis\.title : NULL\\n \.\.\$ axis\.title\.x : list\(\)\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_blank" "element"\\n \.\.\$ axis\.title\.x\.top :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : num 0\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 0points 2\.75points 0points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.title\.x\.bottom : NULL\\n \.\.\$ axis\.title\.y :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : num 1\\n \.\. \.\.\$ angle : num 90\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 2\.75points 0points 0points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.title\.y\.left : NULL\\n \.\.\$ axis\.title\.y\.right :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : num 1\\n \.\. \.\.\$ angle : num -90\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 0points 0points 2\.75points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.text :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : chr "grey30"\\n \.\. \.\.\$ size : 'rel' num 0\.8\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : NULL\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : NULL\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.text\.x :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : num 1\\n \.\. \.\.\$ angle : num 90\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 2\.2points 0points 0points 0points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi FALSE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.text\.x\.top :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : num 0\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 0points 2\.2points 0points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.text\.x\.bottom : NULL\\n \.\.\$ axis\.text\.y :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : num 1\\n \.\. \.\.\$ vjust : NULL\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 2\.2points 0points 0points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.text\.y\.left : NULL\\n \.\.\$ axis\.text\.y\.right :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : num 0\\n \.\. \.\.\$ vjust : NULL\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 0points 0points 2\.2points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.text\.theta : NULL\\n \.\.\$ axis\.text\.r :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : num 0\.5\\n \.\. \.\.\$ vjust : NULL\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : 'margin' num \[1:4\] 0points 2\.2points 0points 2\.2points\\n \.\. \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ axis\.ticks :List of 6\\n \.\. \.\.\$ colour : chr "grey20"\\n \.\. \.\.\$ linewidth : NULL\\n \.\. \.\.\$ linetype : NULL\\n \.\. \.\.\$ lineend : NULL\\n \.\. \.\.\$ arrow : logi FALSE\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_line" "element"\\n \.\.\$ axis\.ticks\.x : NULL\\n \.\.\$ axis\.ticks\.x\.top : NULL\\n \.\.\$ axis\.ticks\.x\.bottom : NULL\\n \.\.\$ axis\.ticks\.y : NULL\\n \.\.\$ axis\.ticks\.y\.left : NULL\\n \.\.\$ axis\.ticks\.y\.right : NULL\\n \.\.\$ axis\.ticks\.theta : NULL\\n \.\.\$ axis\.ticks\.r : NULL\\n \.\.\$ axis\.minor\.ticks\.x\.top : NULL\\n \.\.\$ axis\.minor\.ticks\.x\.bottom : NULL\\n \.\.\$ axis\.minor\.ticks\.y\.left : NULL\\n \.\.\$ axis\.minor\.ticks\.y\.right : NULL\\n \.\.\$ axis\.minor\.ticks\.theta : NULL\\n \.\.\$ axis\.minor\.ticks\.r : NULL\\n \.\.\$ axis\.ticks\.length : 'simpleUnit' num 2\.75points\\n \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\.\$ axis\.ticks\.length\.x : NULL\\n \.\.\$ axis\.ticks\.length\.x\.top : NULL\\n \.\.\$ axis\.ticks\.length\.x\.bottom : NULL\\n \.\.\$ axis\.ticks\.length\.y : NULL\\n \.\.\$ axis\.ticks\.length\.y\.left : NULL\\n \.\.\$ axis\.ticks\.length\.y\.right : NULL\\n \.\.\$ axis\.ticks\.length\.theta : NULL\\n \.\.\$ axis\.ticks\.length\.r : NULL\\n \.\.\$ axis\.minor\.ticks\.length : 'rel' num 0\.75\\n \.\.\$ axis\.minor\.ticks\.length\.x : NULL\\n \.\.\$ axis\.minor\.ticks\.length\.x\.top : NULL\\n \.\.\$ axis\.minor\.ticks\.length\.x\.bottom: NULL\\n \.\.\$ axis\.minor\.ticks\.length\.y : NULL\\n \.\.\$ axis\.minor\.ticks\.length\.y\.left : NULL\\n \.\.\$ axis\.minor\.ticks\.length\.y\.right : NULL\\n \.\.\$ axis\.minor\.ticks\.length\.theta : NULL\\n \.\.\$ axis\.minor\.ticks\.length\.r : NULL\\n \.\.\$ axis\.line : list\(\)\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_blank" "element"\\n \.\.\$ axis\.line\.x : NULL\\n \.\.\$ axis\.line\.x\.top : NULL\\n \.\.\$ axis\.line\.x\.bottom : NULL\\n \.\.\$ axis\.line\.y : NULL\\n \.\.\$ axis\.line\.y\.left : NULL\\n \.\.\$ axis\.line\.y\.right : NULL\\n \.\.\$ axis\.line\.theta : NULL\\n \.\.\$ axis\.line\.r : NULL\\n \.\.\$ legend\.background :List of 5\\n \.\. \.\.\$ fill : NULL\\n \.\. \.\.\$ colour : logi NA\\n \.\. \.\.\$ linewidth : NULL\\n \.\. \.\.\$ linetype : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_rect" "element"\\n \.\.\$ legend\.margin : 'margin' num \[1:4\] 5\.5points 5\.5points 5\.5points 5\.5points\\n \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\.\$ legend\.spacing : 'simpleUnit' num 11points\\n \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\.\$ legend\.spacing\.x : NULL\\n \.\.\$ legend\.spacing\.y : NULL\\n \.\.\$ legend\.key : NULL\\n \.\.\$ legend\.key\.size : 'simpleUnit' num 1\.2lines\\n \.\. \.\.- attr\(\*, "unit"\)= int 3\\n \.\.\$ legend\.key\.height : NULL\\n \.\.\$ legend\.key\.width : NULL\\n \.\.\$ legend\.key\.spacing : 'simpleUnit' num 5\.5points\\n \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\.\$ legend\.key\.spacing\.x : NULL\\n \.\.\$ legend\.key\.spacing\.y : NULL\\n \.\.\$ legend\.frame : NULL\\n \.\.\$ legend\.ticks : NULL\\n \.\.\$ legend\.ticks\.length : 'rel' num 0\.2\\n \.\.\$ legend\.axis\.line : NULL\\n \.\.\$ legend\.text :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : 'rel' num 0\.8\\n \.\. \.\.\$ hjust : NULL\\n \.\. \.\.\$ vjust : NULL\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : NULL\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ legend\.text\.position : NULL\\n \.\.\$ legend\.title :List of 11\\n \.\. \.\.\$ family : NULL\\n \.\. \.\.\$ face : NULL\\n \.\. \.\.\$ colour : NULL\\n \.\. \.\.\$ size : NULL\\n \.\. \.\.\$ hjust : num 0\\n \.\. \.\.\$ vjust : NULL\\n \.\. \.\.\$ angle : NULL\\n \.\. \.\.\$ lineheight : NULL\\n \.\. \.\.\$ margin : NULL\\n \.\. \.\.\$ debug : NULL\\n \.\. \.\.\$ inherit\.blank: logi TRUE\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_text" "element"\\n \.\.\$ legend\.title\.position : NULL\\n \.\.\$ legend\.position : chr "right"\\n \.\.\$ legend\.position\.inside : NULL\\n \.\.\$ legend\.direction : NULL\\n \.\.\$ legend\.byrow : NULL\\n \.\.\$ legend\.justification : chr "center"\\n \.\.\$ legend\.justification\.top : NULL\\n \.\.\$ legend\.justification\.bottom : NULL\\n \.\.\$ legend\.justification\.left : NULL\\n \.\.\$ legend\.justification\.right : NULL\\n \.\.\$ legend\.justification\.inside : NULL\\n \.\.\$ legend\.location : NULL\\n \.\.\$ legend\.box : NULL\\n \.\.\$ legend\.box\.just : NULL\\n \.\.\$ legend\.box\.margin : 'margin' num \[1:4\] 0cm 0cm 0cm 0cm\\n \.\. \.\.- attr\(\*, "unit"\)= int 1\\n \.\.\$ legend\.box\.background : list\(\)\\n \.\. \.\.- attr\(\*, "class"\)= chr \[1:2\] "element_blank" "element"\\n \.\.\$ legend\.box\.spacing : 'simpleUnit' num 11points\\n \.\. \.\.- attr\(\*, "unit"\)= int 8\\n \.\. \[list output truncated\]\\n \.\.- attr\(\*, "class"\)= chr \[1:2\] "theme" "gg"\\n \.\.- attr\(\*, "complete"\)= logi TRUE\\n \.\.- attr\(\*, "validate"\)= logi TRUE\\n \$ coordinates:Classes 'CoordCartesian', 'Coord', 'ggproto', 'gg' \\n aspect: function\\n backtransform_range: function\\n clip: on\\n default: FALSE\\n distance: function\\n expand: TRUE\\n is_free: function\\n is_linear: function\\n labels: function\\n limits: list\\n modify_scales: function\\n range: function\\n render_axis_h: function\\n render_axis_v: function\\n render_bg: function\\n render_fg: function\\n setup_data: function\\n setup_layout: function\\n setup_panel_guides: function\\n setup_panel_params: function\\n setup_params: function\\n train_panel_guides: function\\n transform: function\\n super: \\n \$ facet :Classes 'FacetGrid', 'Facet', 'ggproto', 'gg' \\n compute_layout: function\\n draw_back: function\\n draw_front: function\\n draw_labels: function\\n draw_panels: function\\n finish_data: function\\n init_scales: function\\n map_data: function\\n params: list\\n setup_data: function\\n setup_params: function\\n shrink: TRUE\\n train_scales: function\\n vars: function\\n super: \\n \$ plot_env : \\n \$ layout :Classes 'Layout', 'ggproto', 'gg' \\n coord: NULL\\n coord_params: list\\n facet: NULL\\n facet_params: list\\n finish_data: function\\n get_scales: function\\n layout: NULL\\n map_position: function\\n panel_params: NULL\\n panel_scales_x: NULL\\n panel_scales_y: NULL\\n render: function\\n render_labels: function\\n reset_scales: function\\n resolve_label: function\\n setup: function\\n setup_panel_guides: function\\n setup_panel_params: function\\n train_position: function\\n super: \\n \$ labels :List of 4\\n \.\.\$ title: chr "K = 3 "\\n \.\.\$ y : chr "Probability"\\n \.\.\$ x : chr "Ind\.ID"\\n \.\.\$ fill : chr "variable"\\n - attr\(\*, "class"\)= chr \[1:2\] "gg" "ggplot""
+ Backtrace:
+ ▆
+ 1. └─testthat::expect_output(str(plot), "List of 10") at test_membership.R:5:3
+ 2. └─testthat::expect_match(...)
+ 3. └─testthat:::expect_match_(...)
+
+ [ FAIL 3 | WARN 1 | SKIP 0 | PASS 39 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# bioassays
+
+
+
+* Version: 1.0.1
+* GitHub: NA
+* Source code: https://github.com/cran/bioassays
+* Date/Publication: 2020-10-09 20:10:02 UTC
+* Number of recursive dependencies: 73
+
+Run `revdepcheck::cloud_details(, "bioassays")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(bioassays)
+ >
+ > test_check("bioassays")
+ F1
+ F2
+ F3
+ ...
+ 1. ├─testthat::expect_identical(eg4$guides[[1]], NULL) at test_heatmap.R:43:3
+ 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
+ 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
+ 4. ├─eg4$guides[[1]]
+ 5. └─ggplot2:::`[[.ggproto`(eg4$guides, 1)
+ 6. └─ggplot2:::fetch_ggproto(x, name)
+
+ [ FAIL 4 | WARN 5 | SKIP 0 | PASS 48 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# BOSO
+
+
+
+* Version: 1.0.3
+* GitHub: NA
+* Source code: https://github.com/cran/BOSO
+* Date/Publication: 2021-07-01 07:40:11 UTC
+* Number of recursive dependencies: 153
+
+Run `revdepcheck::cloud_details(, "BOSO")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘BOSO.Rmd’ using rmarkdown
+
+ Quitting from lines 475-492 [plot_comparison_BOSOvsREST] (BOSO.Rmd)
+ Error: processing vignette 'BOSO.Rmd' failed with diagnostics:
+ The `legend.pos` theme element is not defined in the element hierarchy.
+ --- failed re-building ‘BOSO.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘BOSO.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+## In both
+
+* checking package dependencies ... NOTE
+ ```
+ Packages suggested but not available for checking: 'cplexAPI', 'bestsubset'
+ ```
+
+# breakDown
+
+
+
+* Version: 0.2.1
+* GitHub: https://github.com/pbiecek/breakDown
+* Source code: https://github.com/cran/breakDown
+* Date/Publication: 2021-01-20 12:30:06 UTC
+* Number of recursive dependencies: 119
+
+Run `revdepcheck::cloud_details(, "breakDown")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(breakDown)
+ >
+ > test_check("breakDown")
+ contribution
+ (Intercept) 0.240
+ - number_project = 2 -0.050
+ ...
+ ── Failure ('test_plot.R:38:3'): Output format ─────────────────────────────────
+ plot(broken_rf_classif) has length 11, not length 9.
+ ── Failure ('test_plot.R:39:3'): Output format ─────────────────────────────────
+ plot(broken_lm_regr) has length 11, not length 9.
+ ── Failure ('test_plot.R:40:3'): Output format ─────────────────────────────────
+ plot(broken_glm_classif) has length 11, not length 9.
+
+ [ FAIL 3 | WARN 12 | SKIP 0 | PASS 30 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# canadianmaps
+
+
+
+* Version: 1.3.0
+* GitHub: https://github.com/joellecayen/canadianmaps
+* Source code: https://github.com/cran/canadianmaps
+* Date/Publication: 2023-07-10 22:30:20 UTC
+* Number of recursive dependencies: 82
+
+Run `revdepcheck::cloud_details(, "canadianmaps")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(canadianmaps)
+ >
+ > test_check("canadianmaps")
+ [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ...
+ `expected` is a character vector ('manual')
+ ── Failure ('test-functions.R:23:3'): check-functions: scale_color_map() returns a ggplot manual fill object ──
+ output$scale_name (`actual`) not equal to "manual" (`expected`).
+
+ `actual` is NULL
+ `expected` is a character vector ('manual')
+
+ [ FAIL 2 | WARN 0 | SKIP 0 | PASS 4 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking dependencies in R code ... NOTE
+ ```
+ Namespace in Imports field not imported from: ‘sf’
+ All declared Imports should be used.
+ ```
+
+* checking data for non-ASCII characters ... NOTE
+ ```
+ Note: found 2992 marked UTF-8 strings
+ ```
+
+# CAST
+
+
+
+* Version: 0.9.0
+* GitHub: https://github.com/HannaMeyer/CAST
+* Source code: https://github.com/cran/CAST
+* Date/Publication: 2024-01-09 05:40:02 UTC
+* Number of recursive dependencies: 159
+
+Run `revdepcheck::cloud_details(, "CAST")` for more info
+
+
+
+## Newly broken
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 5.0Mb
+ sub-directories of 1Mb or more:
+ doc 2.9Mb
+ extdata 1.6Mb
+ ```
+
+# CEDA
+
+
+
+* Version: 1.1.0
+* GitHub: NA
+* Source code: https://github.com/cran/CEDA
+* Date/Publication: 2022-08-11 13:50:12 UTC
+* Number of recursive dependencies: 80
+
+Run `revdepcheck::cloud_details(, "CEDA")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘Userguide.Rmd’ using rmarkdown
+
+ Quitting from lines 190-191 [fig3] (Userguide.Rmd)
+ Error: processing vignette 'Userguide.Rmd' failed with diagnostics:
+ The `legend.text.align` theme element is not defined in the element
+ hierarchy.
+ --- failed re-building ‘Userguide.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘Userguide.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# cobalt
+
+
+
+* Version: 4.5.3
+* GitHub: https://github.com/ngreifer/cobalt
+* Source code: https://github.com/cran/cobalt
+* Date/Publication: 2024-01-10 03:23:07 UTC
+* Number of recursive dependencies: 176
+
+Run `revdepcheck::cloud_details(, "cobalt")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘cobalt-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: balance-statistics
+ > ### Title: Balance Statistics in 'bal.tab' and 'love.plot'
+ > ### Aliases: balance-statistics
+ >
+ > ### ** Examples
+ >
+ > data(lalonde)
+ ...
+ Warning: No shared levels found between `names(values)` of the manual scale and the
+ data's fill values.
+ Warning: No shared levels found between `names(values)` of the manual scale and the
+ data's fill values.
+ Warning: No shared levels found between `names(values)` of the manual scale and the
+ data's fill values.
+ Error in legg$grobs[[which(legg$layout$name == "guide-box")]] :
+ attempt to select less than one element in get1index
+ Calls: love.plot -> eval.parent -> eval -> eval -> love.plot
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘cobalt.Rmd’ using rmarkdown
+
+ Quitting from lines 347-366 [unnamed-chunk-17] (cobalt.Rmd)
+ Error: processing vignette 'cobalt.Rmd' failed with diagnostics:
+ attempt to select less than one element in get1index
+ --- failed re-building ‘cobalt.Rmd’
+
+ --- re-building ‘longitudinal-treat.Rmd’ using rmarkdown
+ --- finished re-building ‘longitudinal-treat.Rmd’
+ ...
+ --- finished re-building ‘other-packages.Rmd’
+
+ --- re-building ‘segmented-data.Rmd’ using rmarkdown
+ --- finished re-building ‘segmented-data.Rmd’
+
+ SUMMARY: processing the following files failed:
+ ‘cobalt.Rmd’ ‘love.plot.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# constructive
+
+
+
+* Version: 0.2.0
+* GitHub: https://github.com/cynkra/constructive
+* Source code: https://github.com/cran/constructive
+* Date/Publication: 2023-11-13 17:33:24 UTC
+* Number of recursive dependencies: 112
+
+Run `revdepcheck::cloud_details(, "constructive")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(constructive)
+ >
+ > test_check("constructive")
+ [ FAIL 3 | WARN 0 | SKIP 58 | PASS 10 ]
+
+ ══ Skipped tests (58) ══════════════════════════════════════════════════════════
+ ...
+ 20. │ └─utils::getFromNamespace(fun, pkg)
+ 21. │ └─base::get(x, envir = ns, inherits = FALSE)
+ 22. └─base::.handleSimpleError(...)
+ 23. └─rlang (local) h(simpleError(msg, call))
+ 24. └─handlers[[1L]](cnd)
+ 25. └─rlang::abort(...)
+
+ [ FAIL 3 | WARN 0 | SKIP 58 | PASS 10 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# docxtools
+
+
+
+* Version: 0.3.0
+* GitHub: https://github.com/graphdr/docxtools
+* Source code: https://github.com/cran/docxtools
+* Date/Publication: 2022-11-12 00:40:02 UTC
+* Number of recursive dependencies: 74
+
+Run `revdepcheck::cloud_details(, "docxtools")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(docxtools)
+ >
+ > test_check("docxtools")
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure ('test_put.R:21:3'): put_axes() attributes match expectations ───────
+ p$layers[[1]]$geom$non_missing_aes not identical to c("linetype", "linewidth", "shape").
+ Lengths differ: 2 is not 3
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 22 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# dynamAedes
+
+
+
+* Version: 2.2.8
+* GitHub: https://github.com/mattmar/dynamAedes
+* Source code: https://github.com/cran/dynamAedes
+* Date/Publication: 2024-01-08 23:00:03 UTC
+* Number of recursive dependencies: 127
+
+Run `revdepcheck::cloud_details(, "dynamAedes")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘dynamAedes_01_punctual.Rmd’ using rmarkdown
+ starting worker pid=5564 on localhost:11930 at 08:51:28.686
+ Loading required package: dynamAedes
+ loaded dynamAedes and set parent environment
+
+ |
+ |%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%| 100%
+ Quitting from lines 182-199 [unnamed-chunk-14] (dynamAedes_01_punctual.Rmd)
+ Error: processing vignette 'dynamAedes_01_punctual.Rmd' failed with diagnostics:
+ ...
+
+ --- re-building ‘dynamAedes_05_spreader.Rmd’ using rmarkdown
+ --- finished re-building ‘dynamAedes_05_spreader.Rmd’
+
+ SUMMARY: processing the following files failed:
+ ‘dynamAedes_01_punctual.Rmd’ ‘dynamAedes_02_local.Rmd’
+ ‘dynamAedes_03_regional.Rmd’ ‘dynamAedes_04_uncompModel.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# EcoDiet
+
+
+
+* Version: 2.0.0
+* GitHub: https://github.com/pyhernvann/EcoDiet
+* Source code: https://github.com/cran/EcoDiet
+* Date/Publication: 2023-01-06 23:50:02 UTC
+* Number of recursive dependencies: 136
+
+Run `revdepcheck::cloud_details(, "EcoDiet")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘convergence_problems.Rmd’ using rmarkdown
+ --- finished re-building ‘convergence_problems.Rmd’
+
+ --- re-building ‘introduction_EcoDiet.Rmd’ using rmarkdown
+
+ Quitting from lines 373-374 [unnamed-chunk-35] (introduction_EcoDiet.Rmd)
+ Error: processing vignette 'introduction_EcoDiet.Rmd' failed with diagnostics:
+ The `legend.byrow` theme element must be a object.
+ ...
+ --- failed re-building ‘introduction_EcoDiet.Rmd’
+
+ --- re-building ‘realistic_example.Rmd’ using rmarkdown
+ --- finished re-building ‘realistic_example.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘introduction_EcoDiet.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# epos
+
+
+
+* Version: 1.0
+* GitHub: NA
+* Source code: https://github.com/cran/epos
+* Date/Publication: 2021-02-20 01:10:14 UTC
+* Number of recursive dependencies: 98
+
+Run `revdepcheck::cloud_details(, "epos")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(epos)
+ >
+ > test_check("epos")
+ [ FAIL 1 | WARN 12 | SKIP 0 | PASS 13 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ...
+ [1] 11 - 9 == 2
+ Backtrace:
+ ▆
+ 1. └─testthat::expect_that(length(tanimotobaseline), equals(9)) at test_createTanimotoBaseline.R:39:3
+ 2. └─testthat (local) condition(object)
+ 3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
+
+ [ FAIL 1 | WARN 12 | SKIP 0 | PASS 13 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking dependencies in R code ... NOTE
+ ```
+ Namespace in Imports field not imported from: ‘testthat’
+ All declared Imports should be used.
+ ```
+
+* checking data for non-ASCII characters ... NOTE
+ ```
+ Note: found 15 marked UTF-8 strings
+ ```
+
+# feasts
+
+
+
+* Version: 0.3.1
+* GitHub: https://github.com/tidyverts/feasts
+* Source code: https://github.com/cran/feasts
+* Date/Publication: 2023-03-22 14:20:10 UTC
+* Number of recursive dependencies: 101
+
+Run `revdepcheck::cloud_details(, "feasts")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘feasts-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: gg_season
+ > ### Title: Seasonal plot
+ > ### Aliases: gg_season
+ >
+ > ### ** Examples
+ >
+ > library(tsibble)
+ ...
+ 14. ├─rlang::inject(self$extract_key(scale, !!!params))
+ 15. └─self$extract_key(...)
+ 16. └─ggplot2 (local) extract_key(...)
+ 17. └─Guide$extract_key(scale, aesthetic, ...)
+ 18. └─ggplot2 (local) extract_key(...)
+ 19. └─scale$get_labels(breaks)
+ 20. └─ggplot2 (local) get_labels(..., self = self)
+ 21. └─cli::cli_abort(...)
+ 22. └─rlang::abort(...)
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(feasts)
+ Loading required package: fabletools
+ >
+ > test_check("feasts")
+ [ FAIL 2 | WARN 0 | SKIP 0 | PASS 98 ]
+
+ ...
+ 15. └─Guide$extract_key(scale, aesthetic, ...)
+ 16. └─ggplot2 (local) extract_key(...)
+ 17. └─scale$get_labels(breaks)
+ 18. └─ggplot2 (local) get_labels(..., self = self)
+ 19. └─cli::cli_abort(...)
+ 20. └─rlang::abort(...)
+
+ [ FAIL 2 | WARN 0 | SKIP 0 | PASS 98 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘feasts.Rmd’ using rmarkdown
+
+ Quitting from lines 49-51 [season-plot] (feasts.Rmd)
+ Error: processing vignette 'feasts.Rmd' failed with diagnostics:
+ `breaks` and `labels` have different lengths.
+ --- failed re-building ‘feasts.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘feasts.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# fitODBODRshiny
+
+
+
+* Version: 1.0.0
+* GitHub: https://github.com/Amalan-ConStat/fitODBODRshiny,https:
+* Source code: https://github.com/cran/fitODBODRshiny
+* Date/Publication: 2024-02-09 18:10:02 UTC
+* Number of recursive dependencies: 92
+
+Run `revdepcheck::cloud_details(, "fitODBODRshiny")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘fitODBODRshiny-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: All_Plots
+ > ### Title: All Plots data
+ > ### Aliases: All_Plots
+ > ### Keywords: datasets
+ >
+ > ### ** Examples
+ >
+ ...
+ 11. │ │ └─base::withCallingHandlers(...)
+ 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
+ 13. │ └─l$compute_aesthetics(d, plot)
+ 14. │ └─ggplot2 (local) compute_aesthetics(..., self = self)
+ 15. └─base::.handleSimpleError(...)
+ 16. └─rlang (local) h(simpleError(msg, call))
+ 17. └─handlers[[1L]](cnd)
+ 18. └─cli::cli_abort(...)
+ 19. └─rlang::abort(...)
+ Execution halted
+ ```
+
+## In both
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 8.2Mb
+ sub-directories of 1Mb or more:
+ data 8.0Mb
+ ```
+
+# fmeffects
+
+
+
+* Version: 0.1.1
+* GitHub: https://github.com/holgstr/fmeffects
+* Source code: https://github.com/cran/fmeffects
+* Date/Publication: 2023-09-26 15:10:02 UTC
+* Number of recursive dependencies: 158
+
+Run `revdepcheck::cloud_details(, "fmeffects")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘fmeffects-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: ForwardMarginalEffect
+ > ### Title: R6 Class representing a forward marginal effect (FME)
+ > ### Aliases: ForwardMarginalEffect
+ >
+ > ### ** Examples
+ >
+ >
+ ...
+ Warning in ggplot2::geom_segment(ggplot2::aes(x = (0.5 * min(x1) + 0.5 * :
+ All aesthetics have length 1, but the data has 699 rows.
+ ℹ Did you mean to use `annotate()`?
+ Warning in ggplot2::geom_segment(ggplot2::aes(y = (0.5 * min(x2) + 0.5 * :
+ All aesthetics have length 1, but the data has 699 rows.
+ ℹ Did you mean to use `annotate()`?
+ Error in as.vector(x, "character") :
+ cannot coerce type 'environment' to vector of type 'character'
+ Calls: ... validDetails.text -> as.character -> as.character.default
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘fme_theory.Rmd’ using rmarkdown
+ --- finished re-building ‘fme_theory.Rmd’
+
+ --- re-building ‘fmeffects.Rmd’ using rmarkdown
+
+ Quitting from lines 92-100 [unnamed-chunk-7] (fmeffects.Rmd)
+ Error: processing vignette 'fmeffects.Rmd' failed with diagnostics:
+ cannot coerce type 'environment' to vector of type 'character'
+ --- failed re-building ‘fmeffects.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘fmeffects.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# genekitr
+
+
+
+* Version: 1.2.5
+* GitHub: https://github.com/GangLiLab/genekitr
+* Source code: https://github.com/cran/genekitr
+* Date/Publication: 2023-09-07 08:50:09 UTC
+* Number of recursive dependencies: 211
+
+Run `revdepcheck::cloud_details(, "genekitr")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘genekitr-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: plotVenn
+ > ### Title: Venn plot for groups of genes
+ > ### Aliases: plotVenn
+ >
+ > ### ** Examples
+ >
+ > library(ggplot2)
+ ...
+ 7. └─ggplot2::ggplotGrob(x)
+ 8. ├─ggplot2::ggplot_gtable(ggplot_build(x))
+ 9. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x))
+ 10. └─ggplot2:::plot_theme(plot)
+ 11. └─ggplot2:::validate_theme(theme)
+ 12. └─base::mapply(...)
+ 13. └─ggplot2 (local) ``(...)
+ 14. └─cli::cli_abort(...)
+ 15. └─rlang::abort(...)
+ Execution halted
+ ```
+
+# geomtextpath
+
+
+
+* Version: 0.1.1
+* GitHub: https://github.com/AllanCameron/geomtextpath
+* Source code: https://github.com/cran/geomtextpath
+* Date/Publication: 2022-08-30 17:00:05 UTC
+* Number of recursive dependencies: 95
+
+Run `revdepcheck::cloud_details(, "geomtextpath")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(geomtextpath)
+ Loading required package: ggplot2
+ >
+ > test_check("geomtextpath")
+ [ FAIL 1 | WARN 7 | SKIP 3 | PASS 460 ]
+
+ ...
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure ('test-coord_curvedpolar.R:76:3'): wrapping first and last labels works as expected ──
+ make_label(axis_labels$textpath$label[[9]]$glyph) (`actual`) not identical to expression(paste(1, "/", 10)) (`expected`).
+
+ `actual[[1]]`: `paste(1L, "/", 10L)`
+ `expected[[1]]`: `paste(1, "/", 10)`
+
+ [ FAIL 1 | WARN 7 | SKIP 3 | PASS 460 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# ggedit
+
+
+
+* Version: 0.3.1
+* GitHub: https://github.com/yonicd/ggedit
+* Source code: https://github.com/cran/ggedit
+* Date/Publication: 2020-06-02 11:50:06 UTC
+* Number of recursive dependencies: 96
+
+Run `revdepcheck::cloud_details(, "ggedit")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggedit-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: cloneFacet
+ > ### Title: Clone ggplot facet object
+ > ### Aliases: cloneFacet
+ >
+ > ### ** Examples
+ >
+ > obj=ggplot2::facet_grid(a+b~c+d,scales = 'free',as.table = FALSE,switch = 'x',shrink = FALSE)
+ >
+ > cloneFacet(obj)
+ Error in if (use.names && nt[i] == nc[i]) dQuote(nt[i]) else i :
+ missing value where TRUE/FALSE needed
+ Calls: cloneFacet ... lapply -> FUN -> all.equal -> all.equal.list -> paste0
+ Execution halted
+ ```
+
+## In both
+
+* checking dependencies in R code ... NOTE
+ ```
+ Namespace in Imports field not imported from: ‘magrittr’
+ All declared Imports should be used.
+ ```
+
+# gghdr
+
+
+
+* Version: 0.2.0
+* GitHub: https://github.com/Sayani07/gghdr
+* Source code: https://github.com/cran/gghdr
+* Date/Publication: 2022-10-27 15:15:19 UTC
+* Number of recursive dependencies: 92
+
+Run `revdepcheck::cloud_details(, "gghdr")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘gghdr-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: geom_hdr_boxplot
+ > ### Title: Box plot for the highest density region
+ > ### Aliases: geom_hdr_boxplot
+ >
+ > ### ** Examples
+ >
+ > library(ggplot2)
+ ...
+ the data.
+ ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
+ variable into a factor?
+ Warning: The `scale_name` argument of `discrete_scale()` is deprecated as of ggplot2
+ 3.5.0.
+ Warning: The S3 guide system was deprecated in ggplot2 3.5.0.
+ ℹ It has been replaced by a ggproto system that can be extended.
+ Error in if (guide$reverse) { : argument is of length zero
+ Calls: ... -> train -> guide_train -> guide_train.prob_guide
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(gghdr)
+ > library(ggplot2)
+ > library(vdiffr)
+ >
+ > test_check("gghdr")
+ ...
+ 14. └─base::mapply(FUN = f, ..., SIMPLIFY = FALSE)
+ 15. └─ggplot2 (local) ``(...)
+ 16. └─guide$train(param, scale, aes, title = labels[[aes]])
+ 17. └─ggplot2 (local) train(..., self = self)
+ 18. ├─ggplot2::guide_train(params, scale, aesthetic)
+ 19. └─gghdr:::guide_train.prob_guide(params, scale, aesthetic)
+
+ [ FAIL 3 | WARN 6 | SKIP 1 | PASS 8 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘gghdr.Rmd’ using rmarkdown
+
+ Quitting from lines 93-98 [setup] (gghdr.Rmd)
+ Error: processing vignette 'gghdr.Rmd' failed with diagnostics:
+ argument is of length zero
+ --- failed re-building ‘gghdr.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘gghdr.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# ggiraph
+
+
+
+* Version: 0.8.8
+* GitHub: https://github.com/davidgohel/ggiraph
+* Source code: https://github.com/cran/ggiraph
+* Date/Publication: 2023-12-09 15:50:02 UTC
+* Number of recursive dependencies: 98
+
+Run `revdepcheck::cloud_details(, "ggiraph")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggiraph-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: geom_boxplot_interactive
+ > ### Title: Create interactive boxplot
+ > ### Aliases: geom_boxplot_interactive
+ >
+ > ### ** Examples
+ >
+ > # add interactive boxplot -------
+ ...
+ 24. │ └─ggplot2 (local) draw_panel(..., self = self)
+ 25. │ └─base::lapply(...)
+ 26. │ └─ggplot2 (local) FUN(X[[i]], ...)
+ 27. │ └─self$draw_group(group, panel_params, coord, ...)
+ 28. └─base::.handleSimpleError(...)
+ 29. └─rlang (local) h(simpleError(msg, call))
+ 30. └─handlers[[1L]](cnd)
+ 31. └─cli::cli_abort(...)
+ 32. └─rlang::abort(...)
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘tinytest.R’
+ Running the tests in ‘tests/tinytest.R’ failed.
+ Complete output:
+ > if (requireNamespace("tinytest", quietly = TRUE)) {
+ + tinytest::test_package("ggiraph")
+ + }
+
+ test-annotate_interactive.R... 0 tests
+ test-annotate_interactive.R... 0 tests
+ test-annotate_interactive.R... 0 tests
+ ...
+
+ test-geom_label_interactive.R. 0 tests
+ test-geom_label_interactive.R. 0 tests
+ test-geom_label_interactive.R. 0 tests
+ test-geom_label_interactive.R. 0 tests
+ test-geom_label_interactive.R. 0 tests
+ test-geom_label_interactive.R. 8 tests [0;32mOK[0m Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
+ 'x' must be atomic
+ Calls: ... FUN -> eval -> eval -> sort -> sort.default -> sort.int
+ Execution halted
+ ```
+
+## In both
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 11.9Mb
+ sub-directories of 1Mb or more:
+ libs 9.5Mb
+ ```
+
+# ggiraphExtra
+
+
+
+* Version: 0.3.0
+* GitHub: https://github.com/cardiomoon/ggiraphExtra
+* Source code: https://github.com/cran/ggiraphExtra
+* Date/Publication: 2020-10-06 07:00:02 UTC
+* Number of recursive dependencies: 125
+
+Run `revdepcheck::cloud_details(, "ggiraphExtra")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggiraphExtra-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: ggBoxplot
+ > ### Title: Draw boxplots of a data.frame
+ > ### Aliases: ggBoxplot
+ >
+ > ### ** Examples
+ >
+ > require(ggplot2)
+ ...
+ 21. │ └─ggplot2 (local) draw_panel(..., self = self)
+ 22. │ └─base::lapply(...)
+ 23. │ └─ggplot2 (local) FUN(X[[i]], ...)
+ 24. │ └─self$draw_group(group, panel_params, coord, ...)
+ 25. └─base::.handleSimpleError(...)
+ 26. └─rlang (local) h(simpleError(msg, call))
+ 27. └─handlers[[1L]](cnd)
+ 28. └─cli::cli_abort(...)
+ 29. └─rlang::abort(...)
+ Execution halted
+ ```
+
+# ggparallel
+
+
+
+* Version: 0.3.0
+* GitHub: https://github.com/heike/ggparallel
+* Source code: https://github.com/cran/ggparallel
+* Date/Publication: 2024-01-29 18:50:06 UTC
+* Number of recursive dependencies: 51
+
+Run `revdepcheck::cloud_details(, "ggparallel")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > # This file is part of the standard setup for testthat.
+ > # It is recommended that you do not modify it.
+ > #
+ > # Where should you do additional test configuration?
+ > # Learn more about the roles of various files in:
+ > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+ > # * https://testthat.r-lib.org/articles/special-files.html
+ ...
+ 12. │ └─ggplot2 (local) compute_aesthetics(..., self = self)
+ 13. └─base::.handleSimpleError(...)
+ 14. └─rlang (local) h(simpleError(msg, call))
+ 15. └─handlers[[1L]](cnd)
+ 16. └─cli::cli_abort(...)
+ 17. └─rlang::abort(...)
+
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# ggprism
+
+
+
+* Version: 1.0.4
+* GitHub: https://github.com/csdaw/ggprism
+* Source code: https://github.com/cran/ggprism
+* Date/Publication: 2022-11-04 15:20:05 UTC
+* Number of recursive dependencies: 106
+
+Run `revdepcheck::cloud_details(, "ggprism")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggprism-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: annotation_ticks
+ > ### Title: Add ticks as ggplot annotation
+ > ### Aliases: annotation_ticks
+ >
+ > ### ** Examples
+ >
+ > ## Generally it is better to use the guide_prism_minor function.
+ ...
+ 2. └─ggplot2:::print.ggplot(x)
+ 3. ├─ggplot2::ggplot_gtable(data)
+ 4. └─ggplot2:::ggplot_gtable.ggplot_built(data)
+ 5. └─ggplot2:::plot_theme(plot)
+ 6. └─ggplot2:::validate_theme(theme)
+ 7. └─base::mapply(...)
+ 8. └─ggplot2 (local) ``(...)
+ 9. └─cli::cli_abort(...)
+ 10. └─rlang::abort(...)
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘tinytest.R’
+ Running the tests in ‘tests/tinytest.R’ failed.
+ Complete output:
+ >
+ > if ( requireNamespace("tinytest", quietly=TRUE) ){
+ + tinytest::test_package("ggprism")
+ + }
+
+ test-add_pvalue.R............. 0 tests
+ test-add_pvalue.R............. 0 tests
+ ...
+ test-annotation_ticks.R....... 21 tests [0;32mOK[0m [0;34m0.9s[0m
+
+ test-guide_prism_bracket.R.... 0 tests
+ test-guide_prism_bracket.R.... 0 tests
+ test-guide_prism_bracket.R.... 0 tests
+ test-guide_prism_bracket.R.... 0 tests
+ test-guide_prism_bracket.R.... 0 tests
+ test-guide_prism_bracket.R.... 1 tests [0;32mOK[0m Error in if (msg != "") { : the condition has length > 1
+ Calls: ... lapply -> FUN -> eval -> eval -> expect_silent -> fun
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘axes.Rmd’ using rmarkdown
+
+ Quitting from lines 38-48 [unnamed-chunk-2] (axes.Rmd)
+ Error: processing vignette 'axes.Rmd' failed with diagnostics:
+ classes have been rewritten as classes.
+ The old S3 guide methods have been superseded.
+ --- failed re-building ‘axes.Rmd’
+
+ --- re-building ‘colours.Rmd’ using rmarkdown
+ ...
+ Error: processing vignette 'themes.Rmd' failed with diagnostics:
+ The `legend.text.align` theme element is not defined in the element
+ hierarchy.
+ --- failed re-building ‘themes.Rmd’
+
+ SUMMARY: processing the following files failed:
+ ‘axes.Rmd’ ‘colours.Rmd’ ‘ggprism.Rmd’ ‘pvalues.Rmd’ ‘themes.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# ggraph
+
+
+
+* Version: 2.1.0
+* GitHub: https://github.com/thomasp85/ggraph
+* Source code: https://github.com/cran/ggraph
+* Date/Publication: 2022-10-09 20:33:19 UTC
+* Number of recursive dependencies: 100
+
+Run `revdepcheck::cloud_details(, "ggraph")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggraph-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: geom_edge_density
+ > ### Title: Show edges as a density map
+ > ### Aliases: geom_edge_density
+ >
+ > ### ** Examples
+ >
+ > require(tidygraph)
+ ...
+ ℹ This can happen when ggplot fails to infer the correct grouping structure in
+ the data.
+ ℹ Did you forget to specify a `group` aesthetic or to convert a numerical
+ variable into a factor?
+ Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
+ ℹ Consider using `geom_tile()` instead.
+ Warning: Raster pixels are placed at uneven horizontal intervals and will be shifted
+ ℹ Consider using `geom_tile()` instead.
+ Error: Unknown colour name: TRUE
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘Edges.Rmd’ using rmarkdown
+
+ Quitting from lines 142-145 [unnamed-chunk-7] (Edges.Rmd)
+ Error: processing vignette 'Edges.Rmd' failed with diagnostics:
+ Unknown colour name: TRUE
+ --- failed re-building ‘Edges.Rmd’
+
+ --- re-building ‘Layouts.Rmd’ using rmarkdown
+ ...
+ --- finished re-building ‘Nodes.Rmd’
+
+ --- re-building ‘tidygraph.Rmd’ using rmarkdown
+ --- finished re-building ‘tidygraph.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘Edges.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+## In both
+
+* checking C++ specification ... NOTE
+ ```
+ Specified C++11: please drop specification unless essential
+ ```
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 11.0Mb
+ sub-directories of 1Mb or more:
+ doc 3.5Mb
+ libs 5.9Mb
+ ```
+
+# ggside
+
+
+
+* Version: 0.2.3
+* GitHub: https://github.com/jtlandis/ggside
+* Source code: https://github.com/cran/ggside
+* Date/Publication: 2023-12-10 06:00:06 UTC
+* Number of recursive dependencies: 77
+
+Run `revdepcheck::cloud_details(, "ggside")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggside-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: geom_xsidebar
+ > ### Title: Side bar Charts
+ > ### Aliases: geom_xsidebar geom_*sidebar geom_ysidebar geom_xsidecol
+ > ### geom_ysidecol
+ >
+ > ### ** Examples
+ >
+ ...
+ > p <-ggplot(iris, aes(Sepal.Width, Sepal.Length, color = Species, fill = Species)) +
+ + geom_point()
+ >
+ > #sidebar - uses StatCount
+ > p +
+ + geom_xsidebar() +
+ + geom_ysidebar()
+ Error in guide$position : object of type 'closure' is not subsettable
+ Calls: ... panel_guides_grob -> %||% -> guide_for_position -> vapply -> FUN
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(vdiffr)
+ > library(ggplot2)
+ > library(ggside)
+ Registered S3 method overwritten by 'ggside':
+ method from
+ +.gg ggplot2
+ ...
+ • non_aes_mapping_legend/non-aes-color-blue.svg
+ • non_aes_mapping_legend/non-aes-xcolor-red.svg
+ • vdiff_irisScatter/collapsed-histo.svg
+ • vdiff_irisScatter/facetgrid-collapsed-density.svg
+ • vdiff_irisScatter/facetgrid-histo.svg
+ • vdiff_irisScatter/facetgrid-side-density.svg
+ • vdiff_irisScatter/stacked-side-density.svg
+ • vdiff_irisScatter/yside-histo.svg
+ Error: Test failures
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘ggside_aes_mapping.Rmd’ using rmarkdown
+
+ Quitting from lines 78-79 [ggside_legacy_example] (ggside_aes_mapping.Rmd)
+ Error: processing vignette 'ggside_aes_mapping.Rmd' failed with diagnostics:
+ object of type 'closure' is not subsettable
+ --- failed re-building ‘ggside_aes_mapping.Rmd’
+
+ --- re-building ‘ggside_basic_usage.Rmd’ using rmarkdown
+ ...
+ Quitting from lines 73-77 [ggside_summarise_diamond_base] (ggside_basic_usage.Rmd)
+ Error: processing vignette 'ggside_basic_usage.Rmd' failed with diagnostics:
+ object of type 'closure' is not subsettable
+ --- failed re-building ‘ggside_basic_usage.Rmd’
+
+ SUMMARY: processing the following files failed:
+ ‘ggside_aes_mapping.Rmd’ ‘ggside_basic_usage.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# ggstance
+
+
+
+* Version: 0.3.6
+* GitHub: https://github.com/lionel-/ggstance
+* Source code: https://github.com/cran/ggstance
+* Date/Publication: 2022-11-16 00:20:02 UTC
+* Number of recursive dependencies: 93
+
+Run `revdepcheck::cloud_details(, "ggstance")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > .libPaths()
+ [1] "/tmp/workdir/ggstance/new/ggstance.Rcheck"
+ [2] "/tmp/workdir/ggstance/new"
+ [3] "/opt/R/4.3.1/lib/R/site-library"
+ [4] "/opt/R/4.3.1/lib/R/library"
+ > library("testthat")
+ > library("ggstance")
+ ...
+ • geoms/geom-boxploth-facet-wrap-with-fill.svg
+ • geoms/geom-boxploth-with-fill.svg
+ • geoms/geom-histogramh-position-nudge-with-fill.svg
+ • geoms/geom-histogramh-position-stack-with-fill.svg
+ • geoms/geom-pointrangeh-facet-wrap.svg
+ • geoms/geom-pointrangeh-position-dodgev.svg
+ • geoms/geom-violinh-draw-quantiles.svg
+ • geoms/geom-violinh-facet-wrap.svg
+ Error: Test failures
+ Execution halted
+ ```
+
+# ggstatsplot
+
+
+
+* Version: 0.12.2
+* GitHub: https://github.com/IndrajeetPatil/ggstatsplot
+* Source code: https://github.com/cran/ggstatsplot
+* Date/Publication: 2024-01-14 14:30:02 UTC
+* Number of recursive dependencies: 166
+
+Run `revdepcheck::cloud_details(, "ggstatsplot")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘ggstatsplot-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: ggscatterstats
+ > ### Title: Scatterplot with marginal distributions and statistical results
+ > ### Aliases: ggscatterstats
+ >
+ > ### ** Examples
+ >
+ > set.seed(123)
+ ...
+ 11. │ │ └─base::withCallingHandlers(...)
+ 12. │ └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
+ 13. │ └─l$compute_aesthetics(d, plot)
+ 14. │ └─ggplot2 (local) compute_aesthetics(..., self = self)
+ 15. └─base::.handleSimpleError(...)
+ 16. └─rlang (local) h(simpleError(msg, call))
+ 17. └─handlers[[1L]](cnd)
+ 18. └─cli::cli_abort(...)
+ 19. └─rlang::abort(...)
+ Execution halted
+ ```
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > # graphics engine changed in this version, and so snapshots generated on
+ > # previous R version won't work
+ > if (getRversion() < "4.4.0") {
+ + library(testthat)
+ + suppressPackageStartupMessages(library(ggstatsplot))
+ +
+ + test_check("ggstatsplot")
+ ...
+ • pairwise-ggsignif/within-non-parametric-all.svg
+ • pairwise-ggsignif/within-non-parametric-only-non-significant.svg
+ • pairwise-ggsignif/within-non-parametric-only-significant.svg
+ • pairwise-ggsignif/within-parametric-all.svg
+ • pairwise-ggsignif/within-parametric-only-significant.svg
+ • pairwise-ggsignif/within-robust-all.svg
+ • pairwise-ggsignif/within-robust-only-non-significant.svg
+ • pairwise-ggsignif/within-robust-only-significant.svg
+ Error: Test failures
+ Execution halted
+ ```
+
+# ggtern
+
+
+
+* Version: 3.4.2
+* GitHub: NA
+* Source code: https://github.com/cran/ggtern
+* Date/Publication: 2023-06-06 11:10:02 UTC
+* Number of recursive dependencies: 42
+
+Run `revdepcheck::cloud_details(, "ggtern")` for more info
+
+
+
+## Newly broken
+
+* checking whether package ‘ggtern’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/00install.out’ for details.
+ ```
+
+## Newly fixed
+
+* checking Rd cross-references ... NOTE
+ ```
+ Package unavailable to check Rd xrefs: ‘chemometrics’
+ ```
+
+## In both
+
+* checking package dependencies ... NOTE
+ ```
+ Package which this enhances but not available for checking: ‘sp’
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘ggtern’ ...
+** package ‘ggtern’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+** demo
+** inst
+** byte-compile and prepare package for lazy loading
+Error in get(x, envir = ns, inherits = FALSE) :
+ object 'build_guides' not found
+Error: unable to load R code in package ‘ggtern’
+Execution halted
+ERROR: lazy loading failed for package ‘ggtern’
+* removing ‘/tmp/workdir/ggtern/new/ggtern.Rcheck/ggtern’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘ggtern’ ...
+** package ‘ggtern’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+** demo
+** inst
+** byte-compile and prepare package for lazy loading
+** help
+*** installing help indices
+** building package indices
+** testing if installed package can be loaded from temporary location
+** testing if installed package can be loaded from final location
+** testing if installed package keeps a record of temporary installation path
+* DONE (ggtern)
+
+
+```
+# ghibli
+
+
+
+* Version: 0.3.3
+* GitHub: https://github.com/ewenme/ghibli
+* Source code: https://github.com/cran/ghibli
+* Date/Publication: 2022-08-26 13:52:03 UTC
+* Number of recursive dependencies: 72
+
+Run `revdepcheck::cloud_details(, "ghibli")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(ghibli)
+ >
+ > test_check("ghibli")
+ [ FAIL 2 | WARN 1 | SKIP 0 | PASS 8 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure ('test-scales.R:40:3'): scale_colour_ghibli_d fails as expected ─────
+ `base_color_plot + scale_colour_ghibli_d()` did not throw an error.
+ ── Failure ('test-scales.R:67:3'): scale_fill_ghibli_d fails as expected ───────
+ `base_fill_plot + scale_fill_ghibli_d()` did not throw an error.
+
+ [ FAIL 2 | WARN 1 | SKIP 0 | PASS 8 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+# glancedata
+
+
+
+* Version: 1.0.1
+* GitHub: NA
+* Source code: https://github.com/cran/glancedata
+* Date/Publication: 2019-11-22 23:10:05 UTC
+* Number of recursive dependencies: 109
+
+Run `revdepcheck::cloud_details(, "glancedata")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘spelling.R’
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(glancedata)
+ >
+ > test_check("glancedata")
+ [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
+
+ ...
+ `expected`: TRUE
+ ── Failure ('test-plot_numerical_vars.R:37:3'): qqplot is a list of length 9 ───
+ mymode == "list" & mylength == 9 is not TRUE
+
+ `actual`: FALSE
+ `expected`: TRUE
+
+ [ FAIL 5 | WARN 4 | SKIP 0 | PASS 13 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking LazyData ... NOTE
+ ```
+ 'LazyData' is specified without a 'data' directory
+ ```
+
+# grafify
+
+
+
+* Version: 4.0
+* GitHub: https://github.com/ashenoy-cmbi/grafify
+* Source code: https://github.com/cran/grafify
+* Date/Publication: 2023-10-07 11:10:02 UTC
+* Number of recursive dependencies: 107
+
+Run `revdepcheck::cloud_details(, "grafify")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(grafify)
+ Loading required package: ggplot2
+ > library(rlang)
+
+ Attaching package: 'rlang'
+
+ ...
+ ── Error ('test-scale_colour_grafify.R:20:3'): Check colour and fill scales ────
+ Error in `expect_match(db1$scales$scales[[1]]$scale_name, "muted")`: is.character(act$val) is not TRUE
+ Backtrace:
+ ▆
+ 1. └─testthat::expect_match(db1$scales$scales[[1]]$scale_name, "muted") at test-scale_colour_grafify.R:20:3
+ 2. └─base::stopifnot(is.character(act$val))
+
+ [ FAIL 21 | WARN 22 | SKIP 0 | PASS 225 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 5.7Mb
+ sub-directories of 1Mb or more:
+ help 5.4Mb
+ ```
+
+* checking Rd cross-references ... NOTE
+ ```
+ Package unavailable to check Rd xrefs: ‘gratia’
+ ```
+
+# inTextSummaryTable
+
+
+
+* Version: 3.3.1
+* GitHub: https://github.com/openanalytics/inTextSummaryTable
+* Source code: https://github.com/cran/inTextSummaryTable
+* Date/Publication: 2023-09-12 10:20:02 UTC
+* Number of recursive dependencies: 121
+
+Run `revdepcheck::cloud_details(, "inTextSummaryTable")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(inTextSummaryTable)
+ >
+ > test_check("inTextSummaryTable")
+ [ FAIL 2 | WARN 167 | SKIP 0 | PASS 991 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure ('test_subjectProfileSummaryPlot-general.R:25:2'): The plot is correctly facetted based on a variable ──
+ `... <- NULL` produced warnings.
+ ── Failure ('test_subjectProfileSummaryPlot-table.R:356:2'): The size of the points (in the legend) is correctly set ──
+ gg$guides$colour$override.aes$size not equal to `pointSize`.
+ target is NULL, current is numeric
+
+ [ FAIL 2 | WARN 167 | SKIP 0 | PASS 991 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 10.9Mb
+ sub-directories of 1Mb or more:
+ doc 9.9Mb
+ ```
+
+# LMoFit
+
+
+
+* Version: 0.1.6
+* GitHub: NA
+* Source code: https://github.com/cran/LMoFit
+* Date/Publication: 2020-11-26 11:10:02 UTC
+* Number of recursive dependencies: 65
+
+Run `revdepcheck::cloud_details(, "LMoFit")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘LMoFit.Rmd’ using rmarkdown
+
+ Quitting from lines 236-237 [unnamed-chunk-15] (LMoFit.Rmd)
+ Error: processing vignette 'LMoFit.Rmd' failed with diagnostics:
+ Problem while computing aesthetics.
+ ℹ Error occurred in the 1st layer.
+ Caused by error in `scales_add_defaults()`:
+ ! could not find function "scales_add_defaults"
+ --- failed re-building ‘LMoFit.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘LMoFit.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# manydata
+
+
+
+* Version: 0.8.3
+* GitHub: https://github.com/globalgov/manydata
+* Source code: https://github.com/cran/manydata
+* Date/Publication: 2023-06-15 11:30:03 UTC
+* Number of recursive dependencies: 134
+
+Run `revdepcheck::cloud_details(, "manydata")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(manydata)
+ >
+ > test_check("manydata")
+ There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 5 matched observations by manyID variable across datasets in database.There were 116 matched observations by ID variable across datasets in database.There were 116 matched observations by ID variable across datasets in database.There were 116 matched observations by ID variable across datasets in database.There were 116 matched observations by ID variable across datasets in database.[ FAIL 3 | WARN 4 | SKIP 0 | PASS 111 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ...
+ `db` has length 11, not length 9.
+ ── Failure ('test_db.R:6:3'): dbplot() returns the correct output format ───────
+ Names of `db` ('data', 'layers', 'scales', 'guides', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'layout', 'labels') don't match 'data', 'layers', 'scales', 'mapping', 'theme', 'coordinates', 'facet', 'plot_env', 'labels'
+ ── Failure ('test_releases.R:8:3'): Plotting function visualises historical
+ milestones/releases of a repository ──
+ `testplot` has length 11, not length 9.
+
+ [ FAIL 3 | WARN 4 | SKIP 0 | PASS 111 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking data for non-ASCII characters ... NOTE
+ ```
+ Note: found 3 marked UTF-8 strings
+ ```
+
+# MiscMetabar
+
+
+
+* Version: 0.7.9
+* GitHub: https://github.com/adrientaudiere/MiscMetabar
+* Source code: https://github.com/cran/MiscMetabar
+* Date/Publication: 2024-02-17 21:10:16 UTC
+* Number of recursive dependencies: 414
+
+Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info
+
+
+
+## Newly broken
+
+* checking examples ... ERROR
+ ```
+ Running examples in ‘MiscMetabar-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: upset_pq
+ > ### Title: Make upset plot for phyloseq object.
+ > ### Aliases: upset_pq
+ >
+ > ### ** Examples
+ >
+ >
+ ...
+ 7. └─ggplot2::ggplotGrob(x)
+ 8. ├─ggplot2::ggplot_gtable(ggplot_build(x))
+ 9. └─ggplot2:::ggplot_gtable.ggplot_built(ggplot_build(x))
+ 10. └─ggplot2:::plot_theme(plot)
+ 11. └─ggplot2:::validate_theme(theme)
+ 12. └─base::mapply(...)
+ 13. └─ggplot2 (local) ``(...)
+ 14. └─cli::cli_abort(...)
+ 15. └─rlang::abort(...)
+ Execution halted
+ ```
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘MiscMetabar.Rmd’ using rmarkdown
+
+ Quitting from lines 68-69 [unnamed-chunk-4] (MiscMetabar.Rmd)
+ Error: processing vignette 'MiscMetabar.Rmd' failed with diagnostics:
+ The `legend.text.align` theme element is not defined in the element
+ hierarchy.
+ --- failed re-building ‘MiscMetabar.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘MiscMetabar.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# miWQS
+
+
+
+* Version: 0.4.4
+* GitHub: https://github.com/phargarten2/miWQS
+* Source code: https://github.com/cran/miWQS
+* Date/Publication: 2021-04-02 21:50:02 UTC
+* Number of recursive dependencies: 152
+
+Run `revdepcheck::cloud_details(, "miWQS")` for more info
+
+
+
+## Newly broken
+
+* checking re-building of vignette outputs ... ERROR
+ ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘README.Rmd’ using rmarkdown
+ tlmgr: package repository https://ctan.mirrors.hoobly.com/systems/texlive/tlnet (verified)
+ [1/2, ??:??/??:??] install: biblatex [249k]
+ [2/2, 00:00/00:00] install: logreq [4k]
+ running mktexlsr ...
+ done running mktexlsr.
+ tlmgr: package log updated: /opt/TinyTeX/texmf-var/web2c/tlmgr.log
+ tlmgr: command log updated: /opt/TinyTeX/texmf-var/web2c/tlmgr-commands.log
+ tlmgr: package repository https://ctan.mirrors.hoobly.com/systems/texlive/tlnet (verified)
+ ...
+ Warning: (biblatex) and rerun LaTeX afterwards.
+ Error: processing vignette 'README.Rmd' failed with diagnostics:
+ Failed to build the bibliography via biber
+ --- failed re-building ‘README.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘README.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+## Newly fixed
+
+* checking re-building of vignette outputs ... WARNING
+ ```
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘README.Rmd’ using rmarkdown
+
+ tlmgr: Remote database (revision 69978 of the texlive-scripts package)
+ seems to be older than the local installation (rev 70006 of
+ texlive-scripts); please use a different mirror and/or wait a day or two.
+
+ Warning in system2("tlmgr", args, ...) :
+ running command ''tlmgr' search --file --global '/biblatex.sty'' had status 1
+ ...
+
+ Error: processing vignette 'README.Rmd' failed with diagnostics:
+ LaTeX failed to compile /tmp/workdir/miWQS/old/miWQS.Rcheck/vign_test/miWQS/vignettes/README.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See README.log for more info.
+ --- failed re-building ‘README.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘README.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+# NAIR
+
+
+
+* Version: 1.0.3
+* GitHub: https://github.com/mlizhangx/Network-Analysis-for-Repertoire-Sequencing-
+* Source code: https://github.com/cran/NAIR
+* Date/Publication: 2024-01-09 17:00:02 UTC
+* Number of recursive dependencies: 86
+
+Run `revdepcheck::cloud_details(, "NAIR")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(NAIR)
+ Welcome to NAIR: Network Analysis of Immune Repertoire.
+ Get started using `vignette("NAIR")`, or by visiting
+ https://mlizhangx.github.io/Network-Analysis-for-Repertoire-Sequencing-/
+ >
+ > test_check("NAIR")
+ ...
+ `expected` is a character vector ('UMIs')
+ ── Failure ('test_functions.R:1419:3'): plots legends behave correctly ─────────
+ sc_net$plots$SampleID$guides$size$name (`actual`) not equal to "legend" (`expected`).
+
+ `actual` is NULL
+ `expected` is a character vector ('legend')
+
+ [ FAIL 48 | WARN 0 | SKIP 0 | PASS 1171 ]
+ Error: Test failures
+ Execution halted
+ ```
+
+## In both
+
+* checking installed package size ... NOTE
+ ```
+ installed size is 8.1Mb
+ sub-directories of 1Mb or more:
+ libs 6.6Mb
+ ```
+
+# OpenLand
+
+
+
+* Version: 1.0.2
+* GitHub: https://github.com/reginalexavier/OpenLand
+* Source code: https://github.com/cran/OpenLand
+* Date/Publication: 2021-11-02 07:20:02 UTC
+* Number of recursive dependencies: 121
+
+Run `revdepcheck::cloud_details(, "OpenLand")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
+ ```
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(OpenLand)
+ >
+ > test_check("OpenLand")
+ [ FAIL 2 | WARN 1 | SKIP 0 | PASS 110 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ...
+ Actual value: "List of 11\\n \$ data : tibble \[200 × 5\] \(S3: tbl_df/tbl/data\.frame\)\\n \.\.\$ Period : chr \[1:200\] "2000-2001" "2000-2001" "2000-2001" "2000-2001" \.\.\.\\n \.\.\$ area_gross: num \[1:200\] 0\.000388 0\.000379 0\.00038 0\.000411 0\.000403 0\.000416 0\.000368 0\.000445 0\.000387 0\.000399 \.\.\.\\n \.\.\$ From : Factor w/ 5 levels "GUP","OZS","PSN",\.\.: 3 3 3 3 4 4 4 4 2 2 \.\.\.\\n \.\.\$ To : Factor w/ 5 levels "GUP","OZS","PSN",\.\.: 4 2 1 5 3 2 1 5 3 4 \.\.\.\\n \.\.\$ changes : chr \[1:200\] "Gain" "Gain" "Gain" "Gain" \.\.\.\\n \$ layers :List of 4\\n \.\.\$ :Classes 'LayerInstance', 'Layer', 'ggproto', 'gg' \\n aes_params: list\\n compute_aesthetics: function\\n compute_geom_1: function\\n compute_geom_2: function\\n compute_position: function\\n compute_statistic: function\\n computed_geom_params: NULL\\n computed_mapping: NULL\\n computed_stat_params: NULL\\n constructor: call\\n data: waiver\\n draw_geom: function\\n finish_statistics: function\\n geom: \\n aesthetics: function\\n default_aes: uneval\\n draw_group: function\\n draw_key: function\\n draw_layer: function\\n draw_panel: function\\n extra_params: just na\.rm orientation\\n handle_na: function\\n non_missing_aes: xmin xmax ymin ymax\\n optional_aes: \\n parameters: function\\n rename_size: TRUE\\n required_aes: x y\\n setup_data: function\\n setup_params: function\\n use_defaults: function\\n super: \\n geom_params: list\\n inherit\.aes: TRUE\\n layer_data: function\\n map_statistic: function\\n mapping: uneval\\n position: \\n compute_layer: function\\n compute_panel: function\\n fill: FALSE\\n required_aes: \\n reverse: FALSE\\n setup_data: function\\n setup_params: function\\n type: NULL\\n vjust: 1\\n super: \\n print: function\\n setup_layer: function\\n show\.legend: NA\\n stat: \\n aesthetics: function\\n compute_group: function\\n compute_layer: function\\n compute_panel: function\\n default_aes: uneval\\n dropped_aes: \\n extra_params: na\.rm\\n finish_layer: function\\n non_missing_aes: \\n optional_aes: \\n parameters: function\\n required_aes: \\n retransform: TRUE\\n setup_data: function\\n setup_params: function\\n super: \\n stat_params: list\\n super: \\n \.\.\$ :Classes 'LayerInstance', 'Layer', 'ggproto', 'gg'