diff --git a/R/coord-radial.R b/R/coord-radial.R
index d60479b506..32dd33599e 100644
--- a/R/coord-radial.R
+++ b/R/coord-radial.R
@@ -136,7 +136,7 @@ coord_radial <- function(theta = "x",
}
if (lifecycle::is_present(direction)) {
deprecate_warn0(
- "3.5.2", "coord_radial(direction)", "coord_radial(reverse)"
+ "4.0.0", "coord_radial(direction)", "coord_radial(reverse)"
)
reverse <- switch(reverse, "r" = "thetar", "theta")
}
diff --git a/R/coord-transform.R b/R/coord-transform.R
index 145a5f8117..89922b09c6 100644
--- a/R/coord-transform.R
+++ b/R/coord-transform.R
@@ -113,7 +113,7 @@ coord_transform <- function(x = "identity", y = "identity", xlim = NULL, ylim =
#' @export
coord_trans <- function(...) {
deprecate_soft0(
- "3.5.2",
+ "4.0.0",
"coord_trans()",
"coord_transform()"
)
diff --git a/R/facet-wrap.R b/R/facet-wrap.R
index 2481bb5e6a..51fccb37b7 100644
--- a/R/facet-wrap.R
+++ b/R/facet-wrap.R
@@ -569,7 +569,7 @@ wrap_layout <- function(id, dims, dir) {
# Should only occur when `as.table` was not incorporated into `dir`
dir <- switch(dir, h = "lt", v = "tl")
deprecate_soft0(
- "3.5.2",
+ "4.0.0",
what = I("Internal use of `dir = \"h\"` and `dir = \"v\"` in `facet_wrap()`"),
details = I(c(
"The `dir` argument should incorporate the `as.table` argument.",
diff --git a/R/geom-boxplot.R b/R/geom-boxplot.R
index a43009545d..78bdbacc30 100644
--- a/R/geom-boxplot.R
+++ b/R/geom-boxplot.R
@@ -241,7 +241,7 @@ GeomBoxplot <- ggproto("GeomBoxplot", Geom,
setup_params = function(data, params) {
if ("fatten" %in% names(params)) {
deprecate_soft0(
- "3.6.0", "geom_boxplot(fatten)",
+ "4.0.0", "geom_boxplot(fatten)",
"geom_boxplot(median.linewidth)"
)
} else {
diff --git a/R/geom-crossbar.R b/R/geom-crossbar.R
index e0c98621fd..2547219ac6 100644
--- a/R/geom-crossbar.R
+++ b/R/geom-crossbar.R
@@ -62,7 +62,7 @@ GeomCrossbar <- ggproto("GeomCrossbar", Geom,
setup_params = function(data, params) {
if (lifecycle::is_present(params$fatten %||% deprecated())) {
deprecate_soft0(
- "3.6.0", "geom_crossbar(fatten)",
+ "4.0.0", "geom_crossbar(fatten)",
"geom_crossbar(middle.linewidth)"
)
} else {
diff --git a/R/geom-errorbar.R b/R/geom-errorbar.R
index 62808d86e3..cd56d59193 100644
--- a/R/geom-errorbar.R
+++ b/R/geom-errorbar.R
@@ -69,7 +69,7 @@ GeomErrorbarh <- ggproto(
"GeomErrorbarh", GeomErrorbar,
setup_params = function(data, params) {
deprecate_soft0(
- "3.5.2", "geom_errobarh()", "geom_errorbar(orientation = \"y\")",
+ "4.0.0", "geom_errobarh()", "geom_errorbar(orientation = \"y\")",
id = "no-more-errorbarh"
)
GeomLinerange$setup_params(data, params)
@@ -87,7 +87,7 @@ geom_errorbar <- make_constructor(GeomErrorbar, orientation = NA)
#' `geom_errorbar(orientation = "y")` instead.
geom_errorbarh <- function(..., orientation = "y") {
deprecate_soft0(
- "3.5.2", "geom_errobarh()", "geom_errorbar(orientation = \"y\")",
+ "4.0.0", "geom_errobarh()", "geom_errorbar(orientation = \"y\")",
id = "no-more-errorbarh"
)
geom_errorbar(..., orientation = orientation)
diff --git a/R/geom-label.R b/R/geom-label.R
index 15120bf6fd..f250089435 100644
--- a/R/geom-label.R
+++ b/R/geom-label.R
@@ -28,7 +28,7 @@ geom_label <- function(mapping = NULL, data = NULL,
extra_args <- list2(...)
if (lifecycle::is_present(label.size)) {
- deprecate_warn0("3.5.0", "geom_label(label.size)", "geom_label(linewidth)")
+ deprecate_soft0("3.5.0", "geom_label(label.size)", "geom_label(linewidth)")
extra_args$linewidth <- extra_args$linewidth %||% label.size
}
diff --git a/R/geom-pointrange.R b/R/geom-pointrange.R
index 9029805aa4..4f3603f485 100644
--- a/R/geom-pointrange.R
+++ b/R/geom-pointrange.R
@@ -16,7 +16,7 @@ GeomPointrange <- ggproto("GeomPointrange", Geom,
setup_params = function(data, params) {
if (lifecycle::is_present(params$fatten %||% deprecated())) {
- deprecate_soft0("3.6.0", "geom_pointrange(fatten)", I("the `size` aesthetic"))
+ deprecate_soft0("4.0.0", "geom_pointrange(fatten)", I("the `size` aesthetic"))
} else {
# For backward compatibility reasons
params$fatten <- 4
diff --git a/R/geom-violin.R b/R/geom-violin.R
index 1640e4c893..c8d9dc47fb 100644
--- a/R/geom-violin.R
+++ b/R/geom-violin.R
@@ -111,7 +111,7 @@ geom_violin <- function(mapping = NULL, data = NULL,
extra <- list()
if (lifecycle::is_present(draw_quantiles)) {
deprecate_soft0(
- "3.6.0",
+ "4.0.0",
what = "geom_violin(draw_quantiles)",
with = "geom_violin(quantiles.linetype)"
)
diff --git a/R/guide-colorsteps.R b/R/guide-colorsteps.R
index 2a9f291477..83cdf53508 100644
--- a/R/guide-colorsteps.R
+++ b/R/guide-colorsteps.R
@@ -194,7 +194,7 @@ GuideColoursteps <- ggproto(
params$title <- scale$make_title(params$title, scale$name, title)
limits <- c(params$decor$min[1], params$decor$max[nrow(params$decor)])
- if (params$reverse) {
+ if (isTRUE(params$reverse)) {
limits <- rev(limits)
}
params$key$.value <- rescale(params$key$.value, from = limits)
diff --git a/R/guides-.R b/R/guides-.R
index a72e7d60db..e4a96242d1 100644
--- a/R/guides-.R
+++ b/R/guides-.R
@@ -274,7 +274,7 @@ Guides <- ggproto(
#
# The resulting guide is then drawn in ggplot_gtable
- build = function(self, scales, layers, labels, layer_data, theme = theme()) {
+ build = function(self, scales, layers, labels, layer_data, theme = NULL) {
# Empty guides list
custom <- self$get_custom()
@@ -300,6 +300,7 @@ Guides <- ggproto(
}
# Merge and process layers
+ theme <- theme %||% theme()
guides$merge()
guides$process_layers(layers, layer_data, theme)
if (length(guides$guides) == 0) {
diff --git a/R/labels.R b/R/labels.R
index 0c2cd1c7d4..a0991fed03 100644
--- a/R/labels.R
+++ b/R/labels.R
@@ -78,7 +78,8 @@ setup_plot_labels <- function(plot, layers, data) {
# `geom_function()`. We can display these labels anyway, so we include them.
plot_labels <- plot@labels
known_labels <- c(names(labels), fn_fmls_names(labs), "x", "y")
- extra_labels <- setdiff(names(plot_labels), known_labels)
+ extra_labels <- names(plot_labels)[lengths(plot_labels) > 0]
+ extra_labels <- setdiff(extra_labels, known_labels)
if (length(extra_labels) > 0) {
@@ -92,7 +93,7 @@ setup_plot_labels <- function(plot, layers, data) {
extra_labels <- paste0("{.field ", extra_labels, "} : ", warn_labels)
names(extra_labels) <- rep("*", length(extra_labels))
- cli::cli_warn(c(
+ cli::cli_inform(c(
"Ignoring unknown labels:",
extra_labels
))
diff --git a/R/layer-sf.R b/R/layer-sf.R
index 65eeda8b38..3695084aa9 100644
--- a/R/layer-sf.R
+++ b/R/layer-sf.R
@@ -78,7 +78,12 @@ LayerSf <- ggproto("LayerSf", Layer,
geom_column <- function(data) {
w <- which(vapply(data, inherits, TRUE, what = "sfc"))
if (length(w) == 0) {
- "geometry" # avoids breaks when objects without geometry list-column are examined
+ if (!is.character(data[["geometry"]])) {
+ "geometry" # avoids breaks when objects without geometry list-column are examined
+ } else {
+ # Avoids a rare case where computed_geom_params$legend is present but there is no actual geometry column
+ ""
+ }
} else {
# this may not be best in case more than one geometry list-column is present:
if (length(w) > 1)
diff --git a/R/plot-build.R b/R/plot-build.R
index d92ce633e2..ecd94621c2 100644
--- a/R/plot-build.R
+++ b/R/plot-build.R
@@ -317,13 +317,13 @@ S7::method(gtable_ggplot, class_ggplot_built) <- function(data) {
# TODO: the S3 generic should be phased out once S7 is adopted more widely
#' @rdname gtable_ggplot
#' @export
-ggplot_gtable <- function(plot) {
+ggplot_gtable <- function(data) {
UseMethod("ggplot_gtable")
}
#' @export
-ggplot_gtable.default <- function(plot) {
- gtable_ggplot(plot)
+ggplot_gtable.default <- function(data) {
+ gtable_ggplot(data)
}
#' Generate a ggplot2 plot grob.
diff --git a/R/plot.R b/R/plot.R
index 9749859c6f..19511bcc46 100644
--- a/R/plot.R
+++ b/R/plot.R
@@ -276,13 +276,14 @@ S7::method(plot, class_ggplot) <- `print.ggplot2::ggplot`
`[[<-.ggplot2::gg` <- `$<-.ggplot2::gg`
#' @importFrom S7 convert
-S7::method(convert, list(from = class_ggplot, to = S7::class_list)) <-
- function(from, to) {
- S7::props(from)
- }
-
# S7 currently attaches the S3 method to the calling environment which gives `ggplot2:::as.list`
# Wrap in `local()` to provide a temp environment which throws away the attachment
local({
- S7::method(as.list, class_ggplot) <- function(x, ...) convert(x, S7::class_list)
+ S7::method(convert, list(from = class_ggplot, to = S7::class_list)) <-
+ function(from, to) {
+ S7::props(from)
+ }
+
+ S7::method(as.list, class_ggplot) <-
+ function(x, ...) convert(x, S7::class_list)
})
diff --git a/R/position-dodge.R b/R/position-dodge.R
index 393d13d8a0..9382bb2815 100644
--- a/R/position-dodge.R
+++ b/R/position-dodge.R
@@ -152,7 +152,7 @@ PositionDodge <- ggproto("PositionDodge", Position,
data$order <- xtfrm( # xtfrm makes anything 'sortable'
data$order %||% ave(data$group, data$x, data$PANEL, FUN = match_sorted)
)
- if (params$reverse) {
+ if (isTRUE(params$reverse)) {
data$order <- -data$order
}
if (is.null(params$n)) { # preserve = "total"
diff --git a/R/position-stack.R b/R/position-stack.R
index f2bc62ac34..50a0ef4ac7 100644
--- a/R/position-stack.R
+++ b/R/position-stack.R
@@ -154,7 +154,7 @@ PositionStack <- ggproto("PositionStack", Position,
flipped_aes <- has_flipped_aes(data)
data <- flip_data(data, flipped_aes)
var <- self$var %||% stack_var(data)
- if (!vec_duplicate_any(data$x)) {
+ if (!vec_duplicate_any(data$x) && !isTRUE(self$fill)) {
# We skip stacking when all data have different x positions so that
# there is nothing to stack
var <- NULL
diff --git a/R/scale-.R b/R/scale-.R
index ae2100a0d3..490c163fff 100644
--- a/R/scale-.R
+++ b/R/scale-.R
@@ -1331,7 +1331,7 @@ ScaleDiscrete <- ggproto("ScaleDiscrete", Scale,
vec_slice(pal, match(as.character(x), limits, nomatch = vec_size(pal)))
if (!is.na(na_value)) {
- vec_slice(pal_match, is.na(x)) <- na_value
+ vec_slice(pal_match, vec_detect_missing(x)) <- na_value
}
pal_match
},
diff --git a/R/stat-summary-2d.R b/R/stat-summary-2d.R
index 84e79c63d9..847cb68bfc 100644
--- a/R/stat-summary-2d.R
+++ b/R/stat-summary-2d.R
@@ -15,7 +15,7 @@ StatSummary2d <- ggproto(
params$drop <- !identical(params$drop, "none")
}
- params <- fix_bin_params(params, fun = snake_class(self), version = "3.5.2")
+ params <- fix_bin_params(params, fun = snake_class(self), version = "4.0.0")
vars <- c("origin", "binwidth", "breaks", "center", "boundary")
params[vars] <- lapply(params[vars], dual_param, default = NULL)
params$closed <- dual_param(params$closed, list(x = "right", y = "right"))
diff --git a/R/stat-summary-bin.R b/R/stat-summary-bin.R
index a8449950c9..d86936163a 100644
--- a/R/stat-summary-bin.R
+++ b/R/stat-summary-bin.R
@@ -108,6 +108,13 @@ make_summary_fun <- function(fun.data, fun, fun.max, fun.min, fun.args) {
force(fun.min)
force(fun.args)
+ as_function <- function(x) {
+ if (is.character(x)) {
+ x <- match.fun(x)
+ }
+ rlang::as_function(x)
+ }
+
if (!is.null(fun.data)) {
# Function that takes complete data frame as input
fun.data <- as_function(fun.data)
diff --git a/R/stat-ydensity.R b/R/stat-ydensity.R
index e568196743..969723ebd4 100644
--- a/R/stat-ydensity.R
+++ b/R/stat-ydensity.R
@@ -12,7 +12,7 @@ StatYdensity <- ggproto(
if (!is.null(params$draw_quantiles)) {
deprecate_soft0(
- "3.6.0",
+ "4.0.0",
what = "stat_ydensity(draw_quantiles)",
with = "stat_ydensity(quantiles)"
)
diff --git a/R/theme.R b/R/theme.R
index 703d2a5326..6c654bcb7e 100644
--- a/R/theme.R
+++ b/R/theme.R
@@ -518,9 +518,9 @@ fix_theme_deprecations <- function(elements) {
)
if (is.null(elements[["legend.title"]])) {
elements$legend.title <- element_text(hjust = elements$legend.title.align)
- } else {
- elements$legend.title$hjust <- elements$legend.title$hjust %||%
- elements$legend.title.align
+ } else if (!is_theme_element(elements$legend.title, "blank")) {
+ elements$legend.title$hjust <-
+ try_prop(elements$legend.title, "hjust", elements$legend.title.align)
}
elements$legend.title.align <- NULL
}
@@ -531,9 +531,9 @@ fix_theme_deprecations <- function(elements) {
)
if (is.null(elements[["legend.text"]])) {
elements$legend.text <- element_text(hjust = elements$legend.text.align)
- } else {
- elements$legend.text$hjust <- elements$legend.text$hjust %||%
- elements$legend.text.align
+ } else if (!is_theme_element(elements$legend.text, "blank")) {
+ elements$legend.text$hjust <-
+ try_prop(elements$legend.text, "hjust", elements$legend.text.align)
}
elements$legend.text.align <- NULL
}
@@ -980,7 +980,7 @@ combine_elements <- function(e1, e2) {
# Backward compatbility
# TODO: deprecate next release cycle
is_old_element <- !S7::S7_inherits(e1) && inherits(e1, "element")
- if (is_old_element && is_theme_element(e2)) {
+ if (is_old_element && (is_theme_element(e2) || inherits(e2, "element"))) {
return(combine_s3_elements(e1, e2))
}
@@ -999,22 +999,24 @@ combine_elements <- function(e1, e2) {
}
}
+ parent_props <- if (S7::S7_inherits(e2)) S7::props(e2) else unclass(e2)
+
# If e1 has any NULL properties, inherit them from e2
n <- S7::prop_names(e1)[lengths(S7::props(e1)) == 0]
- S7::props(e1)[n] <- S7::props(e2)[n]
+ S7::props(e1)[n] <- parent_props[n]
# Calculate relative sizes
if (is_rel(try_prop(e1, "size"))) {
- e1@size <- e2@size * unclass(e1@size)
+ e1@size <- parent_props$size * unclass(e1@size)
}
# Calculate relative linewidth
if (is_rel(try_prop(e1, "linewidth"))) {
- e1@linewidth <- e2@linewidth * unclass(e1@linewidth)
+ e1@linewidth <- parent_props$linewidth * unclass(e1@linewidth)
}
if (is_theme_element(e1, "text")) {
- e1@margin <- combine_elements(e1@margin, e2@margin)
+ e1@margin <- combine_elements(e1@margin, parent_props$margin)
}
# If e2 is 'richer' than e1, fill e2 with e1 parameters
diff --git a/man/gtable_ggplot.Rd b/man/gtable_ggplot.Rd
index 67959e831b..3d02793a54 100644
--- a/man/gtable_ggplot.Rd
+++ b/man/gtable_ggplot.Rd
@@ -7,7 +7,7 @@
\usage{
gtable_ggplot(data)
-ggplot_gtable(plot)
+ggplot_gtable(data)
}
\arguments{
\item{data}{plot data generated by \code{\link[=ggplot_build]{ggplot_build()}}}
diff --git a/revdep/README.md b/revdep/README.md
index d3a6471eb5..ca67010418 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -8,8 +8,8 @@
|bayesdfa |1.3.4 |1 | | |
|[cocktailApp](failures.md#cocktailapp)|0.2.3 |__+1__ | |-1 |
|[coda.plot](failures.md#codaplot)|0.1.9 |__+1__ | | |
-|ctsem |3.10.2 |1 | |1 |
-|[deeptime](failures.md#deeptime)|2.1.0 |__+1__ | | |
+|cry |? | | | |
+|ctsem |3.10.3 |1 | |1 |
|EcoEnsemble |1.1.2 |1 | | |
|fio |0.1.6 |1 | | |
|[GGally](failures.md#ggally)|2.2.1 |__+1__ | | |
@@ -17,11 +17,11 @@
|[ggmulti](failures.md#ggmulti)|1.0.7 |__+1__ | | |
|ggRandomForests |2.2.1 |1 | | |
|[ggtern](failures.md#ggtern)|3.5.0 |__+1__ | |1 -1 |
-|[inventorize](failures.md#inventorize)|1.1.2 |__+1__ | | |
|metabolic |? | | | |
|multinma |0.8.1 |1 | | |
|[MultiTraits](failures.md#multitraits)|0.5.0 |__+1__ | | |
|OpenMx |? | | | |
+|pacta.loanbook |0.1.0 |1 | | |
|[PieGlyph](failures.md#pieglyph)|1.0.0 |__+1__ | | |
|rmsb |1.1-2 |1 | | |
|rshift |3.1.2 |1 | | |
@@ -36,16 +36,13 @@
|TriDimRegression |1.0.2 |1 | | |
|[xpose](failures.md#xpose)|0.4.19 |__+1__ | | |
-## New problems (498)
+## New problems (327)
-|package |version |error |warning |note |
-|:----------------------|:---------|:--------|:--------|:------|
-|[activAnalyzer](problems.md#activanalyzer)|2.1.2 |__+1__ | |1 |
-|[actxps](problems.md#actxps)|1.6.0 |__+1__ | | |
+|package |version |error |warning |note |
+|:---------------------|:---------|:--------|:--------|:------|
|[adklakedata](problems.md#adklakedata)|0.6.1 |__+1__ | |1 |
|[adsoRptionCMF](problems.md#adsorptioncmf)|0.1.0 |__+1__ | | |
-|[adw](problems.md#adw) |0.4.0 |__+2__ | | |
-|[AeRobiology](problems.md#aerobiology)|2.0.1 |__+1__ | | |
+|[adw](problems.md#adw)|0.4.0 |__+2__ | | |
|[afex](problems.md#afex)|1.4-1 |__+1__ | | |
|[AgroR](problems.md#agror)|1.3.6 |__+1__ | | |
|[AgroReg](problems.md#agroreg)|1.2.10 |__+1__ | | |
@@ -55,196 +52,129 @@
|[animbook](problems.md#animbook)|1.0.0 |__+1__ | | |
|[ANN2](problems.md#ann2)|2.3.4 |__+1__ | |3 |
|[APackOfTheClones](problems.md#apackoftheclones)|1.2.4 |__+3__ |1 |1 |
-|[APCtools](problems.md#apctools)|1.0.4 |__+3__ | | |
-|[aplot](problems.md#aplot)|0.2.5 | |__+1__ | |
|[applicable](problems.md#applicable)|0.1.1 |__+1__ | | |
|[arena2r](problems.md#arena2r)|1.0.0 |__+1__ | |1 |
-|[ARUtools](problems.md#arutools)|0.7.2 |__+3__ | | |
|[ASRgenomics](problems.md#asrgenomics)|1.1.4 |__+1__ | |1 |
|[assignPOP](problems.md#assignpop)|1.3.0 |__+1__ | | |
|[autocogs](problems.md#autocogs)|0.1.4 |__+1__ | |1 |
-|[autoplotly](problems.md#autoplotly)|0.1.4 |__+2__ | | |
-|[autoReg](problems.md#autoreg)|0.3.3 |__+2__ | | |
+|[autoplotly](problems.md#autoplotly)|0.1.4 |__+1__ | | |
|[bayesAB](problems.md#bayesab)|1.1.3 |__+1__ | |1 |
|[bayesassurance](problems.md#bayesassurance)|0.1.0 |__+1__ | | |
|[BayesCVI](problems.md#bayescvi)|1.0.1 | |__+1__ | |
-|[BayesERtools](problems.md#bayesertools)|0.2.2 |__+1__ | | |
|[BayesianReasoning](problems.md#bayesianreasoning)|0.4.2 |__+1__ | | |
-|[BayesMallows](problems.md#bayesmallows)|2.2.3 |__+1__ | |1 |
|[BayesMultiMode](problems.md#bayesmultimode)|0.7.3 | |__+1__ |1 |
-|[bayesplot](problems.md#bayesplot)|1.12.0 |__+1__ | |1 |
|[BCEA](problems.md#bcea)|2.4.7 |__+1__ | | |
|[bdsm](problems.md#bdsm)|0.2.1 |__+1__ |1 | |
|[BeeBDC](problems.md#beebdc)|1.2.1 |__+1__ | |1 |
|[benchr](problems.md#benchr)|0.2.5 |__+1__ | |2 |
|[biclustermd](problems.md#biclustermd)|0.2.3 |__+1__ | |1 |
-|[biometryassist](problems.md#biometryassist)|1.2.2 |__+1__ | |2 |
+|[biometryassist](problems.md#biometryassist)|1.3.0 |__+1__ | |2 |
|[BiVariAn](problems.md#bivarian)|1.0.1 |__+2__ | | |
-|[blockCV](problems.md#blockcv)|3.1-5 |__+1__ | | |
-|[boxly](problems.md#boxly)|0.1.1 |__+1__ | | |
|[brolgar](problems.md#brolgar)|1.0.1 |__+2__ | | |
|[bullseye](problems.md#bullseye)|1.0.0 |__+2__ | | |
-|[calibmsm](problems.md#calibmsm)|1.1.2 |__+1__ | | |
|[calmr](problems.md#calmr)|0.7.0 |__+1__ | | |
|[canvasXpress](problems.md#canvasxpress)|1.56.1 |__+1__ | | |
|[carbonr](problems.md#carbonr)|0.2.1 |__+1__ | |2 |
-|[cartograflow](problems.md#cartograflow)|1.0.5 |__+1__ | | |
+|[caretEnsemble](problems.md#caretensemble)|4.0.1 | | |__+1__ |
|[cartographr](problems.md#cartographr)|0.2.2 |__+1__ | |1 |
-|[cats](problems.md#cats)|1.0.2 |__+1__ | |1 |
|[causact](problems.md#causact)|0.5.7 |__+1__ | | |
|[CausalImpact](problems.md#causalimpact)|1.3.0 |__+1__ | | |
|[centerline](problems.md#centerline)|0.2.2 |__+2__ | | |
|[Certara.Xpose.NLME](problems.md#certaraxposenlme)|2.0.2 |__+1__ | | |
|[cheem](problems.md#cheem)|0.4.0.0 |__+1__ | | |
-|[ChemoSpec](problems.md#chemospec)|6.1.11 |__+1__ | | |
-|[ChemoSpecUtils](problems.md#chemospecutils)|1.0.5 |__+1__ | | |
-|[chillR](problems.md#chillr)|0.76 |__+1__ | | |
-|[chronicle](problems.md#chronicle)|0.3 |__+2__ | |1 |
|[circumplex](problems.md#circumplex)|1.0.0 |__+1__ | | |
-|[classmap](problems.md#classmap)|1.2.4 | |__+1__ |1 |
|[clifro](problems.md#clifro)|3.2-5 |__+1__ | |1 |
|[climwin](problems.md#climwin)|1.2.31 |__+1__ | | |
-|[clinDataReview](problems.md#clindatareview)|1.6.2 |__+3__ | |1 |
-|[clinUtils](problems.md#clinutils)|0.2.0 |__+1__ | |1 |
|[clockSim](problems.md#clocksim)|0.1.2 | |__+1__ | |
-|[clustcurv](problems.md#clustcurv)|2.0.2 |__+1__ | | |
|[cmcR](problems.md#cmcr)|0.1.11 |__+1__ | |1 |
|[cnmap](problems.md#cnmap)|0.1.0 |__+2__ | | |
-|[CNVreg](problems.md#cnvreg)|1.0 |__+1__ | | |
-|[CohortPlat](problems.md#cohortplat)|1.0.5 |__+2__ | | |
-|[colorrepel](problems.md#colorrepel)|0.4.1 |__+1__ | | |
|[conquestr](problems.md#conquestr)|1.5.1 |__+1__ | | |
|[constructive](problems.md#constructive)|1.1.0 |__+1__ | | |
-|[contsurvplot](problems.md#contsurvplot)|0.2.1 |__+1__ | | |
-|[CoreMicrobiomeR](problems.md#coremicrobiomer)|0.1.0 |__+1__ | | |
-|[correlationfunnel](problems.md#correlationfunnel)|0.2.0 |__+1__ | |1 |
-|[corrViz](problems.md#corrviz)|0.1.0 |__+2__ | |1 |
|[CoSMoS](problems.md#cosmos)|2.1.0 |__+1__ | | |
|[countfitteR](problems.md#countfitter)|1.4 |__+1__ | |1 |
-|[countries](problems.md#countries)|1.2.1 |__+1__ | |1 |
|[covidcast](problems.md#covidcast)|0.5.2 |__+2__ | |1 |
|[cowplot](problems.md#cowplot)|1.1.3 |__+1__ | | |
-|[Coxmos](problems.md#coxmos)|1.1.3 |__+1__ | |1 |
-|[cry](problems.md#cry) |0.5.1 |__+2__ | |1 |
|[ctrialsgov](problems.md#ctrialsgov)|0.2.5 |__+1__ | |1 |
-|[cubble](problems.md#cubble)|1.0.0 |__+1__ | |1 |
-|[cutpointr](problems.md#cutpointr)|1.2.0 |__+1__ | | |
|[cvms](problems.md#cvms)|1.7.0 |__+1__ | | |
|[cylcop](problems.md#cylcop)|0.2.0 |__+1__ | |1 |
|[D2MCS](problems.md#d2mcs)|1.0.1 |__+1__ | | |
|[dabestr](problems.md#dabestr)|2025.3.14 |__+1__ | | |
|[daiquiri](problems.md#daiquiri)|1.1.1 |__+2__ | | |
|[DAISIEprep](problems.md#daisieprep)|1.0.0 |__+1__ | | |
-|[daltoolbox](problems.md#daltoolbox)|1.2.707 | |__+1__ | |
|[dams](problems.md#dams)|0.3.0 |__+1__ | |1 |
|[Deducer](problems.md#deducer)|0.9-0 | |__+1__ | |
|[dendextend](problems.md#dendextend)|1.19.0 |__+1__ | |3 |
-|[densityratio](problems.md#densityratio)|0.2.0 |__+1__ | |1 |
-|[diceR](problems.md#dicer)|3.0.0 |__+1__ | | |
|[DImodelsVis](problems.md#dimodelsvis)|1.0.1 |__+2__ | | |
|[directlabels](problems.md#directlabels)|2025.5.20 |__+1__ | | |
|[DiSCos](problems.md#discos)|0.1.1 |__+1__ | | |
|[distributions3](problems.md#distributions3)|0.2.2 |__+1__ | | |
|[dittoViz](problems.md#dittoviz)|1.0.3 |__+2__ | | |
-|[dndR](problems.md#dndr)|3.0.0 |__+1__ | | |
|[duke](problems.md#duke)|0.0.3 |__+2__ | | |
|[easyalluvial](problems.md#easyalluvial)|0.3.2 |__+1__ | | |
|[easysurv](problems.md#easysurv)|2.0.1 |__+2__ | | |
|[ecocbo](problems.md#ecocbo)|0.12.0 |__+1__ | | |
-|[EGM](problems.md#egm) |0.1.0 |__+1__ | | |
-|[eks](problems.md#eks) |1.1.0 | |__+1__ | |
+|[EGM](problems.md#egm)|0.1.0 |__+1__ | | |
+|[eks](problems.md#eks)|1.1.0 | |__+1__ | |
|[ENMTools](problems.md#enmtools)|1.1.2 |__+1__ | | |
-|[epiCleanr](problems.md#epicleanr)|0.2.0 |__+1__ | |1 |
-|[epiphy](problems.md#epiphy)|0.5.0 |__+1__ | | |
|[epos](problems.md#epos)|1.1 |__+1__ | |2 |
|[EQUALSTATS](problems.md#equalstats)|0.5.0 |__+1__ | |1 |
|[equatiomatic](problems.md#equatiomatic)|0.3.6 |__+1__ | | |
-|[errors](problems.md#errors)|0.4.3 |__+2__ | | |
-|[eudract](problems.md#eudract)|1.0.4 |__+3__ | | |
+|[errors](problems.md#errors)|0.4.3 |__+2__ |-1 | |
|[eventstudyr](problems.md#eventstudyr)|1.1.3 |__+1__ | | |
-|[EvoPhylo](problems.md#evophylo)|0.3.2 |__+2__ | |1 |
-|[explainer](problems.md#explainer)|1.0.2 |__+1__ | |1 |
-|[ez](problems.md#ez) |4.4-0 |__+1__ | |1 |
+|[ez](problems.md#ez) |4.4-0 |__+1__ | |1 |
|[ezEDA](problems.md#ezeda)|0.1.1 |__+1__ | | |
-|[EZFragility](problems.md#ezfragility)|1.0.3 |__+2__ | | |
|[ezplot](problems.md#ezplot)|0.7.13 |__+3__ | | |
|[fabletools](problems.md#fabletools)|0.5.0 |__+1__ | | |
|[fairmodels](problems.md#fairmodels)|1.2.1 |__+3__ | |1 |
|[fairness](problems.md#fairness)|1.2.2 | |__+1__ | |
|[faux](problems.md#faux)|1.2.2 |__+2__ | | |
-|[fChange](problems.md#fchange)|2.0.0 |__+1__ | |1 |
|[feasts](problems.md#feasts)|0.4.1 |__+1__ | | |
|[fec16](problems.md#fec16)|0.1.4 |__+1__ | |1 |
-|[fitbitViz](problems.md#fitbitviz)|1.0.6 |__+1__ | |1 |
|[flextable](problems.md#flextable)|0.9.9 |__+1__ | | |
-|[flipr](problems.md#flipr)|0.3.3 |__+1__ | |1 |
-|[fmf](problems.md#fmf) |1.1.1 | |__+1__ |1 |
-|[foqat](problems.md#foqat)|2.0.8.2 |__+1__ | | |
-|[forestly](problems.md#forestly)|0.1.2 |__+1__ | | |
+|[fmf](problems.md#fmf)|1.1.1 | |__+1__ |1 |
|[forestPSD](problems.md#forestpsd)|1.0.0 |__+1__ | |1 |
-|[formods](problems.md#formods)|0.2.0 |__+1__ | | |
-|[fqar](problems.md#fqar)|0.5.4 |__+1__ | | |
-|[frailtyEM](problems.md#frailtyem)|1.0.1 |__+1__ |1 |2 |
-|[funcharts](problems.md#funcharts)|1.7.0 |__+2__ | |1 |
|[FunnelPlotR](problems.md#funnelplotr)|0.5.0 |__+3__ | | |
|[gapfill](problems.md#gapfill)|0.9.6-1 |__+1__ | |2 |
-|[gapminder](problems.md#gapminder)|1.0.0 |__+1__ | | |
|[genekitr](problems.md#genekitr)|1.2.8 |__+1__ | | |
-|[geneSLOPE](problems.md#geneslope)|0.38.2 | |__+1__ | |
+|[geneSLOPE](problems.md#geneslope)|0.38.3 | |__+1__ | |
|[geofacet](problems.md#geofacet)|0.2.1 | |__+1__ |1 |
-|[geoheatmap](problems.md#geoheatmap)|0.1.0 |__+1__ | | |
|[geomtextpath](problems.md#geomtextpath)|0.1.5 |__+2__ | | |
|[gfoRmulaICE](problems.md#gformulaice)|0.1.0 |__+1__ | | |
|[gg1d](problems.md#gg1d)|0.1.0 |__+2__ | | |
|[ggalign](problems.md#ggalign)|1.0.2 |__+2__ |__+3__ |1 -1 |
-|[gganimate](problems.md#gganimate)|1.0.9 |__+2__ |__+1__ | |
|[ggblend](problems.md#ggblend)|0.1.0 |__+1__ | | |
|[ggborderline](problems.md#ggborderline)|0.2.0 |__+1__ | | |
-|[ggbrain](problems.md#ggbrain)|0.9.0 |__+1__ |__+1__ |1 |
-|[ggbreak](problems.md#ggbreak)|0.1.4 |__+2__ |__+1__ | |
+|[ggbrain](problems.md#ggbrain)|0.9.0 | |__+1__ |1 |
+|[ggbreak](problems.md#ggbreak)|0.1.4 |__+1__ |__+1__ | |
|[ggbump](problems.md#ggbump)|0.1.0 |__+1__ | |1 |
|[ggdark](problems.md#ggdark)|0.2.1 |__+2__ | |1 |
|[ggdemetra](problems.md#ggdemetra)|0.2.8 | |__+1__ | |
-|[ggDoE](problems.md#ggdoe)|0.8 |__+1__ | | |
|[ggDoubleHeat](problems.md#ggdoubleheat)|0.1.2 |__+1__ | | |
-|[ggeasy](problems.md#ggeasy)|0.1.5 |__+3__ |__+1__ | |
|[ggEDA](problems.md#ggeda)|0.1.0 |__+2__ | | |
|[ggedit](problems.md#ggedit)|0.4.1 |__+1__ | | |
-|[ggfields](problems.md#ggfields)|0.0.6 |__+1__ | | |
|[ggfixest](problems.md#ggfixest)|0.3.0 |__+1__ | | |
|[ggfocus](problems.md#ggfocus)|1.0.0 |__+1__ |__+1__ |1 |
-|[ggforce](problems.md#ggforce)|0.4.2 |__+1__ | |1 |
|[ggformula](problems.md#ggformula)|0.12.0 | |__+1__ |1 |
|[ggfortify](problems.md#ggfortify)|0.4.17 |__+1__ | | |
-|[ggfun](problems.md#ggfun)|0.1.8 | |__+1__ | |
|[ggfx](problems.md#ggfx)|1.0.1 | |__+1__ |1 |
|[gggenomes](problems.md#gggenomes)|1.0.1 |__+2__ | | |
|[ggghost](problems.md#ggghost)|0.2.2 |__+1__ | | |
|[gghalves](problems.md#gghalves)|0.1.4 |__+2__ | |1 |
-|[gghighlight](problems.md#gghighlight)|0.4.1 |__+3__ |__+1__ | |
-|[gghourglass](problems.md#gghourglass)|0.0.2 |__+2__ | | |
|[ggimage](problems.md#ggimage)|0.3.3 | |__+1__ | |
|[ggiraph](problems.md#ggiraph)|0.8.13 |__+2__ | |1 |
|[ggiraphExtra](problems.md#ggiraphextra)|0.3.0 |__+2__ | | |
-|[gglogger](problems.md#gglogger)|0.1.5 |__+1__ | | |
|[ggmap](problems.md#ggmap)|4.0.1 | |__+1__ |1 |
-|[ggmice](problems.md#ggmice)|0.1.0 |__+1__ | | |
-|[ggnewscale](problems.md#ggnewscale)|0.5.1 |__+1__ |__+1__ | |
|[ggpackets](problems.md#ggpackets)|0.2.1 |__+2__ |__+1__ | |
|[ggparallel](problems.md#ggparallel)|0.4.0 |__+1__ | | |
-|[ggpath](problems.md#ggpath)|1.0.2 |__+2__ | | |
-|[ggpedigree](problems.md#ggpedigree)|0.7.0 |__+2__ | |1 |
+|[ggpath](problems.md#ggpath)|1.0.2 |__+1__ | | |
|[ggplot2.utils](problems.md#ggplot2utils)|0.3.2 |__+1__ | | |
|[ggPMX](problems.md#ggpmx)|1.2.11 |__+1__ | |2 |
|[ggpol](problems.md#ggpol)|0.0.7 |__+1__ | |2 |
|[ggprism](problems.md#ggprism)|1.0.6 |__+3__ | | |
|[ggpubr](problems.md#ggpubr)|0.6.0 |__+1__ | | |
-|[ggquickeda](problems.md#ggquickeda)|0.3.1 |__+1__ | |1 |
|[ggraph](problems.md#ggraph)|2.2.1 |__+2__ |__+1__ |1 |
-|[ggredist](problems.md#ggredist)|0.0.2 |__+1__ | | |
|[ggResidpanel](problems.md#ggresidpanel)|0.3.0 |__+3__ | | |
|[ggRtsy](problems.md#ggrtsy)|0.1.0 |__+2__ | |1 |
-|[ggseas](problems.md#ggseas)|0.5.4 |__+1__ | | |
|[ggseqplot](problems.md#ggseqplot)|0.8.6 |__+3__ | | |
|[ggside](problems.md#ggside)|0.3.1 |__+3__ |__+2__ |__+1__ |
|[ggspatial](problems.md#ggspatial)|1.1.9 | |__+1__ | |
@@ -252,222 +182,143 @@
|[ggstream](problems.md#ggstream)|0.1.0 |__+1__ | |1 |
|[ggswissmaps](problems.md#ggswissmaps)|0.1.1 | |__+1__ |__+1__ |
|[ggtangle](problems.md#ggtangle)|0.0.6 |__+1__ |__+1__ | |
-|[ggtext](problems.md#ggtext)|0.1.2 |__+1__ | | |
-|[ggtibble](problems.md#ggtibble)|1.0.1 |__+1__ | | |
|[ggtime](problems.md#ggtime)|0.1.0 |__+1__ | | |
-|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.2 |__+1__ | |1 |
+|[ggVennDiagram](problems.md#ggvenndiagram)|1.5.4 |__+1__ | |1 |
|[ggview](problems.md#ggview)|0.2.1 | |__+1__ | |
|[grafify](problems.md#grafify)|5.0.0.1 |__+1__ | |2 |
|[graphPAF](problems.md#graphpaf)|2.0.0 |__+1__ | | |
-|[gratia](problems.md#gratia)|0.10.0 |__+2__ | | |
-|[Greymodels](problems.md#greymodels)|2.0.1 |__+1__ | | |
|[GRShiny](problems.md#grshiny)|1.0.0 |__+1__ | |1 |
|[grwat](problems.md#grwat)|0.0.4 |__+1__ | |1 |
|[gtExtras](problems.md#gtextras)|0.6.0 |__+1__ | | |
-|[guideR](problems.md#guider)|0.4.0 |__+2__ | | |
+|[handwriterRF](problems.md#handwriterrf)|1.1.1 |__+1__ | | |
|[harmony](problems.md#harmony)|1.2.3 |__+1__ | |1 |
|[hatchR](problems.md#hatchr)|0.3.2 |__+1__ | |1 |
-|[healthyR](problems.md#healthyr)|0.2.2 |__+1__ | |1 |
-|[healthyR.ai](problems.md#healthyrai)|0.1.1 |__+2__ | | |
-|[healthyR.ts](problems.md#healthyrts)|0.3.1 |__+2__ | |1 |
-|[heatmaply](problems.md#heatmaply)|1.5.0 |__+2__ | |2 |
+|[heatmaply](problems.md#heatmaply)|1.5.0 |__+1__ | |2 |
|[hesim](problems.md#hesim)|0.5.5 |__+1__ | |1 |
-|[hmsidwR](problems.md#hmsidwr)|1.1.2 |__+1__ | |2 |
|[hrbrthemes](problems.md#hrbrthemes)|0.8.7 |__+1__ | | |
-|[HVT](problems.md#hvt) |25.2.4 |__+1__ | | |
|[hyperoverlap](problems.md#hyperoverlap)|1.1.1 | |__+1__ |1 |
-|[hypervolume](problems.md#hypervolume)|3.1.5 | |__+1__ |1 |
|[hypsoLoop](problems.md#hypsoloop)|0.2.0 | |__+1__ | |
|[ImHD](problems.md#imhd)|0.1.0 | |__+1__ | |
|[implicitMeasures](problems.md#implicitmeasures)|0.2.1 |__+2__ | | |
|[imputeTS](problems.md#imputets)|3.3 |__+1__ |1 |1 |
-|[incidence](problems.md#incidence)|1.7.5 |__+3__ | | |
|[infer](problems.md#infer)|1.0.8 |__+1__ |__+1__ | |
-|[inferCSN](problems.md#infercsn)|1.1.7 |__+1__ | |1 |
|[inTextSummaryTable](problems.md#intextsummarytable)|3.3.3 |__+2__ | |1 |
|[iNZightTS](problems.md#inzightts)|2.0.0 |__+1__ | |1 |
|[IRon](problems.md#iron)|0.1.4 |__+1__ | |1 |
|[isoorbi](problems.md#isoorbi)|1.3.1 |__+1__ | |1 |
-|[jskm](problems.md#jskm)|0.5.11 |__+1__ | | |
-|[karel](problems.md#karel)|0.1.1 |__+2__ | |1 |
-|[kDGLM](problems.md#kdglm)|1.2.7 |__+2__ | |1 |
+|[jskm](problems.md#jskm)|0.5.13 |__+1__ | | |
|[lares](problems.md#lares)|5.2.13 |__+1__ | | |
-|[latentcor](problems.md#latentcor)|2.0.1 |__+1__ | |1 |
|[latrend](problems.md#latrend)|1.6.1 |__+2__ | | |
-|[lcars](problems.md#lcars)|0.4.0 |__+2__ | | |
|[legendry](problems.md#legendry)|0.2.2 | |__+3__ |__+2__ |
|[lemon](problems.md#lemon)|0.5.0 |__+3__ |__+1__ | |
|[lfproQC](problems.md#lfproqc)|1.4.0 |__+2__ | | |
|[lgpr](problems.md#lgpr)|1.2.4 |__+1__ | |3 |
-|[lionfish](problems.md#lionfish)|1.0.27 |__+1__ | | |
|[listdown](problems.md#listdown)|0.5.7 |__+2__ | |2 |
-|[LMD](problems.md#lmd) |1.0.0 |__+2__ | | |
-|[lnmixsurv](problems.md#lnmixsurv)|3.1.6 |__+2__ | |4 |
+|[LMD](problems.md#lmd)|1.0.0 |__+2__ | | |
|[longevity](problems.md#longevity)|1.2 |__+2__ | |1 |
-|[LSX](problems.md#lsx) |1.4.4 |__+1__ | |1 |
|[ltertools](problems.md#ltertools)|2.0.0 |__+1__ | | |
-|[manydata](problems.md#manydata)|1.0.2 |__+1__ | | |
|[manymodelr](problems.md#manymodelr)|0.3.9 | |__+1__ | |
|[manynet](problems.md#manynet)|1.3.2 |__+2__ | |3 |
|[marquee](problems.md#marquee)|1.0.0 |__+1__ | |1 |
|[MaxWiK](problems.md#maxwik)|1.0.5 |__+1__ | | |
-|[MBMethPred](problems.md#mbmethpred)|0.1.4.2 |__+1__ | |1 |
-|[mcp](problems.md#mcp) |0.3.4 |__+2__ | | |
|[mcStats](problems.md#mcstats)|0.1.2 |__+1__ | |1 |
|[meme](problems.md#meme)|0.2.3 |__+1__ | | |
-|[MendelianRandomization](problems.md#mendelianrandomization)|0.10.0 |__+1__ | |1 |
|[metagam](problems.md#metagam)|0.4.0 |__+1__ | | |
-|[MetAlyzer](problems.md#metalyzer)|1.1.0 |__+1__ | | |
|[MetaNet](problems.md#metanet)|0.2.5 |__+1__ | | |
-|[metaquant](problems.md#metaquant)|0.1.1 |__+1__ | | |
|[metR](problems.md#metr)|0.18.1 |__+3__ | |1 |
|[mgcViz](problems.md#mgcviz)|0.2.0 |__+1__ | | |
-|[MIC](problems.md#mic) |1.1.0 |__+1__ | | |
-|[migraph](problems.md#migraph)|1.4.5 |__+2__ | | |
+|[MIC](problems.md#mic)|1.1.0 |__+1__ | | |
|[mikropml](problems.md#mikropml)|1.6.1 |__+1__ | |1 |
|[MiMIR](problems.md#mimir)|1.5 |__+1__ | | |
|[miRetrieve](problems.md#miretrieve)|1.3.4 |__+1__ | | |
-|[MiscMetabar](problems.md#miscmetabar)|0.14.2 |__+3__ | |1 |
-|[miscset](problems.md#miscset)|1.1.0 |__+1__ | | |
-|[misspi](problems.md#misspi)|0.1.0 |__+1__ | | |
+|[MiscMetabar](problems.md#miscmetabar)|0.14.3 |__+3__ | |1 |
|[mistral](problems.md#mistral)|2.2.2 | |__+1__ | |
|[misty](problems.md#misty)|0.7.2 |__+1__ | |1 |
-|[mizer](problems.md#mizer)|2.5.3 |__+1__ | |1 |
|[MKpower](problems.md#mkpower)|1.0 |__+1__ | | |
-|[mlr3spatiotempcv](problems.md#mlr3spatiotempcv)|2.3.2 |__+1__ | |1 |
|[modeldb](problems.md#modeldb)|0.3.0 |__+1__ | | |
-|[modeltime.resample](problems.md#modeltimeresample)|0.2.3 |__+1__ | |1 |
|[Momocs](problems.md#momocs)|1.4.1 |__+1__ | | |
-|[mpactr](problems.md#mpactr)|0.2.1 |__+2__ | |1 |
-|[MRZero](problems.md#mrzero)|0.2.0 |__+1__ | | |
+|[mpactr](problems.md#mpactr)|0.2.1 |__+1__ | |1 |
|[mshap](problems.md#mshap)|0.1.0 |__+1__ | |1 |
|[mtdesign](problems.md#mtdesign)|0.1.2 |__+1__ | | |
-|[mvdalab](problems.md#mvdalab)|1.7 |__+1__ | | |
-|[mverse](problems.md#mverse)|0.2.0 |__+1__ | |1 |
+|[mverse](problems.md#mverse)|0.2.2 |__+1__ | |1 |
|[mxnorm](problems.md#mxnorm)|1.0.3 |__+1__ | |1 |
-|[neatmaps](problems.md#neatmaps)|2.1.0 |__+1__ | |1 |
|[NHSRplotthedots](problems.md#nhsrplotthedots)|0.1.0 |__+1__ | |1 |
-|[nichetools](problems.md#nichetools)|0.3.2 |__+1__ | | |
-|[NiLeDAM](problems.md#niledam)|0.3 |__+1__ | | |
-|[NIMAA](problems.md#nimaa)|0.2.1 |__+3__ | |2 |
|[nlmixr2plot](problems.md#nlmixr2plot)|3.0.1 |__+1__ | | |
-|[nonmem2R](problems.md#nonmem2r)|0.2.5 |__+2__ | | |
|[normfluodbf](problems.md#normfluodbf)|2.0.0 |__+1__ | | |
|[nzelect](problems.md#nzelect)|0.4.0 |__+1__ | |2 |
-|[occCite](problems.md#occcite)|0.5.9 |__+1__ | |2 |
|[ofpetrial](problems.md#ofpetrial)|0.1.2 |__+1__ | | |
|[ogrdbstats](problems.md#ogrdbstats)|0.5.2 |__+2__ | | |
|[OmicNavigator](problems.md#omicnavigator)|1.15.0 |__+1__ |1 | |
|[ordinalsimr](problems.md#ordinalsimr)|0.2.1 |__+1__ | | |
|[ordr](problems.md#ordr)|0.1.1 |__+3__ | |2 |
-|[pacu](problems.md#pacu)|0.1.63 |__+1__ | |1 |
|[pafr](problems.md#pafr)|0.0.2 |__+1__ |__+1__ |1 |
|[palettes](problems.md#palettes)|0.2.1 |__+2__ | | |
-|[paramix](problems.md#paramix)|0.0.2 |__+1__ | | |
-|[patchwork](problems.md#patchwork)|1.3.0 |__+2__ |__+1__ | |
-|[pathfindR](problems.md#pathfindr)|2.4.2 |__+1__ | | |
-|[pathviewr](problems.md#pathviewr)|1.1.7 |__+1__ | | |
-|[PatientLevelPrediction](problems.md#patientlevelprediction)|6.4.1 |__+1__ | | |
+|[patchwork](problems.md#patchwork)|1.3.1 | |__+1__ | |
|[patientProfilesVis](problems.md#patientprofilesvis)|2.0.9 |1 __+1__ | |1 |
-|[pcr](problems.md#pcr) |1.2.2 |__+1__ | | |
-|[pdxTrees](problems.md#pdxtrees)|0.4.0 |__+1__ | |1 |
-|[pedbp](problems.md#pedbp)|2.0.2 |__+1__ | |1 |
-|[personalized](problems.md#personalized)|0.2.7 |__+1__ | |1 |
+|[pcr](problems.md#pcr)|1.2.2 |__+1__ | | |
|[phylepic](problems.md#phylepic)|0.2.0 | |__+1__ | |
|[plantTracker](problems.md#planttracker)|1.1.0 |__+1__ | | |
-|[Plasmidprofiler](problems.md#plasmidprofiler)|0.1.6 |__+1__ | | |
|[plotdap](problems.md#plotdap)|1.0.3 |__+2__ | | |
|[plotDK](problems.md#plotdk)|0.1.0 |__+1__ | |2 |
|[PlotFTIR](problems.md#plotftir)|1.2.0 |__+1__ | | |
-|[plotly](problems.md#plotly)|4.10.4 |__+2__ | |1 |
|[plotor](problems.md#plotor)|0.6.0 |__+3__ | | |
|[plotROC](problems.md#plotroc)|2.3.1 |__+3__ | | |
-|[plotthis](problems.md#plotthis)|0.7.0 |__+1__ | |1 |
-|[pmartR](problems.md#pmartr)|2.5.0 |__+1__ | |1 |
+|[plotthis](problems.md#plotthis)|0.7.1 |__+1__ | |1 |
|[pmxTools](problems.md#pmxtools)|1.3 |__+1__ | |2 |
|[pollster](problems.md#pollster)|0.1.6 |__+1__ | | |
-|[poppr](problems.md#poppr)|2.9.6 |__+1__ |1 | |
|[PoweREST](problems.md#powerest)|0.1.0 |__+1__ | | |
-|[PPQplan](problems.md#ppqplan)|1.1.0 |__+1__ | |2 |
-|[ppseq](problems.md#ppseq)|0.2.5 |__+1__ | |1 |
|[precintcon](problems.md#precintcon)|2.3.0 |__+1__ | | |
|[predint](problems.md#predint)|2.2.1 |__+1__ | | |
|[PredPsych](problems.md#predpsych)|0.4 | |__+1__ | |
|[predRupdate](problems.md#predrupdate)|0.2.0 |__+1__ | | |
|[priorsense](problems.md#priorsense)|1.1.0 |__+1__ | | |
|[probably](problems.md#probably)|1.1.0 |__+1__ | | |
-|[processmapR](problems.md#processmapr)|0.5.6 |__+1__ | | |
|[psborrow](problems.md#psborrow)|0.2.2 |__+1__ |__+1__ | |
-|[psc](problems.md#psc) |1.3.0 |__+1__ | | |
+|[psc](problems.md#psc)|1.3.0 |__+1__ | | |
|[pscore](problems.md#pscore)|0.4.0 | |__+1__ | |
|[pubh](problems.md#pubh)|2.0.0 |__+1__ | | |
-|[qad](problems.md#qad) |1.0.4 |__+1__ | |1 |
+|[qad](problems.md#qad)|1.0.4 |__+1__ | |1 |
|[qdap](problems.md#qdap)|2.4.6 |__+1__ | |3 |
|[qgcompint](problems.md#qgcompint)|1.0.0 |__+1__ | | |
-|[qicharts2](problems.md#qicharts2)|0.8.0 |__+1__ | | |
|[quantities](problems.md#quantities)|0.2.3 |__+1__ | | |
|[quickPlot](problems.md#quickplot)|1.0.2 |__+2__ | |1 |
|[quickReg](problems.md#quickreg)|1.5.0 |__+1__ | |3 |
-|[R4GoodPersonalFinances](problems.md#r4goodpersonalfinances)|1.0.0 |__+1__ | | |
|[Radviz](problems.md#radviz)|0.9.4 |__+2__ | |1 |
|[RamanMP](problems.md#ramanmp)|1.0 |__+1__ | |1 |
|[randomForestExplainer](problems.md#randomforestexplainer)|0.10.1 |__+3__ | |1 |
-|[rassta](problems.md#rassta)|1.0.6 |__+2__ | | |
|[rasterdiv](problems.md#rasterdiv)|0.3.6 |__+1__ | | |
|[rater](problems.md#rater)|1.3.1 |__+1__ | |3 |
|[ratlas](problems.md#ratlas)|0.1.0 |__+2__ | |1 |
|[rbioacc](problems.md#rbioacc)|1.2.1 |__+1__ | |2 |
|[rbiom](problems.md#rbiom)|2.2.0 |__+1__ | | |
-|[reda](problems.md#reda)|0.5.4 |__+1__ | |3 |
+|[reda](problems.md#reda)|0.5.5 |__+1__ | |1 |
|[regtomean](problems.md#regtomean)|1.2 | |__+1__ |1 |
|[rempsyc](problems.md#rempsyc)|0.1.9 |__+3__ | | |
-|[RevGadgets](problems.md#revgadgets)|1.2.1 |__+1__ | | |
-|[rifreg](problems.md#rifreg)|0.1.0 |__+1__ | | |
|[rmweather](problems.md#rmweather)|0.2.62 |__+1__ | | |
-|[RNAseqQC](problems.md#rnaseqqc)|0.2.1 |__+1__ | |1 |
-|[roahd](problems.md#roahd)|1.4.3 |__+1__ | |2 |
|[robCompositions](problems.md#robcompositions)|2.4.1 | |1 __+1__ |3 |
-|[romic](problems.md#romic)|1.1.3 |__+1__ | |1 |
-|[roptions](problems.md#roptions)|1.0.3 |__+1__ | |1 |
-|[rPBK](problems.md#rpbk)|0.2.4 |__+1__ |1 |3 |
-|[rrr](problems.md#rrr) |1.0.0 |__+2__ | |1 |
+|[rrr](problems.md#rrr)|1.0.0 |__+2__ | |1 |
|[RSDA](problems.md#rsda)|3.2.4 | |__+1__ |1 |
|[RTIGER](problems.md#rtiger)|2.1.0 | |__+1__ | |
-|[RVA](problems.md#rva) |0.0.5 |__+1__ | |2 |
+|[RVA](problems.md#rva)|0.0.5 |__+1__ | |2 |
|[RVenn](problems.md#rvenn)|1.1.0 |__+1__ | |1 |
|[Rwtss](problems.md#rwtss)|0.9.2 |__+1__ | |1 |
|[saros](problems.md#saros)|1.5.4 |__+2__ | | |
-|[scatterpie](problems.md#scatterpie)|0.2.4 | |__+1__ | |
|[scCustomize](problems.md#sccustomize)|3.0.1 |__+1__ | | |
-|[schtools](problems.md#schtools)|0.4.1 |__+1__ | | |
|[scoringutils](problems.md#scoringutils)|2.1.0 |__+1__ | | |
|[SCpubr](problems.md#scpubr)|2.0.2 |__+1__ | | |
-|[scRNAstat](problems.md#scrnastat)|0.1.1.1 |__+1__ |1 |1 |
|[scrutiny](problems.md#scrutiny)|0.5.0 |__+3__ | |1 |
|[scUtils](problems.md#scutils)|0.1.0 |__+1__ | |1 |
-|[SCVA](problems.md#scva)|1.3.1 |__+1__ | | |
|[SDMtune](problems.md#sdmtune)|1.3.2 |__+1__ | |1 |
|[seAMLess](problems.md#seamless)|0.1.1 |__+1__ | | |
-|[sedproxy](problems.md#sedproxy)|0.7.5 |__+1__ | | |
-|[see](problems.md#see) |0.11.0 |__+2__ | | |
+|[see](problems.md#see)|0.11.0 |__+2__ | | |
|[seedreg](problems.md#seedreg)|1.0.3 |__+1__ | | |
-|[seqHMM](problems.md#seqhmm)|2.0.0 |__+1__ |1 |1 |
-|[Seurat](problems.md#seurat)|5.3.0 |__+1__ | |2 |
-|[sglg](problems.md#sglg)|0.2.2 |__+1__ | | |
-|[sgsR](problems.md#sgsr)|1.4.5 |__+1__ | | |
|[shadowtext](problems.md#shadowtext)|0.1.4 | |__+1__ | |
-|[SHAPforxgboost](problems.md#shapforxgboost)|0.1.3 |__+1__ | | |
|[shiny](problems.md#shiny)|1.10.0 |__+1__ | |1 |
-|[shinyMixR](problems.md#shinymixr)|0.5.0 |__+2__ | | |
-|[shinyMobile](problems.md#shinymobile)|2.0.1 |__+1__ | | |
+|[shinyMixR](problems.md#shinymixr)|0.5.0 |__+1__ | | |
|[simmr](problems.md#simmr)|0.5.1.217 |__+1__ | | |
-|[SimNPH](problems.md#simnph)|0.5.7 |__+1__ | | |
|[simplecolors](problems.md#simplecolors)|0.1.2 |__+1__ | | |
|[sjPlot](problems.md#sjplot)|2.8.17 |__+1__ | | |
-|[smallsets](problems.md#smallsets)|2.0.0 |__+3__ | |1 |
|[smer](problems.md#smer)|0.0.1 |__+1__ | |2 |
-|[SOMbrero](problems.md#sombrero)|1.4-2 |__+1__ | | |
-|[SoupX](problems.md#soupx)|1.6.2 |__+1__ | |1 |
|[spacejamr](problems.md#spacejamr)|0.2.1 |__+1__ | | |
|[spatialwarnings](problems.md#spatialwarnings)|3.1.0 |__+1__ | |1 |
|[spectralR](problems.md#spectralr)|0.1.3 |__+1__ | | |
@@ -475,10 +326,8 @@
|[sport](problems.md#sport)|0.2.1 |__+1__ | |1 |
|[sportyR](problems.md#sportyr)|2.2.2 |__+1__ | | |
|[SPUTNIK](problems.md#sputnik)|1.4.2 | |__+1__ | |
-|[SqueakR](problems.md#squeakr)|1.3.0 |__+1__ | |1 |
|[ssd4mosaic](problems.md#ssd4mosaic)|1.0.3 |__+1__ | |1 |
|[sssc](problems.md#sssc)|1.0.0 | |__+1__ | |
-|[starvz](problems.md#starvz)|0.8.2 |__+1__ | |1 |
|[states](problems.md#states)|0.3.2 |__+1__ | | |
|[statgenGWAS](problems.md#statgengwas)|1.0.11 |__+1__ | |1 |
|[statgenGxE](problems.md#statgengxe)|1.0.9 |__+1__ | |1 |
@@ -487,55 +336,35 @@
|[statgenSTA](problems.md#statgensta)|1.0.14 |__+1__ | |2 |
|[stRoke](problems.md#stroke)|24.10.1 |__+1__ | |1 |
|[Superpower](problems.md#superpower)|0.2.3 |__+1__ | | |
-|[survHE](problems.md#survhe)|2.0.4 |__+1__ | | |
|[synthpop](problems.md#synthpop)|1.9-1.1 |__+1__ |1 | |
-|[tabledown](problems.md#tabledown)|1.0.0 |__+1__ | |1 |
|[tastypie](problems.md#tastypie)|0.1.1 |__+1__ | | |
|[TcGSA](problems.md#tcgsa)|0.12.10 | |__+1__ | |
-|[TCIU](problems.md#tciu)|1.2.7 |__+2__ | |1 |
|[teal.widgets](problems.md#tealwidgets)|0.4.3 |__+1__ | | |
|[TestGardener](problems.md#testgardener)|3.3.5 |__+1__ | | |
-|[thematic](problems.md#thematic)|0.1.6 |__+2__ | | |
-|[tidycat](problems.md#tidycat)|0.1.2 |__+2__ | |1 |
-|[tidyCDISC](problems.md#tidycdisc)|0.2.1 |__+1__ | |1 |
|[tidyEdSurvey](problems.md#tidyedsurvey)|0.1.3 |__+1__ | | |
|[tidypaleo](problems.md#tidypaleo)|0.1.3 | |__+1__ | |
|[tidyposterior](problems.md#tidyposterior)|1.0.1 |__+1__ | | |
-|[tidysdm](problems.md#tidysdm)|1.0.0 |__+2__ | | |
-|[timetk](problems.md#timetk)|2.9.0 |__+1__ | |1 |
-|[tinyarray](problems.md#tinyarray)|2.4.3 |__+1__ | | |
-|[tmt](problems.md#tmt) |0.3.4-0 |__+1__ | |1 |
|[TPMplt](problems.md#tpmplt)|0.1.6 | |__+1__ | |
|[track2KBA](problems.md#track2kba)|1.1.2 |__+1__ | | |
|[tradeoffaucdim](problems.md#tradeoffaucdim)|0.1.0 |__+1__ | |1 |
-|[trajmsm](problems.md#trajmsm)|0.1.3 | |__+1__ | |
-|[TransProR](problems.md#transpror)|1.0.3 |__+1__ | | |
-|[trelliscopejs](problems.md#trelliscopejs)|0.2.6 |__+1__ |__+1__ | |
+|[TransProR](problems.md#transpror)|1.0.5 |__+1__ | | |
+|[trelliscopejs](problems.md#trelliscopejs)|0.2.6 | |__+1__ | |
|[triplot](problems.md#triplot)|1.3.0 |__+2__ | |1 |
-|[triptych](problems.md#triptych)|0.1.3 |__+1__ | | |
-|[tsnet](problems.md#tsnet)|0.1.0 |__+1__ | |2 |
|[ulrb](problems.md#ulrb)|0.1.6 |__+1__ | | |
-|[umiAnalyzer](problems.md#umianalyzer)|1.0.0 |__+1__ | | |
|[UnalR](problems.md#unalr)|1.0.0 |__+1__ | |2 |
-|[usmap](problems.md#usmap)|0.8.0 |__+3__ | |1 |
-|[utile.visuals](problems.md#utilevisuals)|0.3.3 |__+1__ | | |
|[vaccine](problems.md#vaccine)|1.3.0 |__+1__ | | |
|[vaccineff](problems.md#vaccineff)|1.0.0 |__+1__ | | |
-|[valr](problems.md#valr)|0.8.3 |__+1__ | |1 |
|[vanquish](problems.md#vanquish)|1.0.0 | |__+1__ | |
|[VarSelLCM](problems.md#varsellcm)|2.1.3.1 |__+1__ | |1 |
|[vDiveR](problems.md#vdiver)|2.0.1 |__+1__ | |1 |
-|[vip](problems.md#vip) |0.4.1 |__+1__ | |2 |
+|[vip](problems.md#vip)|0.4.1 |__+1__ | |2 |
|[visualpred](problems.md#visualpred)|0.1.1 | |__+1__ | |
-|[vivaldi](problems.md#vivaldi)|1.0.1 |__+3__ | |1 |
|[voluModel](problems.md#volumodel)|0.2.2 |__+2__ | | |
|[vvshiny](problems.md#vvshiny)|0.1.1 |__+1__ | | |
|[washi](problems.md#washi)|0.2.0 |__+1__ | | |
-|[wilson](problems.md#wilson)|2.4.2 |__+1__ | | |
|[windfarmGA](problems.md#windfarmga)|4.0.0 |__+1__ | | |
-|[wql](problems.md#wql) |1.0.2 |__+2__ | | |
+|[wql](problems.md#wql)|1.0.2 |__+2__ | | |
|[xaringanthemer](problems.md#xaringanthemer)|0.4.3 |__+1__ | | |
|[xpose.xtras](problems.md#xposextras)|0.0.2 |__+3__ | |2 |
-|[yamlet](problems.md#yamlet)|1.2.1 | |1 __+1__ | |
|[ZetaSuite](problems.md#zetasuite)|1.0.1 | |__+1__ |1 |
diff --git a/revdep/cran.md b/revdep/cran.md
index 8cbc2b3a39..984c6f80c3 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,21 +1,15 @@
## revdepcheck results
-We checked 5755 reverse dependencies (5753 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 5736 reverse dependencies (5733 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
- * We saw 498 new problems
- * We failed to check 29 packages
+ * We saw 327 new problems
+ * We failed to check 28 packages
Issues with CRAN packages are summarised below.
### New problems
(This reports the first line of each new failure)
-* activAnalyzer
- checking re-building of vignette outputs ... ERROR
-
-* actxps
- checking re-building of vignette outputs ... ERROR
-
* adklakedata
checking examples ... ERROR
@@ -26,9 +20,6 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* AeRobiology
- checking re-building of vignette outputs ... ERROR
-
* afex
checking re-building of vignette outputs ... ERROR
@@ -58,25 +49,12 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* APCtools
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* aplot
- checking S3 generic/method consistency ... WARNING
-
* applicable
checking tests ... ERROR
* arena2r
checking tests ... ERROR
-* ARUtools
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* ASRgenomics
checking tests ... ERROR
@@ -87,13 +65,8 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
* autoplotly
- checking examples ... ERROR
checking tests ... ERROR
-* autoReg
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* bayesAB
checking tests ... ERROR
@@ -103,21 +76,12 @@ Issues with CRAN packages are summarised below.
* BayesCVI
checking whether package ‘BayesCVI’ can be installed ... WARNING
-* BayesERtools
- checking tests ... ERROR
-
* BayesianReasoning
checking tests ... ERROR
-* BayesMallows
- checking tests ... ERROR
-
* BayesMultiMode
checking whether package ‘BayesMultiMode’ can be installed ... WARNING
-* bayesplot
- checking tests ... ERROR
-
* BCEA
checking examples ... ERROR
@@ -140,12 +104,6 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking tests ... ERROR
-* blockCV
- checking tests ... ERROR
-
-* boxly
- checking tests ... ERROR
-
* brolgar
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -154,9 +112,6 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* calibmsm
- checking tests ... ERROR
-
* calmr
checking tests ... ERROR
@@ -166,15 +121,12 @@ Issues with CRAN packages are summarised below.
* carbonr
checking tests ... ERROR
-* cartograflow
- checking examples ... ERROR
+* caretEnsemble
+ checking installed package size ... NOTE
* cartographr
checking tests ... ERROR
-* cats
- checking examples ... ERROR
-
* causact
checking tests ... ERROR
@@ -191,45 +143,18 @@ Issues with CRAN packages are summarised below.
* cheem
checking tests ... ERROR
-* ChemoSpec
- checking re-building of vignette outputs ... ERROR
-
-* ChemoSpecUtils
- checking examples ... ERROR
-
-* chillR
- checking examples ... ERROR
-
-* chronicle
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* circumplex
checking tests ... ERROR
-* classmap
- checking whether package ‘classmap’ can be installed ... WARNING
-
* clifro
checking tests ... ERROR
* climwin
checking tests ... ERROR
-* clinDataReview
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* clinUtils
- checking re-building of vignette outputs ... ERROR
-
* clockSim
checking whether package ‘clockSim’ can be installed ... WARNING
-* clustcurv
- checking re-building of vignette outputs ... ERROR
-
* cmcR
checking tests ... ERROR
@@ -237,44 +162,18 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* CNVreg
- checking re-building of vignette outputs ... ERROR
-
-* CohortPlat
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* colorrepel
- checking examples ... ERROR
-
* conquestr
checking tests ... ERROR
* constructive
checking tests ... ERROR
-* contsurvplot
- checking tests ... ERROR
-
-* CoreMicrobiomeR
- checking examples ... ERROR
-
-* correlationfunnel
- checking tests ... ERROR
-
-* corrViz
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* CoSMoS
checking re-building of vignette outputs ... ERROR
* countfitteR
checking tests ... ERROR
-* countries
- checking tests ... ERROR
-
* covidcast
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -282,22 +181,9 @@ Issues with CRAN packages are summarised below.
* cowplot
checking tests ... ERROR
-* Coxmos
- checking examples ... ERROR
-
-* cry
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* ctrialsgov
checking tests ... ERROR
-* cubble
- checking re-building of vignette outputs ... ERROR
-
-* cutpointr
- checking tests ... ERROR
-
* cvms
checking tests ... ERROR
@@ -317,9 +203,6 @@ Issues with CRAN packages are summarised below.
* DAISIEprep
checking tests ... ERROR
-* daltoolbox
- checking whether package ‘daltoolbox’ can be installed ... WARNING
-
* dams
checking re-building of vignette outputs ... ERROR
@@ -329,12 +212,6 @@ Issues with CRAN packages are summarised below.
* dendextend
checking tests ... ERROR
-* densityratio
- checking tests ... ERROR
-
-* diceR
- checking tests ... ERROR
-
* DImodelsVis
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -352,9 +229,6 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking tests ... ERROR
-* dndR
- checking tests ... ERROR
-
* duke
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -378,12 +252,6 @@ Issues with CRAN packages are summarised below.
* ENMTools
checking tests ... ERROR
-* epiCleanr
- checking examples ... ERROR
-
-* epiphy
- checking examples ... ERROR
-
* epos
checking tests ... ERROR
@@ -397,31 +265,15 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* eudract
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* eventstudyr
checking tests ... ERROR
-* EvoPhylo
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* explainer
- checking examples ... ERROR
-
* ez
checking examples ... ERROR
* ezEDA
checking tests ... ERROR
-* EZFragility
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* ezplot
checking examples ... ERROR
checking tests ... ERROR
@@ -442,49 +294,21 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking tests ... ERROR
-* fChange
- checking tests ... ERROR
-
* feasts
checking tests ... ERROR
* fec16
checking re-building of vignette outputs ... ERROR
-* fitbitViz
- checking tests ... ERROR
-
* flextable
checking examples ... ERROR
-* flipr
- checking re-building of vignette outputs ... ERROR
-
* fmf
checking whether package ‘fmf’ can be installed ... WARNING
-* foqat
- checking re-building of vignette outputs ... ERROR
-
-* forestly
- checking re-building of vignette outputs ... ERROR
-
* forestPSD
checking examples ... ERROR
-* formods
- checking tests ... ERROR
-
-* fqar
- checking tests ... ERROR
-
-* frailtyEM
- checking examples ... ERROR
-
-* funcharts
- checking examples ... ERROR
- checking tests ... ERROR
-
* FunnelPlotR
checking examples ... ERROR
checking tests ... ERROR
@@ -493,9 +317,6 @@ Issues with CRAN packages are summarised below.
* gapfill
checking tests ... ERROR
-* gapminder
- checking examples ... ERROR
-
* genekitr
checking examples ... ERROR
@@ -505,9 +326,6 @@ Issues with CRAN packages are summarised below.
* geofacet
checking S3 generic/method consistency ... WARNING
-* geoheatmap
- checking re-building of vignette outputs ... ERROR
-
* geomtextpath
checking examples ... ERROR
checking tests ... ERROR
@@ -526,11 +344,6 @@ Issues with CRAN packages are summarised below.
checking Rd cross-references ... WARNING
checking for code/documentation mismatches ... WARNING
-* gganimate
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
- checking S3 generic/method consistency ... WARNING
-
* ggblend
checking tests ... ERROR
@@ -538,11 +351,9 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
* ggbrain
- checking re-building of vignette outputs ... ERROR
checking S3 generic/method consistency ... WARNING
* ggbreak
- checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
checking S3 generic/method consistency ... WARNING
@@ -556,18 +367,9 @@ Issues with CRAN packages are summarised below.
* ggdemetra
checking whether package ‘ggdemetra’ can be installed ... WARNING
-* ggDoE
- checking examples ... ERROR
-
* ggDoubleHeat
checking examples ... ERROR
-* ggeasy
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
- checking S3 generic/method consistency ... WARNING
-
* ggEDA
checking examples ... ERROR
checking tests ... ERROR
@@ -575,9 +377,6 @@ Issues with CRAN packages are summarised below.
* ggedit
checking examples ... ERROR
-* ggfields
- checking examples ... ERROR
-
* ggfixest
checking tests ... ERROR
@@ -585,18 +384,12 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking S3 generic/method consistency ... WARNING
-* ggforce
- checking examples ... ERROR
-
* ggformula
checking for code/documentation mismatches ... WARNING
* ggfortify
checking tests ... ERROR
-* ggfun
- checking S3 generic/method consistency ... WARNING
-
* ggfx
checking S3 generic/method consistency ... WARNING
@@ -611,16 +404,6 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* gghighlight
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
- checking S3 generic/method consistency ... WARNING
-
-* gghourglass
- checking examples ... ERROR
- checking tests ... ERROR
-
* ggimage
checking S3 generic/method consistency ... WARNING
@@ -632,19 +415,9 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* gglogger
- checking tests ... ERROR
-
* ggmap
checking whether package ‘ggmap’ can be installed ... WARNING
-* ggmice
- checking re-building of vignette outputs ... ERROR
-
-* ggnewscale
- checking tests ... ERROR
- checking S3 generic/method consistency ... WARNING
-
* ggpackets
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -654,12 +427,7 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
* ggpath
- checking examples ... ERROR
- checking tests ... ERROR
-
-* ggpedigree
checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
* ggplot2.utils
checking tests ... ERROR
@@ -678,17 +446,11 @@ Issues with CRAN packages are summarised below.
* ggpubr
checking tests ... ERROR
-* ggquickeda
- checking examples ... ERROR
-
* ggraph
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
checking S3 generic/method consistency ... WARNING
-* ggredist
- checking examples ... ERROR
-
* ggResidpanel
checking examples ... ERROR
checking tests ... ERROR
@@ -698,9 +460,6 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* ggseas
- checking tests ... ERROR
-
* ggseqplot
checking examples ... ERROR
checking tests ... ERROR
@@ -731,12 +490,6 @@ Issues with CRAN packages are summarised below.
checking re-building of vignette outputs ... ERROR
checking S3 generic/method consistency ... WARNING
-* ggtext
- checking re-building of vignette outputs ... ERROR
-
-* ggtibble
- checking tests ... ERROR
-
* ggtime
checking tests ... ERROR
@@ -752,13 +505,6 @@ Issues with CRAN packages are summarised below.
* graphPAF
checking examples ... ERROR
-* gratia
- checking examples ... ERROR
- checking tests ... ERROR
-
-* Greymodels
- checking examples ... ERROR
-
* GRShiny
checking tests ... ERROR
@@ -768,8 +514,7 @@ Issues with CRAN packages are summarised below.
* gtExtras
checking tests ... ERROR
-* guideR
- checking examples ... ERROR
+* handwriterRF
checking tests ... ERROR
* harmony
@@ -778,39 +523,18 @@ Issues with CRAN packages are summarised below.
* hatchR
checking tests ... ERROR
-* healthyR
- checking re-building of vignette outputs ... ERROR
-
-* healthyR.ai
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* healthyR.ts
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* heatmaply
checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
* hesim
checking tests ... ERROR
-* hmsidwR
- checking re-building of vignette outputs ... ERROR
-
* hrbrthemes
checking tests ... ERROR
-* HVT
- checking examples ... ERROR
-
* hyperoverlap
checking whether package ‘hyperoverlap’ can be installed ... WARNING
-* hypervolume
- checking whether package ‘hypervolume’ can be installed ... WARNING
-
* hypsoLoop
checking whether package ‘hypsoLoop’ can be installed ... WARNING
@@ -824,18 +548,10 @@ Issues with CRAN packages are summarised below.
* imputeTS
checking tests ... ERROR
-* incidence
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* infer
checking tests ... ERROR
checking S3 generic/method consistency ... WARNING
-* inferCSN
- checking examples ... ERROR
-
* inTextSummaryTable
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -852,28 +568,13 @@ Issues with CRAN packages are summarised below.
* jskm
checking re-building of vignette outputs ... ERROR
-* karel
- checking examples ... ERROR
- checking tests ... ERROR
-
-* kDGLM
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* lares
checking examples ... ERROR
-* latentcor
- checking examples ... ERROR
-
* latrend
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* lcars
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* legendry
checking whether the package can be loaded with stated dependencies ... WARNING
checking whether the package can be unloaded cleanly ... WARNING
@@ -894,9 +595,6 @@ Issues with CRAN packages are summarised below.
* lgpr
checking tests ... ERROR
-* lionfish
- checking re-building of vignette outputs ... ERROR
-
* listdown
checking examples ... ERROR
checking tests ... ERROR
@@ -905,23 +603,13 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* lnmixsurv
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* longevity
checking examples ... ERROR
checking tests ... ERROR
-* LSX
- checking tests ... ERROR
-
* ltertools
checking tests ... ERROR
-* manydata
- checking tests ... ERROR
-
* manymodelr
checking whether package ‘manymodelr’ can be installed ... WARNING
@@ -935,34 +623,18 @@ Issues with CRAN packages are summarised below.
* MaxWiK
checking re-building of vignette outputs ... ERROR
-* MBMethPred
- checking tests ... ERROR
-
-* mcp
- checking examples ... ERROR
- checking tests ... ERROR
-
* mcStats
checking tests ... ERROR
* meme
checking re-building of vignette outputs ... ERROR
-* MendelianRandomization
- checking examples ... ERROR
-
* metagam
checking re-building of vignette outputs ... ERROR
-* MetAlyzer
- checking examples ... ERROR
-
* MetaNet
checking examples ... ERROR
-* metaquant
- checking examples ... ERROR
-
* metR
checking examples ... ERROR
checking tests ... ERROR
@@ -974,10 +646,6 @@ Issues with CRAN packages are summarised below.
* MIC
checking examples ... ERROR
-* migraph
- checking examples ... ERROR
- checking tests ... ERROR
-
* mikropml
checking tests ... ERROR
@@ -992,42 +660,23 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* miscset
- checking re-building of vignette outputs ... ERROR
-
-* misspi
- checking examples ... ERROR
-
* mistral
checking whether package ‘mistral’ can be installed ... WARNING
* misty
checking examples ... ERROR
-* mizer
- checking tests ... ERROR
-
* MKpower
checking examples ... ERROR
-* mlr3spatiotempcv
- checking tests ... ERROR
-
* modeldb
checking tests ... ERROR
-* modeltime.resample
- checking tests ... ERROR
-
* Momocs
checking examples ... ERROR
* mpactr
checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* MRZero
- checking examples ... ERROR
* mshap
checking tests ... ERROR
@@ -1035,48 +684,24 @@ Issues with CRAN packages are summarised below.
* mtdesign
checking tests ... ERROR
-* mvdalab
- checking examples ... ERROR
-
* mverse
checking re-building of vignette outputs ... ERROR
* mxnorm
checking tests ... ERROR
-* neatmaps
- checking examples ... ERROR
-
* NHSRplotthedots
checking tests ... ERROR
-* nichetools
- checking re-building of vignette outputs ... ERROR
-
-* NiLeDAM
- checking tests ... ERROR
-
-* NIMAA
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* nlmixr2plot
checking tests ... ERROR
-* nonmem2R
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* normfluodbf
checking tests ... ERROR
* nzelect
checking re-building of vignette outputs ... ERROR
-* occCite
- checking tests ... ERROR
-
* ofpetrial
checking examples ... ERROR
@@ -1095,9 +720,6 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* pacu
- checking re-building of vignette outputs ... ERROR
-
* pafr
checking tests ... ERROR
checking S3 generic/method consistency ... WARNING
@@ -1106,47 +728,21 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
-* paramix
- checking re-building of vignette outputs ... ERROR
-
* patchwork
- checking examples ... ERROR
- checking tests ... ERROR
checking S3 generic/method consistency ... WARNING
-* pathfindR
- checking tests ... ERROR
-
-* pathviewr
- checking tests ... ERROR
-
-* PatientLevelPrediction
- checking examples ... ERROR
-
* patientProfilesVis
checking re-building of vignette outputs ... ERROR
* pcr
checking tests ... ERROR
-* pdxTrees
- checking re-building of vignette outputs ... ERROR
-
-* pedbp
- checking tests ... ERROR
-
-* personalized
- checking tests ... ERROR
-
* phylepic
checking S3 generic/method consistency ... WARNING
* plantTracker
checking re-building of vignette outputs ... ERROR
-* Plasmidprofiler
- checking examples ... ERROR
-
* plotdap
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -1157,10 +753,6 @@ Issues with CRAN packages are summarised below.
* PlotFTIR
checking tests ... ERROR
-* plotly
- checking examples ... ERROR
- checking tests ... ERROR
-
* plotor
checking examples ... ERROR
checking tests ... ERROR
@@ -1174,27 +766,15 @@ Issues with CRAN packages are summarised below.
* plotthis
checking examples ... ERROR
-* pmartR
- checking tests ... ERROR
-
* pmxTools
checking tests ... ERROR
* pollster
checking re-building of vignette outputs ... ERROR
-* poppr
- checking examples ... ERROR
-
* PoweREST
checking examples ... ERROR
-* PPQplan
- checking re-building of vignette outputs ... ERROR
-
-* ppseq
- checking re-building of vignette outputs ... ERROR
-
* precintcon
checking examples ... ERROR
@@ -1213,9 +793,6 @@ Issues with CRAN packages are summarised below.
* probably
checking tests ... ERROR
-* processmapR
- checking tests ... ERROR
-
* psborrow
checking tests ... ERROR
checking whether package ‘psborrow’ can be installed ... WARNING
@@ -1238,9 +815,6 @@ Issues with CRAN packages are summarised below.
* qgcompint
checking examples ... ERROR
-* qicharts2
- checking examples ... ERROR
-
* quantities
checking re-building of vignette outputs ... ERROR
@@ -1251,9 +825,6 @@ Issues with CRAN packages are summarised below.
* quickReg
checking re-building of vignette outputs ... ERROR
-* R4GoodPersonalFinances
- checking examples ... ERROR
-
* Radviz
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -1266,10 +837,6 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* rassta
- checking examples ... ERROR
- checking tests ... ERROR
-
* rasterdiv
checking re-building of vignette outputs ... ERROR
@@ -1297,33 +864,12 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* RevGadgets
- checking tests ... ERROR
-
-* rifreg
- checking tests ... ERROR
-
* rmweather
checking tests ... ERROR
-* RNAseqQC
- checking re-building of vignette outputs ... ERROR
-
-* roahd
- checking examples ... ERROR
-
* robCompositions
checking whether package ‘robCompositions’ can be installed ... WARNING
-* romic
- checking tests ... ERROR
-
-* roptions
- checking examples ... ERROR
-
-* rPBK
- checking tests ... ERROR
-
* rrr
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -1347,24 +893,15 @@ Issues with CRAN packages are summarised below.
checking examples ... ERROR
checking tests ... ERROR
-* scatterpie
- checking S3 generic/method consistency ... WARNING
-
* scCustomize
checking examples ... ERROR
-* schtools
- checking re-building of vignette outputs ... ERROR
-
* scoringutils
checking examples ... ERROR
* SCpubr
checking tests ... ERROR
-* scRNAstat
- checking examples ... ERROR
-
* scrutiny
checking examples ... ERROR
checking tests ... ERROR
@@ -1373,18 +910,12 @@ Issues with CRAN packages are summarised below.
* scUtils
checking tests ... ERROR
-* SCVA
- checking examples ... ERROR
-
* SDMtune
checking tests ... ERROR
* seAMLess
checking examples ... ERROR
-* sedproxy
- checking tests ... ERROR
-
* see
checking examples ... ERROR
checking tests ... ERROR
@@ -1392,60 +923,27 @@ Issues with CRAN packages are summarised below.
* seedreg
checking examples ... ERROR
-* seqHMM
- checking examples ... ERROR
-
-* Seurat
- checking examples ... ERROR
-
-* sglg
- checking examples ... ERROR
-
-* sgsR
- checking tests ... ERROR
-
* shadowtext
checking dependencies in R code ... WARNING
-* SHAPforxgboost
- checking examples ... ERROR
-
* shiny
checking tests ... ERROR
* shinyMixR
checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* shinyMobile
- checking examples ... ERROR
* simmr
checking re-building of vignette outputs ... ERROR
-* SimNPH
- checking tests ... ERROR
-
* simplecolors
checking tests ... ERROR
* sjPlot
checking re-building of vignette outputs ... ERROR
-* smallsets
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* smer
checking re-building of vignette outputs ... ERROR
-* SOMbrero
- checking tests ... ERROR
-
-* SoupX
- checking re-building of vignette outputs ... ERROR
-
* spacejamr
checking tests ... ERROR
@@ -1467,18 +965,12 @@ Issues with CRAN packages are summarised below.
* SPUTNIK
checking whether package ‘SPUTNIK’ can be installed ... WARNING
-* SqueakR
- checking re-building of vignette outputs ... ERROR
-
* ssd4mosaic
checking tests ... ERROR
* sssc
checking whether package ‘sssc’ can be installed ... WARNING
-* starvz
- checking tests ... ERROR
-
* states
checking tests ... ERROR
@@ -1503,42 +995,21 @@ Issues with CRAN packages are summarised below.
* Superpower
checking tests ... ERROR
-* survHE
- checking tests ... ERROR
-
* synthpop
checking examples ... ERROR
-* tabledown
- checking examples ... ERROR
-
* tastypie
checking tests ... ERROR
* TcGSA
checking Rd cross-references ... WARNING
-* TCIU
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* teal.widgets
checking tests ... ERROR
* TestGardener
checking examples ... ERROR
-* thematic
- checking examples ... ERROR
- checking tests ... ERROR
-
-* tidycat
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* tidyCDISC
- checking tests ... ERROR
-
* tidyEdSurvey
checking tests ... ERROR
@@ -1548,19 +1019,6 @@ Issues with CRAN packages are summarised below.
* tidyposterior
checking tests ... ERROR
-* tidysdm
- checking examples ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* timetk
- checking tests ... ERROR
-
-* tinyarray
- checking examples ... ERROR
-
-* tmt
- checking tests ... ERROR
-
* TPMplt
checking whether package ‘TPMplt’ can be installed ... WARNING
@@ -1570,52 +1028,28 @@ Issues with CRAN packages are summarised below.
* tradeoffaucdim
checking tests ... ERROR
-* trajmsm
- checking whether package ‘trajmsm’ can be installed ... WARNING
-
* TransProR
checking examples ... ERROR
* trelliscopejs
- checking tests ... ERROR
checking S3 generic/method consistency ... WARNING
* triplot
checking examples ... ERROR
checking tests ... ERROR
-* triptych
- checking examples ... ERROR
-
-* tsnet
- checking tests ... ERROR
-
* ulrb
checking re-building of vignette outputs ... ERROR
-* umiAnalyzer
- checking examples ... ERROR
-
* UnalR
checking tests ... ERROR
-* usmap
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
-* utile.visuals
- checking examples ... ERROR
-
* vaccine
checking tests ... ERROR
* vaccineff
checking tests ... ERROR
-* valr
- checking tests ... ERROR
-
* vanquish
checking whether package ‘vanquish’ can be installed ... WARNING
@@ -1631,11 +1065,6 @@ Issues with CRAN packages are summarised below.
* visualpred
checking whether package ‘visualpred’ can be installed ... WARNING
-* vivaldi
- checking examples ... ERROR
- checking tests ... ERROR
- checking re-building of vignette outputs ... ERROR
-
* voluModel
checking examples ... ERROR
checking re-building of vignette outputs ... ERROR
@@ -1646,9 +1075,6 @@ Issues with CRAN packages are summarised below.
* washi
checking tests ... ERROR
-* wilson
- checking tests ... ERROR
-
* windfarmGA
checking tests ... ERROR
@@ -1664,9 +1090,6 @@ Issues with CRAN packages are summarised below.
checking tests ... ERROR
checking re-building of vignette outputs ... ERROR
-* yamlet
- checking S3 generic/method consistency ... WARNING
-
* ZetaSuite
checking whether package ‘ZetaSuite’ can be installed ... WARNING
@@ -1677,7 +1100,6 @@ Issues with CRAN packages are summarised below.
* cocktailApp (NA)
* coda.plot (NA)
* ctsem (NA)
-* deeptime (NA)
* EcoEnsemble (NA)
* fio (NA)
* GGally (NA)
@@ -1685,10 +1107,10 @@ Issues with CRAN packages are summarised below.
* ggmulti (NA)
* ggRandomForests (NA)
* ggtern (NA)
-* inventorize (NA)
* metabolic (NA)
* multinma (NA)
* MultiTraits (NA)
+* pacta.loanbook (NA)
* PieGlyph (NA)
* rmsb (NA)
* rshift (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 2a220a0a47..b252e91055 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -6,7 +6,7 @@
* GitHub: NA
* Source code: https://github.com/cran/bartMan
* Date/Publication: 2024-07-24 12:10:02 UTC
-* Number of recursive dependencies: 133
+* Number of recursive dependencies: 132
Run `revdepcheck::cloud_details(, "bartMan")` for more info
@@ -243,16 +243,51 @@ ERROR: lazy loading failed for package ‘coda.plot’
* DONE (coda.plot)
+```
+# cry
+
+
+
+* Version: NA
+* GitHub: NA
+* Source code: https://github.com/cran/cry
+* Number of recursive dependencies: 50
+
+Run `revdepcheck::cloud_details(, "cry")` for more info
+
+
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
```
# ctsem
-* Version: 3.10.2
+* Version: 3.10.3
* GitHub: https://github.com/cdriveraus/ctsem
* Source code: https://github.com/cran/ctsem
-* Date/Publication: 2025-01-13 11:00:08 UTC
-* Number of recursive dependencies: 158
+* Date/Publication: 2025-06-21 11:00:02 UTC
+* Number of recursive dependencies: 164
Run `revdepcheck::cloud_details(, "ctsem")` for more info
@@ -326,80 +361,6 @@ ERROR: compilation failed for package ‘ctsem’
* removing ‘/tmp/workdir/ctsem/old/ctsem.Rcheck/ctsem’
-```
-# deeptime
-
-
-
-* Version: 2.1.0
-* GitHub: https://github.com/willgearty/deeptime
-* Source code: https://github.com/cran/deeptime
-* Date/Publication: 2024-10-25 23:30:02 UTC
-* Number of recursive dependencies: 195
-
-Run `revdepcheck::cloud_details(, "deeptime")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘deeptime’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/deeptime/new/deeptime.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘deeptime’ ...
-** package ‘deeptime’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-** help
-*** installing help indices
-...
-** testing if installed package can be loaded from temporary location
-Error: package or namespace load failed for ‘deeptime’:
- .onLoad failed in loadNamespace() for 'deeptime', details:
- call: NULL
- error: object properties are invalid:
-- @hjust must be , , or , not
-Error: loading failed
-Execution halted
-ERROR: loading failed
-* removing ‘/tmp/workdir/deeptime/new/deeptime.Rcheck/deeptime’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘deeptime’ ...
-** package ‘deeptime’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-** help
-*** installing help indices
-*** copying figures
-** building package indices
-** installing vignettes
-** 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 (deeptime)
-
-
```
# EcoEnsemble
@@ -547,7 +508,7 @@ ERROR: configuration failed for package ‘fio’
* GitHub: https://github.com/ggobi/ggally
* Source code: https://github.com/cran/GGally
* Date/Publication: 2024-02-14 00:53:32 UTC
-* Number of recursive dependencies: 143
+* Number of recursive dependencies: 142
Run `revdepcheck::cloud_details(, "GGally")` for more info
@@ -881,65 +842,6 @@ ERROR: lazy loading failed for package ‘ggtern’
* DONE (ggtern)
-```
-# inventorize
-
-
-
-* Version: 1.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/inventorize
-* Date/Publication: 2025-05-28 13:20:02 UTC
-* Number of recursive dependencies: 68
-
-Run `revdepcheck::cloud_details(, "inventorize")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘inventorize’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘inventorize’ ...
-** package ‘inventorize’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** byte-compile and prepare package for lazy loading
-Error in pm[[2]] : subscript out of bounds
-Error: unable to load R code in package ‘inventorize’
-Execution halted
-ERROR: lazy loading failed for package ‘inventorize’
-* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘inventorize’ ...
-** package ‘inventorize’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** byte-compile and prepare package for lazy loading
-Warning in qgamma(service_level, alpha, beta) : NaNs produced
-** 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 (inventorize)
-
-
```
# metabolic
@@ -964,9 +866,9 @@ Run `revdepcheck::cloud_details(, "metabolic")` for more info
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
+ gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+ GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘metabolic/DESCRIPTION’ ... OK
@@ -994,9 +896,9 @@ Status: 2 NOTEs
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
+ gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+ GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘metabolic/DESCRIPTION’ ... OK
@@ -1197,6 +1099,64 @@ Run `revdepcheck::cloud_details(, "OpenMx")` for more info
+```
+# pacta.loanbook
+
+
+
+* Version: 0.1.0
+* GitHub: https://github.com/RMI-PACTA/pacta.loanbook
+* Source code: https://github.com/cran/pacta.loanbook
+* Date/Publication: 2025-03-17 20:50:02 UTC
+* Number of recursive dependencies: 115
+
+Run `revdepcheck::cloud_details(, "pacta.loanbook")` for more info
+
+
+
+## In both
+
+* checking whether package ‘pacta.loanbook’ can be installed ... ERROR
+ ```
+ Installation failed.
+ See ‘/tmp/workdir/pacta.loanbook/new/pacta.loanbook.Rcheck/00install.out’ for details.
+ ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘pacta.loanbook’ ...
+** package ‘pacta.loanbook’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+Error : 'market_share' is not an exported object from 'namespace:r2dii.plot'
+Error: unable to load R code in package ‘pacta.loanbook’
+Execution halted
+ERROR: lazy loading failed for package ‘pacta.loanbook’
+* removing ‘/tmp/workdir/pacta.loanbook/new/pacta.loanbook.Rcheck/pacta.loanbook’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘pacta.loanbook’ ...
+** package ‘pacta.loanbook’ successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** inst
+** byte-compile and prepare package for lazy loading
+Error : 'market_share' is not an exported object from 'namespace:r2dii.plot'
+Error: unable to load R code in package ‘pacta.loanbook’
+Execution halted
+ERROR: lazy loading failed for package ‘pacta.loanbook’
+* removing ‘/tmp/workdir/pacta.loanbook/old/pacta.loanbook.Rcheck/pacta.loanbook’
+
+
```
# PieGlyph
@@ -1653,9 +1613,9 @@ Run `revdepcheck::cloud_details(, "streamDAG")` for more info
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
+ gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+ GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘streamDAG/DESCRIPTION’ ... OK
@@ -1681,9 +1641,9 @@ Status: 1 ERROR
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
- gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
- GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
-* running under: Ubuntu 24.04.1 LTS
+ gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+ GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
+* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘streamDAG/DESCRIPTION’ ... OK
@@ -1958,7 +1918,7 @@ ERROR: configuration failed for package ‘TriDimRegression’
* GitHub: https://github.com/UUPharmacometrics/xpose
* Source code: https://github.com/cran/xpose
* Date/Publication: 2025-01-07 20:00:02 UTC
-* Number of recursive dependencies: 105
+* Number of recursive dependencies: 104
Run `revdepcheck::cloud_details(, "xpose")` for more info
diff --git a/revdep/problems.md b/revdep/problems.md
index 4739d325b9..075f42dd58 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,77 +1,3 @@
-# activAnalyzer
-
-
-
-* Version: 2.1.2
-* GitHub: https://github.com/pydemull/activAnalyzer
-* Source code: https://github.com/cran/activAnalyzer
-* Date/Publication: 2024-09-23 23:40:02 UTC
-* Number of recursive dependencies: 145
-
-Run `revdepcheck::cloud_details(, "activAnalyzer")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘activAnalyzer.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.8Mb
- sub-directories of 1Mb or more:
- R 1.5Mb
- doc 1.0Mb
- extdata 2.0Mb
- ```
-
-# actxps
-
-
-
-* Version: 1.6.0
-* GitHub: https://github.com/mattheaphy/actxps
-* Source code: https://github.com/cran/actxps
-* Date/Publication: 2025-01-07 13:00:02 UTC
-* Number of recursive dependencies: 129
-
-Run `revdepcheck::cloud_details(, "actxps")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘actxps.Rmd’ using rmarkdown
-
- Quitting from actxps.Rmd:10-18 [setup]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `get()`:
- ! object 'ggplot_build.ggplot' not found
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'transactions.Rmd' failed with diagnostics:
- object 'ggplot_build.ggplot' not found
- --- failed re-building ‘transactions.Rmd’
-
- SUMMARY: processing the following files failed:
- ‘actxps.Rmd’ ‘misc.Rmd’ ‘transactions.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
# adklakedata
@@ -222,28 +148,6 @@ Run `revdepcheck::cloud_details(, "adw")` for more info
Execution halted
```
-# AeRobiology
-
-
-
-* Version: 2.0.1
-* GitHub: NA
-* Source code: https://github.com/cran/AeRobiology
-* Date/Publication: 2019-06-03 06:20:03 UTC
-* Number of recursive dependencies: 94
-
-Run `revdepcheck::cloud_details(, "AeRobiology")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘my-vignette.Rmd’ using rmarkdown
- ```
-
# afex
@@ -410,16 +314,17 @@ Run `revdepcheck::cloud_details(, "AnalysisLin")` for more info
Running examples in ‘AnalysisLin-Ex.R’ failed
The error most likely occurred in:
- > ### Name: bar_plot
- > ### Title: Bar Plots for Categorical Variables
- > ### Aliases: bar_plot
+ > ### Name: qq_plot
+ > ### Title: QQ Plots for Numerical Variables
+ > ### Aliases: qq_plot
>
> ### ** Examples
>
- > data(iris)
- > bar_plot(iris)
- Error in pm[[2]] : subscript out of bounds
- Calls: bar_plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list
+ > data(mtcars)
+ > qq_plot(mtcars)
+ Error in eval(substitute(expr), data, enclos = parent.frame()) :
+ object 'x' not found
+ Calls: qq_plot ... to_basic.GeomAbline -> with -> with.default -> eval -> eval
Execution halted
```
@@ -662,109 +567,6 @@ Run `revdepcheck::cloud_details(, "APackOfTheClones")` for more info
libs 5.3Mb
```
-# APCtools
-
-
-
-* Version: 1.0.4
-* GitHub: https://github.com/bauer-alex/APCtools
-* Source code: https://github.com/cran/APCtools
-* Date/Publication: 2023-01-13 23:30:02 UTC
-* Number of recursive dependencies: 112
-
-Run `revdepcheck::cloud_details(, "APCtools")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘APCtools-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_densityMatrix
- > ### Title: Create a matrix of density plots
- > ### Aliases: plot_densityMatrix
- >
- > ### ** Examples
- >
- > library(APCtools)
- ...
- 2.2.0 and is now defunct.
- ℹ Please use the `rows` argument instead.
- Backtrace:
- ▆
- 1. └─APCtools::plot_densityMatrix(...)
- 2. └─ggplot2::facet_grid(facets = facet_formula, switch = "y")
- 3. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
- 4. └─lifecycle:::deprecate_stop0(msg)
- 5. └─rlang::cnd_signal(...)
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(APCtools)
- >
- > test_check("APCtools")
- Loading required package: nlme
- This is mgcv 1.9-1. For overview type 'help("mgcv-package")'.
- Excluding 9565 missing observations of mainTrip_distance...
- ...
- ▆
- 1. └─APCtools::plot_densityMatrix(...) at test-plots_descriptive.R:148:3
- 2. └─ggplot2::facet_grid(facets = facet_formula, switch = "y")
- 3. └─lifecycle::deprecate_stop("2.2.0", "facet_grid(facets)", "facet_grid(rows)")
- 4. └─lifecycle:::deprecate_stop0(msg)
- 5. └─rlang::cnd_signal(...)
-
- [ FAIL 2 | WARN 51 | SKIP 0 | PASS 84 ]
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘main_functionality.Rmd’ using rmarkdown
- ```
-
-# aplot
-
-
-
-* Version: 0.2.5
-* GitHub: https://github.com/YuLab-SMU/aplot
-* Source code: https://github.com/cran/aplot
-* Date/Publication: 2025-02-27 03:50:02 UTC
-* Number of recursive dependencies: 47
-
-Run `revdepcheck::cloud_details(, "aplot")` for more info
-
-
-
-## Newly broken
-
-* checking S3 generic/method consistency ... WARNING
- ```
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.axisAlign:
- function(object, plot, object_name)
-
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.alab:
- function(object, plot, object_name)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
- ```
-
# applicable
@@ -856,97 +658,6 @@ Run `revdepcheck::cloud_details(, "arena2r")` for more info
All declared Imports should be used.
```
-# ARUtools
-
-
-
-* Version: 0.7.2
-* GitHub: https://github.com/ARUtools/ARUtools
-* Source code: https://github.com/cran/ARUtools
-* Date/Publication: 2025-03-19 19:20:05 UTC
-* Number of recursive dependencies: 140
-
-Run `revdepcheck::cloud_details(, "ARUtools")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ARUtools-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: calc_selection_weights
- > ### Title: Calculate Selection Weights
- > ### Aliases: calc_selection_weights
- >
- > ### ** Examples
- >
- > s <- clean_site_index(example_sites_clean,
- ...
- + calc_sun()
- Extracting ARU info...
- Extracting Dates and Times...
- Joining by columns `date_time_start` and `date_time_end`
- >
- > params <- sim_selection_weights()
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(ARUtools)
- >
- > test_check("ARUtools")
- sh: 1: sox: not found
- Extracting Dates and Times...
- ! Omitted 1 extra, non-json/GPS files
- ...
- 13. │ └─base::force(code)
- 14. └─S7:::Ops.S7_object((p1 + p2)/p3, ggplot2::theme_minimal(base_size = 14))
-
- [ FAIL 1 | WARN 0 | SKIP 5 | PASS 567 ]
- Deleting unused snapshots:
- • 08_selections/sim-selection-weights1.svg
- • 08_selections/sim-selection-weights2.svg
- • 08_selections/sim-selection-weights3.svg
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘ARUtools.Rmd’ using rmarkdown
- --- finished re-building ‘ARUtools.Rmd’
-
- --- re-building ‘Misc.Rmd’ using rmarkdown
- --- finished re-building ‘Misc.Rmd’
-
- --- re-building ‘SubSample.Rmd’ using rmarkdown
-
- Quitting from SubSample.Rmd:115-124 [unnamed-chunk-5]
- ...
- --- finished re-building ‘spatial.Rmd’
-
- --- re-building ‘timezones.Rmd’ using rmarkdown
- --- finished re-building ‘timezones.Rmd’
-
- SUMMARY: processing the following files failed:
- ‘SubSample.Rmd’ ‘multisampling.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
# ASRgenomics
@@ -1104,31 +815,6 @@ Run `revdepcheck::cloud_details(, "autoplotly")` for more info
## Newly broken
-* checking examples ... ERROR
- ```
- Running examples in ‘autoplotly-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: autoplotly
- > ### Title: Automatic Visualization of Popular Statistical Results Using
- > ### 'plotly.js' and 'ggplot2'
- > ### Aliases: autoplotly
- >
- > ### ** Examples
- >
- ...
- > p <- autoplotly(prcomp(iris[c(1, 2, 3, 4)]), data = iris,
- + colour = 'Species', label = TRUE, label.size = 3, frame = TRUE)
- Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
- ℹ Please use tidy evaluation idioms with `aes()`.
- ℹ See also `vignette("ggplot2-in-packages")` for more information.
- ℹ The deprecated feature was likely used in the ggfortify package.
- Please report the issue at .
- Error in pm[[2]] : subscript out of bounds
- Calls: autoplotly ... autoplotly.default -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
* checking tests ... ERROR
```
Running ‘testthat.R’
@@ -1138,82 +824,22 @@ Run `revdepcheck::cloud_details(, "autoplotly")` for more info
> library(autoplotly)
>
> test_check("autoplotly")
- [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ]
+ [ FAIL 2 | WARN 1 | SKIP 0 | PASS 5 ]
══ Failed tests ════════════════════════════════════════════════════════════════
...
- ▆
- 1. ├─autoplotly::autoplotly(...) at test_all.R:26:3
- 2. └─autoplotly:::autoplotly.default(...)
- 3. ├─plotly::ggplotly(...)
- 4. └─plotly:::ggplotly.ggplot(...)
- 5. └─plotly::gg2list(...)
+ `expected`: TRUE
+ ── Failure ('test_all.R:16:3'): autoplotly is composable with additional ggplot2 elements ──
+ inherits(p$ggplot_obj, "ggplot") is not TRUE
- [ FAIL 3 | WARN 1 | SKIP 0 | PASS 1 ]
+ `actual`: FALSE
+ `expected`: TRUE
+
+ [ FAIL 2 | WARN 1 | SKIP 0 | PASS 5 ]
Error: Test failures
Execution halted
```
-# autoReg
-
-
-
-* Version: 0.3.3
-* GitHub: https://github.com/cardiomoon/autoReg
-* Source code: https://github.com/cran/autoReg
-* Date/Publication: 2023-11-14 05:53:27 UTC
-* Number of recursive dependencies: 216
-
-Run `revdepcheck::cloud_details(, "autoReg")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘autoReg-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: modelPlot
- > ### Title: Draw coefficients/odds ratio/hazard ratio plot
- > ### Aliases: modelPlot
- >
- > ### ** Examples
- >
- > fit=lm(mpg~wt*hp+am,data=mtcars)
- > modelPlot(fit,widths=c(1,0,2,3))
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘Automatic_Regression_Modeling.Rmd’ using rmarkdown
-
- Quitting from Automatic_Regression_Modeling.Rmd:141-143 [unnamed-chunk-15]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error:
- ! Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- ...
- Error: processing vignette 'Getting_started.Rmd' failed with diagnostics:
- Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- --- failed re-building ‘Getting_started.Rmd’
-
- --- re-building ‘Statiastical_test_in_gaze.Rmd’ using rmarkdown
- --- finished re-building ‘Statiastical_test_in_gaze.Rmd’
-
- --- re-building ‘Survival.Rmd’ using rmarkdown
- ```
-
# bartMan
@@ -1222,7 +848,7 @@ Run `revdepcheck::cloud_details(, "autoReg")` for more info
* GitHub: NA
* Source code: https://github.com/cran/bartMan
* Date/Publication: 2024-07-24 12:10:02 UTC
-* Number of recursive dependencies: 133
+* Number of recursive dependencies: 132
Run `revdepcheck::cloud_details(, "bartMan")` for more info
@@ -1386,58 +1012,17 @@ Run `revdepcheck::cloud_details(, "BayesCVI")` for more info
See ‘/tmp/workdir/BayesCVI/new/BayesCVI.Rcheck/00install.out’ for details.
```
-# BayesERtools
+# BayesianReasoning
-* Version: 0.2.2
-* GitHub: NA
-* Source code: https://github.com/cran/BayesERtools
-* Date/Publication: 2025-06-06 20:20:02 UTC
-* Number of recursive dependencies: 215
+* Version: 0.4.2
+* GitHub: https://github.com/gorkang/BayesianReasoning
+* Source code: https://github.com/cran/BayesianReasoning
+* Date/Publication: 2023-11-14 11:33:20 UTC
+* Number of recursive dependencies: 104
-Run `revdepcheck::cloud_details(, "BayesERtools")` 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
- ...
- ── Failure ('test-plot_ermod.R:183:5'): plot_er show caption ───────────────────
- `plot_er(...)` produced warnings.
- ── Failure ('test-plot_ermod.R:194:3'): plot_er show caption ───────────────────
- `plot_er(...)` produced warnings.
- ── Failure ('test-plot_ermod.R:209:5'): plot_er_gof ────────────────────────────
- `plot_er_gof(ermod_bin, show_coef_exp = TRUE, show_caption = TRUE)` produced warnings.
-
- [ FAIL 8 | WARN 3 | SKIP 0 | PASS 168 ]
- Error: Test failures
- Execution halted
- ```
-
-# BayesianReasoning
-
-
-
-* Version: 0.4.2
-* GitHub: https://github.com/gorkang/BayesianReasoning
-* Source code: https://github.com/cran/BayesianReasoning
-* Date/Publication: 2023-11-14 11:33:20 UTC
-* Number of recursive dependencies: 105
-
-Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info
+Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info
@@ -1468,57 +1053,6 @@ Run `revdepcheck::cloud_details(, "BayesianReasoning")` for more info
Execution halted
```
-# BayesMallows
-
-
-
-* Version: 2.2.3
-* GitHub: https://github.com/ocbe-uio/BayesMallows
-* Source code: https://github.com/cran/BayesMallows
-* Date/Publication: 2025-01-14 11:30:02 UTC
-* Number of recursive dependencies: 78
-
-Run `revdepcheck::cloud_details(, "BayesMallows")` 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
- ...
- `expected` is a character vector ('interaction(chain, cluster)')
- ── Failure ('test-assess_convergence.R:217:3'): assess_convergence.BayesMallowsMixtures works ──
- p$labels$colour (`actual`) not equal to "cluster" (`expected`).
-
- `actual` is NULL
- `expected` is a character vector ('cluster')
-
- [ FAIL 10 | WARN 0 | SKIP 10 | PASS 363 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 23.8Mb
- sub-directories of 1Mb or more:
- doc 2.7Mb
- libs 20.2Mb
- ```
-
# BayesMultiMode
@@ -1551,57 +1085,6 @@ Run `revdepcheck::cloud_details(, "BayesMultiMode")` for more info
help 6.1Mb
```
-# bayesplot
-
-
-
-* Version: 1.12.0
-* GitHub: https://github.com/stan-dev/bayesplot
-* Source code: https://github.com/cran/bayesplot
-* Date/Publication: 2025-04-10 10:10:06 UTC
-* Number of recursive dependencies: 126
-
-Run `revdepcheck::cloud_details(, "bayesplot")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(bayesplot)
- This is bayesplot version 1.12.0
- - Online documentation and vignettes at mc-stan.org/bayesplot
- - bayesplot theme set to bayesplot::theme_default()
- * Does _not_ affect other ggplot2 plots
- * See ?bayesplot_theme_set for details on theme setting
- ...
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Failure ('test-mcmc-traces.R:59:3'): mcmc_trace options work ────────────────
- all(c("xmin", "xmax", "ymin", "ymax") %in% names(ll)) is not TRUE
-
- `actual`: FALSE
- `expected`: TRUE
-
- [ FAIL 1 | WARN 2 | SKIP 74 | PASS 1032 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 9.2Mb
- sub-directories of 1Mb or more:
- R 5.0Mb
- doc 3.5Mb
- ```
-
# BCEA
@@ -1865,11 +1348,11 @@ Run `revdepcheck::cloud_details(, "biclustermd")` for more info
-* Version: 1.2.2
+* Version: 1.3.0
* GitHub: https://github.com/biometryhub/biometryassist
* Source code: https://github.com/cran/biometryassist
-* Date/Publication: 2025-04-23 15:00:07 UTC
-* Number of recursive dependencies: 81
+* Date/Publication: 2025-06-11 11:00:12 UTC
+* Number of recursive dependencies: 85
Run `revdepcheck::cloud_details(, "biometryassist")` for more info
@@ -1887,16 +1370,16 @@ Run `revdepcheck::cloud_details(, "biometryassist")` for more info
>
> test_check("biometryassist")
Starting 2 test processes
- [ FAIL 1 | WARN 4 | SKIP 122 | PASS 170 ]
+ [ FAIL 7 | WARN 0 | SKIP 157 | PASS 311 ]
...
- • resplot/resplot-for-asreml-pt-1.svg
• resplot/resplot-for-asreml-pt-2.svg
• resplot/resplot-for-asreml-pt-3.svg
• resplot/resplot-for-asreml-single.svg
• resplot/resplot-for-lme4.svg
• resplot/resplot-for-sommer-mmer.svg
• resplot/resplot-for-sommer-mmes.svg
+ • resplot/resplot-onepage-true.svg
• resplot/resplot-with-smaller-call.svg
Error: Test failures
Execution halted
@@ -1981,88 +1464,6 @@ Run `revdepcheck::cloud_details(, "BiVariAn")` for more info
Execution halted
```
-# blockCV
-
-
-
-* Version: 3.1-5
-* GitHub: https://github.com/rvalavi/blockCV
-* Source code: https://github.com/cran/blockCV
-* Date/Publication: 2024-11-01 08:20:02 UTC
-* Number of recursive dependencies: 145
-
-Run `revdepcheck::cloud_details(, "blockCV")` 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
- ...
- ── Failure ('test-cv_plot.R:20:13'): test that cv_plot function works ──────────
- `plt` has type 'object', not 'list'.
- ── Failure ('test-cv_similarity.R:23:13'): test that cv_similarity function works with cv_spatil ──
- `plt` has type 'object', not 'list'.
- ── Failure ('test-cv_similarity.R:39:13'): test that cv_similarity function works with cv_buffer ──
- `plt` has type 'object', not 'list'.
-
- [ FAIL 3 | WARN 0 | SKIP 1 | PASS 316 ]
- Error: Test failures
- Execution halted
- ```
-
-# boxly
-
-
-
-* Version: 0.1.1
-* GitHub: https://github.com/Merck/boxly
-* Source code: https://github.com/cran/boxly
-* Date/Publication: 2023-10-24 02:40:02 UTC
-* Number of recursive dependencies: 87
-
-Run `revdepcheck::cloud_details(, "boxly")` 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
- ...
- 16. ├─plotly::add_trace(...)
- 17. │ └─plotly::add_data(p, data)
- 18. │ └─plotly:::is.plotly(p)
- 19. ├─plotly::ggplotly(p, tooltip = "text", dynamicTicks = TRUE)
- 20. └─plotly:::ggplotly.ggplot(p, tooltip = "text", dynamicTicks = TRUE)
- 21. └─plotly::gg2list(...)
-
- [ FAIL 2 | WARN 0 | SKIP 0 | PASS 25 ]
- Error: Test failures
- Execution halted
- ```
-
# brolgar
@@ -2106,21 +1507,6 @@ Run `revdepcheck::cloud_details(, "brolgar")` for more info
```
Error(s) in re-building vignettes:
--- re-building ‘exploratory-modelling.Rmd’ using rmarkdown
-
- Quitting from exploratory-modelling.Rmd:46-56 [use-gg-highlight]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- NULL
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'exploratory-modelling.Rmd' failed with diagnostics:
- ℹ In index: 1.
- ℹ With name: geom_line.
- Caused by error in `aes_param_name %in% names(non_null_default_aes) && is.na(non_null_default_aes[[
- aes_param_name]])`:
- ! 'length = 2' in coercion to 'logical(1)'
- --- failed re-building ‘exploratory-modelling.Rmd’
-
- --- re-building ‘finding-features.Rmd’ using rmarkdown
```
# bullseye
@@ -2173,47 +1559,6 @@ Run `revdepcheck::cloud_details(, "bullseye")` for more info
--- re-building ‘integrating.Rmd’ using rmarkdown
```
-# calibmsm
-
-
-
-* Version: 1.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/calibmsm
-* Date/Publication: 2025-06-06 11:10:02 UTC
-* Number of recursive dependencies: 171
-
-Run `revdepcheck::cloud_details(, "calibmsm")` 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
- ...
- [2] "ggplot" -
- [3] "ggplot2::gg" -
- [4] "S7_object" -
- [5] "gg" | "gg" [1]
- - "ggplot" [2]
- [6] "ggarrange" | "ggarrange" [3]
-
- [ FAIL 5 | WARN 0 | SKIP 15 | PASS 210 ]
- Error: Test failures
- Execution halted
- ```
-
# calmr
@@ -2250,7 +1595,7 @@ Run `revdepcheck::cloud_details(, "calmr")` for more info
── Failure ('test-graphs.R:25:3'): calmr_model_graph takes a trial ─────────────
`g` does not have names.
- [ FAIL 4 | WARN 5 | SKIP 0 | PASS 246 ]
+ [ FAIL 4 | WARN 0 | SKIP 0 | PASS 246 ]
Error: Test failures
Execution halted
```
@@ -2351,45 +1696,27 @@ Run `revdepcheck::cloud_details(, "carbonr")` for more info
Note: found 710 marked UTF-8 strings
```
-# cartograflow
+# caretEnsemble
-* Version: 1.0.5
-* GitHub: https://github.com/fbahoken/cartogRaflow
-* Source code: https://github.com/cran/cartograflow
-* Date/Publication: 2023-10-17 22:40:21 UTC
-* Number of recursive dependencies: 98
+* Version: 4.0.1
+* GitHub: https://github.com/zachmayer/caretEnsemble
+* Source code: https://github.com/cran/caretEnsemble
+* Date/Publication: 2024-09-12 21:50:09 UTC
+* Number of recursive dependencies: 174
-Run `revdepcheck::cloud_details(, "cartograflow")` for more info
+Run `revdepcheck::cloud_details(, "caretEnsemble")` for more info
## Newly broken
-* checking examples ... ERROR
+* checking installed package size ... NOTE
```
- Running examples in ‘cartograflow-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: flowgini
- > ### Title: Analysis of flow concentration (Gini coefficient)
- > ### Aliases: flowgini
- >
- > ### ** Examples
- >
- > library(cartograflow)
- ...
- ℹ Use `flowcum` instead.
- Warning: Use of `x$linkcum` is discouraged.
- ℹ Use `linkcum` instead.
- Warning: Use of `x$flowcum` is discouraged.
- ℹ Use `flowcum` instead.
- Warning: Use of `x$flowcum` is discouraged.
- ℹ Use `flowcum` instead.
- Error in pm[[2]] : subscript out of bounds
- Calls: flowgini ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
+ installed size is 5.2Mb
+ sub-directories of 1Mb or more:
+ data 4.5Mb
```
# cartographr
@@ -2442,56 +1769,6 @@ Run `revdepcheck::cloud_details(, "cartographr")` for more info
data 3.5Mb
```
-# cats
-
-
-
-* Version: 1.0.2
-* GitHub: NA
-* Source code: https://github.com/cran/cats
-* Date/Publication: 2022-03-11 10:20:07 UTC
-* Number of recursive dependencies: 80
-
-Run `revdepcheck::cloud_details(, "cats")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘cats-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: trial_ocs
- > ### Title: Calculates the operating characteristics of the cohort trial
- > ### Aliases: trial_ocs
- >
- > ### ** Examples
- >
- >
- ...
- + safety_prob = safety_prob, Bayes_Sup1 = Bayes_Sup1, Bayes_Sup2 = Bayes_Sup2,
- + cohort_offset = cohort_offset, sr_first_pos = sr_first_pos,
- + missing_prob = missing_prob, cohort_fixed = cohort_fixed, accrual_type = accrual_type,
- + accrual_param = accrual_param, hist_lag = hist_lag, analysis_times = analysis_times,
- + time_trend = time_trend, cohorts_start = cohorts_start, cohorts_sim = cohorts_sim,
- + iter = 2, coresnum = 1, save = FALSE, ret_list = TRUE, plot_ocs = TRUE
- + )
- Error in pm[[2]] : subscript out of bounds
- Calls: trial_ocs -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘epitools’ ‘forcats’ ‘purrr’
- All declared Imports should be used.
- ```
-
# causact
@@ -2648,7 +1925,7 @@ Run `revdepcheck::cloud_details(, "centerline")` for more info
* GitHub: NA
* Source code: https://github.com/cran/Certara.Xpose.NLME
* Date/Publication: 2025-01-28 15:50:10 UTC
-* Number of recursive dependencies: 99
+* Number of recursive dependencies: 98
Run `revdepcheck::cloud_details(, "Certara.Xpose.NLME")` for more info
@@ -2710,208 +1987,18 @@ Run `revdepcheck::cloud_details(, "cheem")` for more info
https://github.com/nspyrison/cheem/issues/
--------------------------------------------------------
...
- 13. │ ├─utils::modifyList(x %||% list(), y %||% list(), ...)
- 14. │ │ └─base::stopifnot(is.list(x), is.list(val))
- 15. │ └─x %||% list()
- 16. ├─plotly::ggplotly(...)
- 17. └─plotly:::ggplotly.ggplot(...)
- 18. └─plotly::gg2list(...)
+ `expected[2:2]`: "ggplot"
+ ── Failure ('test-2_visualization.r:66:3'): radial_cheem_tour ──────────────────
+ class(r_ggt) (`actual`) not equal to c("gg", "ggplot") (`expected`).
+
+ `actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
+ `expected[2:2]`: "ggplot"
- [ FAIL 3 | WARN 0 | SKIP 0 | PASS 8 ]
+ [ FAIL 6 | WARN 0 | SKIP 0 | PASS 10 ]
Error: Test failures
Execution halted
```
-# ChemoSpec
-
-
-
-* Version: 6.1.11
-* GitHub: https://github.com/bryanhanson/ChemoSpec
-* Source code: https://github.com/cran/ChemoSpec
-* Date/Publication: 2025-04-15 15:00:09 UTC
-* Number of recursive dependencies: 160
-
-Run `revdepcheck::cloud_details(, "ChemoSpec")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘ChemoSpec.Rmd’ using rmarkdown
-
- Quitting from ChemoSpec.Rmd:464-468 [load1]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error:
- ! Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- ...
- Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- --- failed re-building ‘ChemoSpec.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘ChemoSpec.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-# ChemoSpecUtils
-
-
-
-* Version: 1.0.5
-* GitHub: https://github.com/bryanhanson/ChemoSpecUtils
-* Source code: https://github.com/cran/ChemoSpecUtils
-* Date/Publication: 2025-04-12 15:30:04 UTC
-* Number of recursive dependencies: 98
-
-Run `revdepcheck::cloud_details(, "ChemoSpecUtils")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ChemoSpecUtils-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: GraphicsOptions
- > ### Title: Graphic Output Options in ChemoSpec and ChemoSpec2D
- > ### Aliases: GraphicsOptions
- > ### Keywords: utilities
- >
- > ### ** Examples
- >
- ...
- ℹ Adding new coordinate system, which will replace the existing one.
- Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
- ℹ Please use tidy evaluation idioms with `aes()`.
- ℹ See also `vignette("ggplot2-in-packages")` for more information.
- ℹ The deprecated feature was likely used in the ChemoSpec package.
- Please report the issue at .
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-# chillR
-
-
-
-* Version: 0.76
-* GitHub: NA
-* Source code: https://github.com/cran/chillR
-* Date/Publication: 2024-11-14 09:40:02 UTC
-* Number of recursive dependencies: 133
-
-Run `revdepcheck::cloud_details(, "chillR")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘chillR-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_scenarios
- > ### Title: Plot historic and future scenarios for climate-related metrics
- > ### (ggplot2 version)
- > ### Aliases: plot_scenarios
- >
- > ### ** Examples
- >
- ...
- > # Plot the climate scenarios
- >
- > plot_scenarios(climate_scenario_list, metric = 'Chill_Portions',
- + add_historic = TRUE, size = 2, shape = 3, color = 'blue',
- + outlier_shape = 12, historic_color = 'skyblue',
- + group_by = c("Year", "Scenario"))
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-# chronicle
-
-
-
-* Version: 0.3
-* GitHub: NA
-* Source code: https://github.com/cran/chronicle
-* Date/Publication: 2021-06-25 05:00:02 UTC
-* Number of recursive dependencies: 143
-
-Run `revdepcheck::cloud_details(, "chronicle")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘chronicle-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: make_barplot
- > ### Title: Create a bar plot from a data frame through ggplotly
- > ### Aliases: make_barplot
- >
- > ### ** Examples
- >
- > make_barplot(dt = iris, bars = 'Species', value = 'Sepal.Length')
- Error in pm[[2]] : subscript out of bounds
- Calls: make_barplot -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- ...
- --- re-building ‘chronicle.Rmd’ using rmarkdown
-
- Quitting from chronicle.Rmd:37-67 [unnamed-chunk-3]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- NULL
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'chronicle.Rmd' failed with diagnostics:
- ...
- ℹ In index: 1.
- Caused by error in `pm[[2]]`:
- ! subscript out of bounds
- --- failed re-building ‘chronicle.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘chronicle.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘DT’ ‘dplyr’ ‘prettydoc’ ‘rmdformats’ ‘skimr’
- All declared Imports should be used.
- ```
-
# circumplex
@@ -2920,7 +2007,7 @@ Run `revdepcheck::cloud_details(, "chronicle")` for more info
* GitHub: https://github.com/jmgirard/circumplex
* Source code: https://github.com/cran/circumplex
* Date/Publication: 2024-10-28 04:30:02 UTC
-* Number of recursive dependencies: 94
+* Number of recursive dependencies: 93
Run `revdepcheck::cloud_details(, "circumplex")` for more info
@@ -2953,36 +2040,6 @@ Run `revdepcheck::cloud_details(, "circumplex")` for more info
Execution halted
```
-# classmap
-
-
-
-* Version: 1.2.4
-* GitHub: NA
-* Source code: https://github.com/cran/classmap
-* Date/Publication: 2025-05-13 22:00:02 UTC
-* Number of recursive dependencies: 132
-
-Run `revdepcheck::cloud_details(, "classmap")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘classmap’ can be installed ... WARNING
- ```
- Found the following significant warnings:
- Warning: replacing previous import ‘ggplot2::element’ by ‘e1071::element’ when loading ‘classmap’
- See ‘/tmp/workdir/classmap/new/classmap.Rcheck/00install.out’ for details.
- ```
-
-## In both
-
-* checking data for non-ASCII characters ... NOTE
- ```
- Note: found 9 marked UTF-8 strings
- ```
-
# clifro
@@ -3074,289 +2131,117 @@ Run `revdepcheck::cloud_details(, "climwin")` for more info
Execution halted
```
-# clinDataReview
+# clockSim
-* Version: 1.6.2
-* GitHub: https://github.com/openanalytics/clinDataReview
-* Source code: https://github.com/cran/clinDataReview
-* Date/Publication: 2025-04-11 22:10:02 UTC
-* Number of recursive dependencies: 117
+* Version: 0.1.2
+* GitHub: https://github.com/yeyuan98/clockSim
+* Source code: https://github.com/cran/clockSim
+* Date/Publication: 2025-04-22 20:10:01 UTC
+* Number of recursive dependencies: 78
-Run `revdepcheck::cloud_details(, "clinDataReview")` for more info
+Run `revdepcheck::cloud_details(, "clockSim")` for more info
## Newly broken
-* checking examples ... ERROR
+* checking whether package ‘clockSim’ can be installed ... WARNING
```
- Running examples in ‘clinDataReview-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: scatterplotClinData
- > ### Title: Scatterplot of variables of interest for clinical data
- > ### visualization.
- > ### Aliases: scatterplotClinData
- >
- > ### ** Examples
- >
- ...
- + data = dataPlot,
- + xVar = "ADY",
- + yVar = "LBSTRESN",
- + aesPointVar = list(color = "TRTP", fill = "TRTP"),
- + aesLineVar = list(group = "USUBJID", color = "TRTP"),
- + labelVars = labelVars
- + )
- Error in pm[[2]] : subscript out of bounds
- Calls: scatterplotClinData -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
+ Found the following significant warnings:
+ Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
+ See ‘/tmp/workdir/clockSim/new/clockSim.Rcheck/00install.out’ for details.
```
+# cmcR
+
+
+
+* Version: 0.1.11
+* GitHub: NA
+* Source code: https://github.com/cran/cmcR
+* Date/Publication: 2022-12-10 14:00:02 UTC
+* Number of recursive dependencies: 120
+
+Run `revdepcheck::cloud_details(, "cmcR")` for more info
+
+
+
+## Newly broken
+
* checking tests ... ERROR
```
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
- > library(clinDataReview)
+ > library(cmcR)
>
- > test_check("clinDataReview")
- adding: report.html (deflated 63%)
- adding: report_dependencies172d6f8f416/ (stored 0%)
- adding: report_dependencies172d6f8f416/file172d481ba5e0.html (deflated 8%)
+ > test_check("cmcR",reporter = SummaryReporter)
+ adding: bindata/ (stored 0%)
+ adding: bindata/data.bin (deflated 58%)
+ adding: main.xml (deflated 62%)
...
- Backtrace:
- ▆
- 1. └─clinDataReview::scatterplotClinData(...) at test_scatterplotClinData.R:1001:3
- 2. ├─plotly::ggplotly(p = gg, width = width, height = height, tooltip = if (!is.null(hoverVars)) "text")
- 3. └─plotly:::ggplotly.ggplot(...)
- 4. └─plotly::gg2list(...)
- [ FAIL 31 | WARN 0 | SKIP 31 | PASS 466 ]
+ ── 2. Failure ('test-diagnosticTools.R:104:3'): diagnosticTools functions work a
+ all(unlist(purrr::map(cmcPlt_list, ~class(.) == c("gg", "ggplot")))) is not TRUE
+
+ `actual`: FALSE
+ `expected`: TRUE
+
+ ══ DONE ════════════════════════════════════════════════════════════════════════
Error: Test failures
Execution halted
```
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘clinDataReview-dataPreprocessing.Rmd’ using rmarkdown
- --- finished re-building ‘clinDataReview-dataPreprocessing.Rmd’
-
- --- re-building ‘clinDataReview-dataVisualization.Rmd’ using rmarkdown
-
- Quitting from clinDataReview-dataVisualization.Rmd:169-211 [timeProfiles]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ...
- --- failed re-building ‘clinDataReview-dataVisualization.Rmd’
-
- --- re-building ‘clinDataReview-reporting.Rmd’ using rmarkdown
- --- finished re-building ‘clinDataReview-reporting.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘clinDataReview-dataVisualization.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
## In both
* checking installed package size ... NOTE
```
- installed size is 5.7Mb
+ installed size is 5.5Mb
sub-directories of 1Mb or more:
- doc 4.3Mb
+ data 2.5Mb
+ doc 2.3Mb
```
-# clinUtils
+# cnmap
-* Version: 0.2.0
-* GitHub: https://github.com/openanalytics/clinUtils
-* Source code: https://github.com/cran/clinUtils
-* Date/Publication: 2024-05-17 14:50:06 UTC
-* Number of recursive dependencies: 107
+* Version: 0.1.0
+* GitHub: https://github.com/PanfengZhang/cnmap
+* Source code: https://github.com/cran/cnmap
+* Date/Publication: 2024-04-02 12:42:06 UTC
+* Number of recursive dependencies: 58
-Run `revdepcheck::cloud_details(, "clinUtils")` for more info
+Run `revdepcheck::cloud_details(, "cnmap")` for more info
## Newly broken
-* checking re-building of vignette outputs ... ERROR
+* checking examples ... ERROR
```
- Error(s) in re-building vignettes:
- --- re-building ‘clinUtils-vignette.Rmd’ using rmarkdown
+ Running examples in ‘cnmap-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: getMap
+ > ### Title: China Map Data from AutoNavi Map
+ > ### Aliases: getMap
+ >
+ > ### ** Examples
+ >
+ > library(cnmap)
+ >
+ > map1 <- getMap(code = "110000") # get the map data of Beijing City
+ Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir, :
+ package tibble not available: install first?
+ Calls: getMap ... st_read -> st_read.character -> process_cpl_read_ogr
+ Execution halted
```
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.7Mb
- sub-directories of 1Mb or more:
- doc 6.5Mb
- ```
-
-# clockSim
-
-
-
-* Version: 0.1.2
-* GitHub: https://github.com/yeyuan98/clockSim
-* Source code: https://github.com/cran/clockSim
-* Date/Publication: 2025-04-22 20:10:01 UTC
-* Number of recursive dependencies: 78
-
-Run `revdepcheck::cloud_details(, "clockSim")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘clockSim’ can be installed ... WARNING
- ```
- Found the following significant warnings:
- Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
- See ‘/tmp/workdir/clockSim/new/clockSim.Rcheck/00install.out’ for details.
- ```
-
-# clustcurv
-
-
-
-* Version: 2.0.2
-* GitHub: https://github.com/noramvillanueva/clustcurv
-* Source code: https://github.com/cran/clustcurv
-* Date/Publication: 2024-10-25 08:20:07 UTC
-* Number of recursive dependencies: 106
-
-Run `revdepcheck::cloud_details(, "clustcurv")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘clustcurv.Rmd’ using rmarkdown
-
- Quitting from clustcurv.Rmd:92-94 [unnamed-chunk-5]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'clustcurv.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘clustcurv.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘clustcurv.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-# cmcR
-
-
-
-* Version: 0.1.11
-* GitHub: NA
-* Source code: https://github.com/cran/cmcR
-* Date/Publication: 2022-12-10 14:00:02 UTC
-* Number of recursive dependencies: 120
-
-Run `revdepcheck::cloud_details(, "cmcR")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(cmcR)
- >
- > test_check("cmcR",reporter = SummaryReporter)
- adding: bindata/ (stored 0%)
- adding: bindata/data.bin (deflated 58%)
- adding: main.xml (deflated 62%)
- ...
- ── 2. Failure ('test-diagnosticTools.R:104:3'): diagnosticTools functions work a
- all(unlist(purrr::map(cmcPlt_list, ~class(.) == c("gg", "ggplot")))) is not TRUE
-
- `actual`: FALSE
- `expected`: TRUE
-
- ══ DONE ════════════════════════════════════════════════════════════════════════
- I believe in you!
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.5Mb
- sub-directories of 1Mb or more:
- data 2.5Mb
- doc 2.3Mb
- ```
-
-# cnmap
-
-
-
-* Version: 0.1.0
-* GitHub: https://github.com/PanfengZhang/cnmap
-* Source code: https://github.com/cran/cnmap
-* Date/Publication: 2024-04-02 12:42:06 UTC
-* Number of recursive dependencies: 58
-
-Run `revdepcheck::cloud_details(, "cnmap")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘cnmap-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: getMap
- > ### Title: China Map Data from AutoNavi Map
- > ### Aliases: getMap
- >
- > ### ** Examples
- >
- > library(cnmap)
- >
- > map1 <- getMap(code = "110000") # get the map data of Beijing City
- Error in process_cpl_read_ogr(x, quiet, check_ring_dir = check_ring_dir, :
- package tibble not available: install first?
- Calls: getMap ... st_read -> st_read.character -> process_cpl_read_ogr
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
+* checking re-building of vignette outputs ... ERROR
```
Error(s) in re-building vignettes:
--- re-building ‘Introduction.Rmd’ using rmarkdown
@@ -3381,47 +2266,6 @@ Run `revdepcheck::cloud_details(, "cnmap")` for more info
Execution halted
```
-# CNVreg
-
-
-
-* Version: 1.0
-* GitHub: NA
-* Source code: https://github.com/cran/CNVreg
-* Date/Publication: 2025-03-10 16:50:21 UTC
-* Number of recursive dependencies: 118
-
-Run `revdepcheck::cloud_details(, "CNVreg")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘CNVReg_vig.Rmd’ using rmarkdown
-
- Quitting from CNVReg_vig.Rmd:322-378 [unnamed-chunk-17]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error:
- ! Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- ...
- Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- --- failed re-building ‘CNVReg_vig.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘CNVReg_vig.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
# cocktailApp
@@ -3554,109 +2398,6 @@ ERROR: lazy loading failed for package ‘coda.plot’
```
-# CohortPlat
-
-
-
-* Version: 1.0.5
-* GitHub: NA
-* Source code: https://github.com/cran/CohortPlat
-* Date/Publication: 2022-02-14 09:30:02 UTC
-* Number of recursive dependencies: 79
-
-Run `revdepcheck::cloud_details(, "CohortPlat")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘CohortPlat-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_trial
- > ### Title: Plots the cohort trial study overview given stage data.
- > ### Aliases: plot_trial
- >
- > ### ** Examples
- >
- >
- ...
- + stage_data = stage_data, cohort_random = cohort_random, cohorts_max = cohorts_max,
- + sr_drugs_pos = sr_drugs_pos, target_rr = target_rr, sharing_type = sharing_type,
- + safety_prob = safety_prob, Bayes_Sup = Bayes_Sup, prob_rr_transform = prob_rr_transform,
- + cohort_offset = cohort_offset, Bayes_Fut = Bayes_Fut, sr_first_pos = sr_first_pos
- + )
- >
- > plot_trial(res_list, unit = "n")
- Error in pm[[2]] : subscript out of bounds
- Calls: plot_trial -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘my-vignette.Rmd’ using rmarkdown
-
- Quitting from my-vignette.Rmd:1042-1073 [unnamed-chunk-20]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘my-vignette.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘my-vignette.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-# colorrepel
-
-
-
-* Version: 0.4.1
-* GitHub: https://github.com/raysinensis/color_repel
-* Source code: https://github.com/cran/colorrepel
-* Date/Publication: 2025-01-19 04:50:02 UTC
-* Number of recursive dependencies: 87
-
-Run `revdepcheck::cloud_details(, "colorrepel")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘colorrepel-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: ggplotly_background
- > ### Title: Prepare ggplot object to ggplotly-compatible layer and image
- > ### layer
- > ### Aliases: ggplotly_background
- >
- > ### ** Examples
- >
- > a <- ggplot2::ggplot(ggplot2::mpg, ggplot2::aes(displ, hwy)) +
- + ggplot2::geom_point(ggplot2::aes(color = as.factor(cyl)))
- > new_colors <- color_repel(a)
- > b <- ggplotly_background(a, filename = NULL)
- Error in pm[[2]] : subscript out of bounds
- Calls: ggplotly_background -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# conquestr
@@ -3734,235 +2475,29 @@ Run `revdepcheck::cloud_details(, "constructive")` for more info
Execution halted
```
-# contsurvplot
+# CoSMoS
-* Version: 0.2.1
-* GitHub: https://github.com/RobinDenz1/contsurvplot
-* Source code: https://github.com/cran/contsurvplot
-* Date/Publication: 2023-08-15 08:00:03 UTC
-* Number of recursive dependencies: 156
+* Version: 2.1.0
+* GitHub: https://github.com/TycheLab/CoSMoS
+* Source code: https://github.com/cran/CoSMoS
+* Date/Publication: 2021-05-29 23:20:08 UTC
+* Number of recursive dependencies: 77
-Run `revdepcheck::cloud_details(, "contsurvplot")` for more info
+Run `revdepcheck::cloud_details(, "CoSMoS")` for more info
## Newly broken
-* checking tests ... ERROR
+* checking re-building of vignette outputs ... ERROR
```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(contsurvplot)
- Please cite as:
-
- Denz R, Timmesfeld N (2023). "Visualizing the (Causal) Effect of a Continuous Variable on a Time-To-Event Outcome." Epidemiology, 34 (5). doi: 10.1097/EDE.0000000000001630.
- > library(survival)
- > library(testthat)
- >
- ...
- • plot_surv_contour/plot-change-horizon.svg
- • plot_surv_contour/plot-cif.svg
- • plot_surv_contour/plot-custom-colors.svg
- • plot_surv_contour/plot-defaults.svg
- • plot_surv_contour/plot-lots-of-stuff.svg
- • plot_surv_contour/plot-panel-border-axis-dist.svg
- • plot_surv_contour/plot-with-group.svg
- • plot_surv_heatmap/plot-contour-lines.svg
- Error: Test failures
- Execution halted
+ Error(s) in re-building vignettes:
+ --- re-building ‘vignette.Rmd’ using rmarkdown
```
-# CoreMicrobiomeR
-
-
-
-* Version: 0.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/CoreMicrobiomeR
-* Date/Publication: 2024-04-03 20:03:02 UTC
-* Number of recursive dependencies: 88
-
-Run `revdepcheck::cloud_details(, "CoreMicrobiomeR")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘CoreMicrobiomeR-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: group_bar_plots
- > ### Title: Grouped Bar Plots Based on Sample Size
- > ### Aliases: group_bar_plots
- >
- > ### ** Examples
- >
- > #To run input data
- ...
- + top_percentage = 10 # Adjust the percentage as needed for core/non-core OTUs
- + )
- Warning encountered during diversity analysis:you have empty rows: their dissimilarities may be
- meaningless in method “bray”
- > #To run grouped bar plot function
- > plot_group_bar <- group_bar_plots(core_1$final_otu_table_bef_filter,
- + core_1$final_otu_aft_filter, 10)
- Error in pm[[2]] : subscript out of bounds
- Calls: group_bar_plots -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-# correlationfunnel
-
-
-
-* Version: 0.2.0
-* GitHub: https://github.com/business-science/correlationfunnel
-* Source code: https://github.com/cran/correlationfunnel
-* Date/Publication: 2020-06-09 04:40:03 UTC
-* Number of recursive dependencies: 113
-
-Run `revdepcheck::cloud_details(, "correlationfunnel")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(dplyr)
-
- Attaching package: 'dplyr'
-
- The following object is masked from 'package:testthat':
-
- ...
- ▆
- 1. ├─correlationfunnel::plot_correlation_funnel(...) at test-plot_correlation_funnel.R:23:1
- 2. └─correlationfunnel:::plot_correlation_funnel.data.frame(...)
- 3. ├─plotly::ggplotly(g, tooltip = "text")
- 4. └─plotly:::ggplotly.ggplot(g, tooltip = "text")
- 5. └─plotly::gg2list(...)
-
- [ FAIL 1 | WARN 3 | SKIP 0 | PASS 17 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespace in Imports field not imported from: ‘utils’
- All declared Imports should be used.
- ```
-
-# corrViz
-
-
-
-* Version: 0.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/corrViz
-* Date/Publication: 2023-06-30 11:40:07 UTC
-* Number of recursive dependencies: 126
-
-Run `revdepcheck::cloud_details(, "corrViz")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘corrViz-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: animSolar
- > ### Title: animSolar
- > ### Aliases: animSolar
- >
- > ### ** Examples
- >
- > cm <- cor(mtcars)
- ...
- All aesthetics have length 1, but the data has 250 rows.
- ℹ Please consider using `annotate()` or provide this layer with data containing
- a single row.
- Warning in geom_text(data = solar_system, aes(x = 0, y = 0, label = sun), :
- All aesthetics have length 1, but the data has 250 rows.
- ℹ Please consider using `annotate()` or provide this layer with data containing
- a single row.
- Error in pm[[2]] : subscript out of bounds
- Calls: animSolar -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘corrViz.Rmd’ using rmarkdown
-
- Quitting from corrViz.Rmd:75-81 [heatmap]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'corrViz.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘corrViz.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘corrViz.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.2Mb
- sub-directories of 1Mb or more:
- doc 6.7Mb
- ```
-
-# CoSMoS
-
-
-
-* Version: 2.1.0
-* GitHub: https://github.com/TycheLab/CoSMoS
-* Source code: https://github.com/cran/CoSMoS
-* Date/Publication: 2021-05-29 23:20:08 UTC
-* Number of recursive dependencies: 77
-
-Run `revdepcheck::cloud_details(, "CoSMoS")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘vignette.Rmd’ using rmarkdown
- ```
-
-# countfitteR
+# countfitteR
@@ -4014,54 +2549,6 @@ Run `revdepcheck::cloud_details(, "countfitteR")` for more info
checkRd: (-1) summary_fitlist.Rd:19: Lost braces in \itemize; \value handles \item{}{} directly
```
-# countries
-
-
-
-* Version: 1.2.1
-* GitHub: https://github.com/fbellelli/countries
-* Source code: https://github.com/cran/countries
-* Date/Publication: 2025-02-22 14:10:02 UTC
-* Number of recursive dependencies: 79
-
-Run `revdepcheck::cloud_details(, "countries")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(countries)
- >
- > test_check("countries")
-
- In total 1 unique country names were provided
- 1/1 have been matched with EXACT matching
- ...
- `expected[2:2]`: "ggplot"
- ── Failure ('test_function_output.R:319:3'): output from quick_map() are as expected ──
- class(quick_map(example, "test", col_na = "black")) (`actual`) not equal to c("gg", "ggplot") (`expected`).
-
- `actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
- `expected[2:2]`: "ggplot"
-
- [ FAIL 9 | WARN 0 | SKIP 2 | PASS 137 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking data for non-ASCII characters ... NOTE
- ```
- Note: found 9044 marked UTF-8 strings
- ```
-
# covidcast
@@ -4160,112 +2647,6 @@ Run `revdepcheck::cloud_details(, "cowplot")` for more info
Execution halted
```
-# Coxmos
-
-
-
-* Version: 1.1.3
-* GitHub: https://github.com/BiostatOmics/Coxmos
-* Source code: https://github.com/cran/Coxmos
-* Date/Publication: 2025-06-02 18:02:02 UTC
-* Number of recursive dependencies: 201
-
-Run `revdepcheck::cloud_details(, "Coxmos")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘Coxmos-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_evaluation
- > ### Title: plot_evaluation
- > ### Aliases: plot_evaluation
- >
- > ### ** Examples
- >
- > data("X_proteomic")
- ...
- > Y_test <- Y_proteomic[-index_train,]
- > coxEN.model <- coxEN(X_train, Y_train, x.center = TRUE, x.scale = TRUE)
- Warning: from glmnet C++ code (error code -10013); Number of nonzero coefficients along the path exceeds pmax=7 at 13th lambda value; solutions for larger lambdas returned
- > eval_results <- eval_Coxmos_models(lst_models = list("coxEN" = coxEN.model), X_test = X_test,
- + Y_test = Y_test)
- > plot_eval_results <- plot_evaluation(eval_results)
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.4Mb
- sub-directories of 1Mb or more:
- R 1.5Mb
- data 2.5Mb
- doc 2.8Mb
- ```
-
-# cry
-
-
-
-* Version: 0.5.1
-* GitHub: NA
-* Source code: https://github.com/cran/cry
-* Date/Publication: 2022-10-10 08:00:05 UTC
-* Number of recursive dependencies: 50
-
-Run `revdepcheck::cloud_details(, "cry")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘cry-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_SHELX
- > ### Title: Plot SHELXC log files
- > ### Aliases: plot_SHELX
- >
- > ### ** Examples
- >
- > datadir <- system.file("extdata",package="cry")
- > ## SHELXC
- > shelxc_log <- file.path(datadir,"shelxc.log")
- > shelxc <- read_SHELX_log(shelxc_log)
- > plot_shelxc <- plot_SHELX(filename = shelxc, var = shelxc$I_sig,
- + type = "shelxc", title_chart = "SHELXC")
- Error in rep(yes, length.out = len) :
- attempt to replicate an object of type 'object'
- Calls: plot_SHELX -> ifelse -> ifelse -> ifelse
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘MTZ.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking Rd files ... NOTE
- ```
- checkRd: (-1) calculate_cell_volume.Rd:16: Lost braces; missing escapes or markup?
- 16 | V A real number. The volume (in angstroms^3 or angstroms^{-3})
- | ^
- ```
-
# ctrialsgov
@@ -4295,14 +2676,14 @@ Run `revdepcheck::cloud_details(, "ctrialsgov")` for more info
[NCT03517995] of Sulforaphane in |Bladder| Cancer Chemoprevent
[NCT04210479] Comparison of |Bladder| Filling vs. Non-Fil
...
- ▆
- 1. ├─ctrialsgov::ctgov_to_plotly(p) at test-plot.R:12:3
- 2. └─ctrialsgov:::ctgov_to_plotly.ctgov_bar_plot(p)
- 3. ├─plotly::ggplotly(p, tooltip = "text")
- 4. └─plotly:::ggplotly.ggplot(p, tooltip = "text")
- 5. └─plotly::gg2list(...)
+ [1] "ctgov_bar_plot" - "gg" [2]
+ [2] "ggplot2::ggplot" -
+ [3] "ggplot" -
+ [4] "ggplot2::gg" -
+ [5] "S7_object" -
+ [6] "gg" - "ggplot" [3]
- [ FAIL 1 | WARN 6 | SKIP 0 | PASS 43 ]
+ [ FAIL 1 | WARN 6 | SKIP 0 | PASS 44 ]
Error: Test failures
Execution halted
```
@@ -4314,105 +2695,23 @@ Run `revdepcheck::cloud_details(, "ctrialsgov")` for more info
Note: found 1350 marked UTF-8 strings
```
-# cubble
+# cvms
-* Version: 1.0.0
-* GitHub: https://github.com/huizezhang-sherry/cubble
-* Source code: https://github.com/cran/cubble
-* Date/Publication: 2024-08-27 15:20:02 UTC
-* Number of recursive dependencies: 130
+* Version: 1.7.0
+* GitHub: https://github.com/ludvigolsen/cvms
+* Source code: https://github.com/cran/cvms
+* Date/Publication: 2025-03-07 11:30:07 UTC
+* Number of recursive dependencies: 152
-Run `revdepcheck::cloud_details(, "cubble")` for more info
+Run `revdepcheck::cloud_details(, "cvms")` for more info
## Newly broken
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘cb1class.Rmd’ using rmarkdown
- --- finished re-building ‘cb1class.Rmd’
-
- --- re-building ‘cb2create.Rmd’ using rmarkdown
- --- finished re-building ‘cb2create.Rmd’
-
- --- re-building ‘cb3tsibblesf.Rmd’ using rmarkdown
- --- finished re-building ‘cb3tsibblesf.Rmd’
-
- --- re-building ‘cb4glyph.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 8.6Mb
- sub-directories of 1Mb or more:
- data 6.0Mb
- doc 1.4Mb
- ```
-
-# cutpointr
-
-
-
-* Version: 1.2.0
-* GitHub: https://github.com/thie1e/cutpointr
-* Source code: https://github.com/cran/cutpointr
-* Date/Publication: 2024-12-10 22:50:02 UTC
-* Number of recursive dependencies: 78
-
-Run `revdepcheck::cloud_details(, "cutpointr")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(cutpointr)
- >
- > test_check("cutpointr")
- [ FAIL 105 | WARN 14 | SKIP 0 | PASS 337 ]
-
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ...
- class(tempplot5) not identical to c("gg", "ggplot").
- Lengths differ: 5 is not 2
- Backtrace:
- ▆
- 1. └─cutpointr (local) test_ggplot_functions(cp, do_plot_metric = FALSE) at test-cutpointr.R:1156:5
- 2. └─testthat::expect_identical(class(tempplot5), c("gg", "ggplot")) at test-cutpointr.R:22:5
-
- [ FAIL 105 | WARN 14 | SKIP 0 | PASS 337 ]
- Error: Test failures
- Execution halted
- ```
-
-# cvms
-
-
-
-* Version: 1.7.0
-* GitHub: https://github.com/ludvigolsen/cvms
-* Source code: https://github.com/cran/cvms
-* Date/Publication: 2025-03-07 11:30:07 UTC
-* Number of recursive dependencies: 152
-
-Run `revdepcheck::cloud_details(, "cvms")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
+* checking tests ... ERROR
```
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
@@ -4675,29 +2974,6 @@ Run `revdepcheck::cloud_details(, "DAISIEprep")` for more info
Execution halted
```
-# daltoolbox
-
-
-
-* Version: 1.2.707
-* GitHub: https://github.com/cefet-rj-dal/daltoolbox
-* Source code: https://github.com/cran/daltoolbox
-* Date/Publication: 2025-05-13 06:20:13 UTC
-* Number of recursive dependencies: 99
-
-Run `revdepcheck::cloud_details(, "daltoolbox")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘daltoolbox’ can be installed ... WARNING
- ```
- Found the following significant warnings:
- Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘daltoolbox’
- See ‘/tmp/workdir/daltoolbox/new/daltoolbox.Rcheck/00install.out’ for details.
- ```
-
# dams
@@ -4750,80 +3026,6 @@ Run `revdepcheck::cloud_details(, "Deducer")` for more info
See ‘/tmp/workdir/Deducer/new/Deducer.Rcheck/00install.out’ for details.
```
-# deeptime
-
-
-
-* Version: 2.1.0
-* GitHub: https://github.com/willgearty/deeptime
-* Source code: https://github.com/cran/deeptime
-* Date/Publication: 2024-10-25 23:30:02 UTC
-* Number of recursive dependencies: 195
-
-Run `revdepcheck::cloud_details(, "deeptime")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘deeptime’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/deeptime/new/deeptime.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘deeptime’ ...
-** package ‘deeptime’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-** help
-*** installing help indices
-...
-** testing if installed package can be loaded from temporary location
-Error: package or namespace load failed for ‘deeptime’:
- .onLoad failed in loadNamespace() for 'deeptime', details:
- call: NULL
- error: object properties are invalid:
-- @hjust must be , , or , not
-Error: loading failed
-Execution halted
-ERROR: loading failed
-* removing ‘/tmp/workdir/deeptime/new/deeptime.Rcheck/deeptime’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘deeptime’ ...
-** package ‘deeptime’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-** help
-*** installing help indices
-*** copying figures
-** building package indices
-** installing vignettes
-** 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 (deeptime)
-
-
-```
# dendextend
@@ -4886,98 +3088,6 @@ Run `revdepcheck::cloud_details(, "dendextend")` for more info
Packages unavailable to check Rd xrefs: ‘WGCNA’, ‘dendroextras’, ‘moduleColor’, ‘distory’, ‘phangorn’, ‘ggdendro’, ‘zoo’
```
-# densityratio
-
-
-
-* Version: 0.2.0
-* GitHub: https://github.com/thomvolker/densityratio
-* Source code: https://github.com/cran/densityratio
-* Date/Publication: 2025-05-19 13:30:05 UTC
-* Number of recursive dependencies: 64
-
-Run `revdepcheck::cloud_details(, "densityratio")` 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
- ...
- ── Failure ('test-ulsif.R:78:3'): multidimensional ULSIF estimation, prediction works ──
- plot_univariate(...) has type 'object', not 'list'.
- ── Failure ('test-ulsif.R:83:3'): multidimensional ULSIF estimation, prediction works ──
- plot_univariate(...) has type 'object', not 'list'.
- ── Failure ('test-lhss.R:29:3'): multidimensional lhss estimation, prediction and plotting works ──
- suppressWarnings(plot(dr)) has type 'object', not 'list'.
-
- [ FAIL 10 | WARN 0 | SKIP 0 | PASS 270 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 11.6Mb
- sub-directories of 1Mb or more:
- data 1.5Mb
- libs 8.9Mb
- ```
-
-# diceR
-
-
-
-* Version: 3.0.0
-* GitHub: https://github.com/AlineTalhouk/diceR
-* Source code: https://github.com/cran/diceR
-* Date/Publication: 2025-02-05 09:40:01 UTC
-* Number of recursive dependencies: 151
-
-Run `revdepcheck::cloud_details(, "diceR")` 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
- ...
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Failure ('test-graphs.R:18:3'): graph_cdf object can have added/modified ggplot layers ──
- isTRUE(all.equal(p1, p2)) is not FALSE
-
- `actual`: TRUE
- `expected`: FALSE
-
- [ FAIL 1 | WARN 0 | SKIP 0 | PASS 113 ]
- Error: Test failures
- Execution halted
- ```
-
# DImodelsVis
@@ -4986,7 +3096,7 @@ Run `revdepcheck::cloud_details(, "diceR")` for more info
* GitHub: NA
* Source code: https://github.com/cran/DImodelsVis
* Date/Publication: 2024-02-26 14:10:15 UTC
-* Number of recursive dependencies: 112
+* Number of recursive dependencies: 111
Run `revdepcheck::cloud_details(, "DImodelsVis")` for more info
@@ -5150,23 +3260,23 @@ Run `revdepcheck::cloud_details(, "dittoViz")` for more info
Running examples in ‘dittoViz-Ex.R’ failed
The error most likely occurred in:
- > ### Name: barPlot
- > ### Title: Outputs a stacked bar plot to show the percent composition of
- > ### samples, groups, clusters, or other groupings
- > ### Aliases: barPlot
+ > ### Name: freqPlot
+ > ### Title: Plot discrete observation frequencies per sample and per
+ > ### grouping
+ > ### Aliases: freqPlot
>
> ### ** Examples
>
...
- 15 3 D 12 32 0.3750000
- 16 4 D 8 32 0.2500000
- > # through hovering the cursor over the relevant parts of the plot
- > if (requireNamespace("plotly", quietly = TRUE)) {
- + barPlot(example_df, "clustering", group.by = "groups",
- + do.hover = TRUE)
- + }
- Error in pm[[2]] : subscript out of bounds
- Calls: barPlot -> -> ggplotly.ggplot -> gg2list
+ ▆
+ 1. └─dittoViz::freqPlot(...)
+ 2. └─dittoViz::yPlot(...)
+ 3. └─dittoViz:::.yPlot_add_data_y_direction(...)
+ 4. └─ggplot2::geom_violin(draw_quantiles = vlnplot.quantiles)
+ 5. └─ggplot2:::check_numeric(draw_quantiles)
+ 6. └─ggplot2:::check_object(x, is.numeric, what, ..., arg = arg, call = call)
+ 7. └─ggplot2:::stop_input_type(...)
+ 8. └─rlang::abort(message, ..., call = call, arg = arg)
Execution halted
```
@@ -5190,48 +3300,7 @@ Run `revdepcheck::cloud_details(, "dittoViz")` for more info
10. └─ggplot2:::stop_input_type(...)
11. └─rlang::abort(message, ..., call = call, arg = arg)
- [ FAIL 47 | WARN 19 | SKIP 0 | PASS 199 ]
- Error: Test failures
- Execution halted
- ```
-
-# dndR
-
-
-
-* Version: 3.0.0
-* GitHub: https://github.com/njlyon0/dndR
-* Source code: https://github.com/cran/dndR
-* Date/Publication: 2025-04-02 18:00:02 UTC
-* Number of recursive dependencies: 67
-
-Run `revdepcheck::cloud_details(, "dndR")` 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
- ...
- `expected[2:2]`: "ggplot"
- ── Failure ('test-probability_plot.R:22:3'): Outputs are as expected ───────────
- class(my_plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
-
- `actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
- `expected[2:2]`: "ggplot"
-
- [ FAIL 2 | WARN 0 | SKIP 0 | PASS 102 ]
+ [ FAIL 37 | WARN 19 | SKIP 0 | PASS 220 ]
Error: Test failures
Execution halted
```
@@ -5506,7 +3575,7 @@ Run `revdepcheck::cloud_details(, "eks")` for more info
* GitHub: NA
* Source code: https://github.com/cran/ENMTools
* Date/Publication: 2024-01-16 12:50:11 UTC
-* Number of recursive dependencies: 285
+* Number of recursive dependencies: 284
Run `revdepcheck::cloud_details(, "ENMTools")` for more info
@@ -5539,126 +3608,34 @@ Run `revdepcheck::cloud_details(, "ENMTools")` for more info
Execution halted
```
-# epiCleanr
+# epos
-* Version: 0.2.0
-* GitHub: https://github.com/truenomad/epiCleanr
-* Source code: https://github.com/cran/epiCleanr
-* Date/Publication: 2023-09-28 12:20:05 UTC
-* Number of recursive dependencies: 128
+* Version: 1.1
+* GitHub: https://github.com/bernd-mueller/epos
+* Source code: https://github.com/cran/epos
+* Date/Publication: 2024-03-15 10:10:02 UTC
+* Number of recursive dependencies: 94
-Run `revdepcheck::cloud_details(, "epiCleanr")` for more info
+Run `revdepcheck::cloud_details(, "epos")` for more info
## Newly broken
-* checking examples ... ERROR
+* checking tests ... ERROR
```
- Running examples in ‘epiCleanr-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: handle_outliers
- > ### Title: Detect and Handle Outliers in Dataset
- > ### Aliases: handle_outliers
- >
- > ### ** Examples
- >
- >
- ...
- 13. │ └─ggplot2 (local) FUN(X[[i]], ...)
- 14. │ └─scale$map_df(df = df)
- 15. │ └─ggplot2 (local) map_df(..., self = self)
- 16. │ └─base::lapply(aesthetics, function(j) self$map(df[[j]]))
- 17. │ └─ggplot2 (local) FUN(X[[i]], ...)
- 18. │ └─self$map(df[[j]])
- 19. │ └─ggplot2 (local) map(..., self = self)
- 20. │ └─vctrs::`vec_slice<-`(`*tmp*`, is.na(x), value = na_value)
- 21. └─rlang::cnd_signal(x)
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.6Mb
- sub-directories of 1Mb or more:
- doc 2.9Mb
- help 2.5Mb
- ```
-
-# epiphy
-
-
-
-* Version: 0.5.0
-* GitHub: https://github.com/chgigot/epiphy
-* Source code: https://github.com/cran/epiphy
-* Date/Publication: 2023-11-16 11:20:10 UTC
-* Number of recursive dependencies: 88
-
-Run `revdepcheck::cloud_details(, "epiphy")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘epiphy-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: clump
- > ### Title: Regroup observational data into even clumps of individuals.
- > ### Aliases: clump clump.intensity
- >
- > ### ** Examples
- >
- > my_incidence <- incidence(tomato_tswv$field_1929)
- ...
- 21. │ └─ggplot2 (local) setup_params(...)
- 22. │ └─ggplot2:::make_summary_fun(...)
- 23. │ └─rlang::as_function(fun.data)
- 24. │ └─base::get(x, envir = env, mode = "function")
- 25. └─base::.handleSimpleError(...)
- 26. └─rlang (local) h(simpleError(msg, call))
- 27. └─handlers[[1L]](cnd)
- 28. └─cli::cli_abort(...)
- 29. └─rlang::abort(...)
- Execution halted
- ```
-
-# epos
-
-
-
-* Version: 1.1
-* GitHub: https://github.com/bernd-mueller/epos
-* Source code: https://github.com/cran/epos
-* Date/Publication: 2024-03-15 10:10:02 UTC
-* Number of recursive dependencies: 94
-
-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 1 | SKIP 0 | PASS 13 ]
-
- ══ Failed tests ════════════════════════════════════════════════════════════════
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(epos)
+ >
+ > test_check("epos")
+ [ FAIL 1 | WARN 1 | SKIP 0 | PASS 13 ]
+
+ ══ Failed tests ════════════════════════════════════════════════════════════════
...
[1] 1 - 11 == -10
Backtrace:
@@ -5833,92 +3810,28 @@ Run `revdepcheck::cloud_details(, "errors")` for more info
Execution halted
```
-# eudract
-
-
-
-* Version: 1.0.4
-* GitHub: https://github.com/shug0131/eudraCT
-* Source code: https://github.com/cran/eudract
-* Date/Publication: 2025-03-20 17:20:02 UTC
-* Number of recursive dependencies: 80
-
-Run `revdepcheck::cloud_details(, "eudract")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘eudract-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: dot_plot
- > ### Title: creates a dot-plot of safety data showing the absolute and
- > ### relative risks
- > ### Aliases: dot_plot
- >
- > ### ** Examples
- >
- ...
-
- $reference
- [1] "Control"
-
- > fig <- dot_plot(safety_statistics, type="non_serious", base=4)
- > fig
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(eudract)
- >
- > test_check("eudract")
- [ FAIL 1 | WARN 3 | SKIP 4 | PASS 75 ]
-
- ══ Skipped tests (4) ═══════════════════════════════════════════════════════════
- ...
-
- [ FAIL 1 | WARN 3 | SKIP 4 | PASS 75 ]
- Deleting unused snapshots:
- • dotplot/dotplot-1group.svg
- • dotplot/dotplot-3groups.svg
- • dotplot/dotplot-ref-rr.svg
- • dotplot/dotplot-ref.svg
- • dotplot/dotplot.svg
- Error: Test failures
- Execution halted
- ```
+## Newly fixed
-* checking re-building of vignette outputs ... ERROR
+* checking re-building of vignette outputs ... WARNING
```
Error(s) in re-building vignettes:
- --- re-building ‘eudract.Rmd’ using rmarkdown
- --- finished re-building ‘eudract.Rmd’
+ ...
+ --- re-building ‘rjournal.Rmd’ using rmarkdown
- --- re-building ‘standard_reporting.Rmd’ using rmarkdown
+ tlmgr: Remote database at https://mirrors.mit.edu/CTAN/systems/texlive/tlnet
+ (revision 75567 of the texlive-scripts package)
+ seems to be older than the local installation
+ (revision 75579 of texlive-scripts);
+ please use a different mirror and/or wait a day or two.
- Quitting from standard_reporting.Rmd:65-67 [dotplot_sae]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error:
...
- Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- --- failed re-building ‘standard_reporting.Rmd’
+
+ Error: processing vignette 'rjournal.Rmd' failed with diagnostics:
+ LaTeX failed to compile /tmp/workdir/errors/old/errors.Rcheck/vign_test/errors/vignettes/rjournal.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See rjournal.log for more info.
+ --- failed re-building ‘rjournal.Rmd’
SUMMARY: processing the following file failed:
- ‘standard_reporting.Rmd’
+ ‘rjournal.Rmd’
Error: Vignette re-building failed.
Execution halted
@@ -5965,132 +3878,6 @@ Run `revdepcheck::cloud_details(, "eventstudyr")` for more info
Execution halted
```
-# EvoPhylo
-
-
-
-* Version: 0.3.2
-* GitHub: https://github.com/tiago-simoes/EvoPhylo
-* Source code: https://github.com/cran/EvoPhylo
-* Date/Publication: 2022-11-03 17:00:02 UTC
-* Number of recursive dependencies: 146
-
-Run `revdepcheck::cloud_details(, "EvoPhylo")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘EvoPhylo-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_treerates_sgn
- > ### Title: Plot Bayesian evolutionary tree with rate thresholds for
- > ### selection mode
- > ### Aliases: plot_treerates_sgn
- >
- > ### ** Examples
- >
- ...
- Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
- ℹ Please use tidy evaluation idioms with `aes()`.
- ℹ See also `vignette("ggplot2-in-packages")` for more information.
- ℹ The deprecated feature was likely used in the ggtree package.
- Please report the issue at .
- Error: .onLoad failed in loadNamespace() for 'deeptime', details:
- call: NULL
- error: object properties are invalid:
- - @hjust must be , , or , not
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘char-part.Rmd’ using rmarkdown
-
- Quitting from char-part.Rmd:28-30 [unnamed-chunk-2]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- NULL
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'char-part.Rmd' failed with diagnostics:
- The package "deeptime" (>= 0.2.0) is required.
- ...
- Error: processing vignette 'rates-selection_MrBayes.Rmd' failed with diagnostics:
- The package "deeptime" (>= 0.2.0) is required.
- --- failed re-building ‘rates-selection_MrBayes.Rmd’
-
- SUMMARY: processing the following files failed:
- ‘char-part.Rmd’ ‘fbd-params.Rmd’ ‘offset_handling.Rmd’
- ‘rates-selection_BEAST2.Rmd’ ‘rates-selection_MrBayes.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.8Mb
- sub-directories of 1Mb or more:
- data 2.5Mb
- doc 1.6Mb
- extdata 2.4Mb
- ```
-
-# explainer
-
-
-
-* Version: 1.0.2
-* GitHub: https://github.com/PERSIMUNE/explainer
-* Source code: https://github.com/cran/explainer
-* Date/Publication: 2024-09-30 17:30:02 UTC
-* Number of recursive dependencies: 184
-
-Run `revdepcheck::cloud_details(, "explainer")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘explainer-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: eDecisionCurve
- > ### Title: Decision Curve Plot
- > ### Aliases: eDecisionCurve
- >
- > ### ** Examples
- >
- > library("explainer")
- ...
- > mylrn$train(maintask, splits$train)
- > myplot <- eDecisionCurve(
- + task = maintask,
- + trained_model = mylrn,
- + splits = splits,
- + seed = seed
- + )
- Error in pm[[2]] : subscript out of bounds
- Calls: eDecisionCurve -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespace in Imports field not imported from: ‘ggpmisc’
- All declared Imports should be used.
- ```
-
# ez
@@ -6193,53 +3980,6 @@ Run `revdepcheck::cloud_details(, "ezEDA")` for more info
Execution halted
```
-# EZFragility
-
-
-
-* Version: 1.0.3
-* GitHub: NA
-* Source code: https://github.com/cran/EZFragility
-* Date/Publication: 2025-04-10 14:40:09 UTC
-* Number of recursive dependencies: 84
-
-Run `revdepcheck::cloud_details(, "EZFragility")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘EZFragility-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plotFragHeatmap
- > ### Title: Visualization functions (raw signal, fragility matrix)
- > ### Aliases: plotFragHeatmap plotFragQuantile plotFragDistribution
- >
- > ### ** Examples
- >
- >
- ...
- >
- > ## precomputed fragility object
- > data("pt01Frag")
- >
- > ## plot the fragility heatmap
- > plotFragHeatmap(frag = pt01Frag, sozIndex = sozIndex)
- Warning: Ignoring unknown labels:
- • size : "2"
- Error: `object` must be an , not a S3
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘Intro_to_EZFragility.Rmd’ using rmarkdown
- ```
-
# ezplot
@@ -6338,11 +4078,11 @@ Run `revdepcheck::cloud_details(, "fabletools")` for more info
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-graphics.R:327:3'): autoplot_dcmp_ts() ───────────────────────
- `print(p)` produced warnings.
+ `print(p)` produced messages.
── Failure ('test-graphics.R:346:3'): autoplot_dcmp_ts() ───────────────────────
- `print(p)` produced warnings.
+ `print(p)` produced messages.
- [ FAIL 2 | WARN 5 | SKIP 1 | PASS 292 ]
+ [ FAIL 2 | WARN 0 | SKIP 1 | PASS 292 ]
Error: Test failures
Execution halted
```
@@ -6535,57 +4275,6 @@ Run `revdepcheck::cloud_details(, "faux")` for more info
Execution halted
```
-# fChange
-
-
-
-* Version: 2.0.0
-* GitHub: NA
-* Source code: https://github.com/cran/fChange
-* Date/Publication: 2025-03-27 18:00:09 UTC
-* Number of recursive dependencies: 206
-
-Run `revdepcheck::cloud_details(, "fChange")` 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
- ...
- `expected`: "gg"
- ── Failure ('test-plot_qq.R:3:3'): QQ Plot ─────────────────────────────────────
- class(tmp)[1] (`actual`) not equal to "gg" (`expected`).
-
- `actual`: "ggplot2::ggplot"
- `expected`: "gg"
-
- [ FAIL 13 | WARN 0 | SKIP 9 | PASS 177 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.0Mb
- sub-directories of 1Mb or more:
- data 2.0Mb
- libs 3.5Mb
- ```
-
# feasts
@@ -6656,57 +4345,7 @@ Run `revdepcheck::cloud_details(, "fec16")` for more info
Note: found 20 marked UTF-8 strings
```
-# fitbitViz
-
-
-
-* Version: 1.0.6
-* GitHub: https://github.com/mlampros/fitbitViz
-* Source code: https://github.com/cran/fitbitViz
-* Date/Publication: 2024-02-08 09:30:02 UTC
-* Number of recursive dependencies: 153
-
-Run `revdepcheck::cloud_details(, "fitbitViz")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(fitbitViz)
- >
- > test_check("fitbitViz")
- [ FAIL 3 | WARN 3 | SKIP 0 | PASS 4 ]
-
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ...
- 4. ├─ggplot2::theme(...)
- 5. │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
- 6. │ └─base::mget(args, envir = env)
- 7. └─ggplot2::element_text(...)
- 8. └─S7::new_object(...)
- 9. └─S7::validate(object, recursive = !parent_validated)
-
- [ FAIL 3 | WARN 3 | SKIP 0 | PASS 4 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.7Mb
- sub-directories of 1Mb or more:
- doc 4.0Mb
- ```
-
-# flextable
+# flextable
@@ -6747,57 +4386,6 @@ Run `revdepcheck::cloud_details(, "flextable")` for more info
Execution halted
```
-# flipr
-
-
-
-* Version: 0.3.3
-* GitHub: https://github.com/LMJL-Alea/flipr
-* Source code: https://github.com/cran/flipr
-* Date/Publication: 2023-08-23 09:00:02 UTC
-* Number of recursive dependencies: 104
-
-Run `revdepcheck::cloud_details(, "flipr")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘alternative.Rmd’ using rmarkdown
- --- finished re-building ‘alternative.Rmd’
-
- --- re-building ‘exactness.Rmd’ using rmarkdown
-
- Quitting from exactness.Rmd:141-177 [unnamed-chunk-1]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ...
- 6. ├─plotly::ggplotly(.)
- 7. └─plotly:::ggplotly.ggplot(.)
- 8. └─plotly::gg2list(...)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'exactness.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘exactness.Rmd’
-
- --- re-building ‘flipr.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 11.2Mb
- sub-directories of 1Mb or more:
- doc 9.1Mb
- libs 1.4Mb
- ```
-
# fmf
@@ -6821,292 +4409,24 @@ Run `revdepcheck::cloud_details(, "fmf")` for more info
See ‘/tmp/workdir/fmf/new/fmf.Rcheck/00install.out’ for details.
```
-## In both
-
-* checking C++ specification ... NOTE
- ```
- Specified C++11: please drop specification unless essential
- ```
-
-# foqat
-
-
-
-* Version: 2.0.8.2
-* GitHub: https://github.com/tianshu129/foqat
-* Source code: https://github.com/cran/foqat
-* Date/Publication: 2023-09-30 06:10:02 UTC
-* Number of recursive dependencies: 72
-
-Run `revdepcheck::cloud_details(, "foqat")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘Air_Quality.Rmd’ using rmarkdown
- --- finished re-building ‘Air_Quality.Rmd’
-
- --- re-building ‘Atmospheric_Radiation.Rmd’ using rmarkdown
- --- finished re-building ‘Atmospheric_Radiation.Rmd’
-
- --- re-building ‘Basic_Functions.Rmd’ using rmarkdown
- --- finished re-building ‘Basic_Functions.Rmd’
-
- --- re-building ‘Particle_Size_Distribution.Rmd’ using rmarkdown
- ```
-
-# forestly
-
-
-
-* Version: 0.1.2
-* GitHub: https://github.com/Merck/forestly
-* Source code: https://github.com/cran/forestly
-* Date/Publication: 2025-01-10 16:20:14 UTC
-* Number of recursive dependencies: 80
-
-Run `revdepcheck::cloud_details(, "forestly")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘forest-plot-static.Rmd’ using rmarkdown
- ```
-
-# forestPSD
-
-
-
-* Version: 1.0.0
-* GitHub: NA
-* Source code: https://github.com/cran/forestPSD
-* Date/Publication: 2024-11-11 16:50:05 UTC
-* Number of recursive dependencies: 44
-
-Run `revdepcheck::cloud_details(, "forestPSD")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘forestPSD-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: psdfun
- > ### Title: Regression analysis for survival curves.
- > ### Aliases: psdfun
- >
- > ### ** Examples
- >
- > data(Npop)
- ...
- 16. │ └─l$compute_geom_2(d, theme = plot@theme)
- 17. │ └─ggplot2 (local) compute_geom_2(..., self = self)
- 18. │ └─self$geom$use_defaults(...)
- 19. │ └─ggplot2 (local) use_defaults(..., self = self)
- 20. │ └─ggplot2:::check_aesthetics(new_params, nrow(data))
- 21. │ └─vctrs::list_sizes(x)
- 22. └─vctrs:::stop_scalar_type(``(``), "x$label", ``)
- 23. └─vctrs:::stop_vctrs(...)
- 24. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘ggplot2’ ‘reshape2’
- All declared Imports should be used.
- ```
-
-# formods
-
-
-
-* Version: 0.2.0
-* GitHub: https://github.com/john-harrold/formods
-* Source code: https://github.com/cran/formods
-* Date/Publication: 2025-01-07 16:20:06 UTC
-* Number of recursive dependencies: 187
-
-Run `revdepcheck::cloud_details(, "formods")` 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
- ...
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Failure ('test-FG_module.R:13:5'): FG -- Forcing builds of figures ──────────
- class(ggplot2::ggplot_build(sess_res[["state"]][["FG"]][["figs"]][[fid]][["fobj"]])) (`actual`) not equal to "ggplot_built" (`expected`).
-
- `actual`: "ggplot2::ggplot_built" "ggplot_built" "ggplot2::gg" "S7_object"
- `expected`: "ggplot_built"
-
- [ FAIL 1 | WARN 32 | SKIP 0 | PASS 39 ]
- Error: Test failures
- Execution halted
- ```
-
-# fqar
-
-
-
-* Version: 0.5.4
-* GitHub: https://github.com/equitable-equations/fqar
-* Source code: https://github.com/cran/fqar
-* Date/Publication: 2024-10-06 18:00:02 UTC
-* Number of recursive dependencies: 72
-
-Run `revdepcheck::cloud_details(, "fqar")` 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
- ...
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Failure ('test-species_profile_plot.R:21:3'): species_profile_plot works ────
- class(p) (`actual`) not equal to c("gg", "ggplot") (`expected`).
-
- `actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
- `expected[2:2]`: "ggplot"
-
- [ FAIL 1 | WARN 0 | SKIP 0 | PASS 365 ]
- Error: Test failures
- Execution halted
- ```
-
-# frailtyEM
-
-
-
-* Version: 1.0.1
-* GitHub: https://github.com/tbalan/frailtyEM
-* Source code: https://github.com/cran/frailtyEM
-* Date/Publication: 2019-09-22 13:00:10 UTC
-* Number of recursive dependencies: 75
-
-Run `revdepcheck::cloud_details(, "frailtyEM")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘frailtyEM-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: summary.emfrail
- > ### Title: Summary for 'emfrail' objects
- > ### Aliases: summary.emfrail
- >
- > ### ** Examples
- >
- > data("bladder")
- ...
- filter
-
- The following object is masked from ‘package:graphics’:
-
- layout
-
- > ggplotly(pl2)
- Error in pm[[2]] : subscript out of bounds
- Calls: ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking re-building of vignette outputs ... WARNING
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘frailtyEM_manual.Rnw’ using Sweave
- Loading required package: survival
- Loading required package: gridExtra
- Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
- ℹ Please use tidy evaluation idioms with `aes()`.
- ℹ See also `vignette("ggplot2-in-packages")` for more
- information.
- ℹ The deprecated feature was likely used in the frailtyEM
- package.
- ...
- l.179 \RequirePackage{grfext}\relax
- ^^M
- ! ==> Fatal error occurred, no output PDF file produced!
- --- failed re-building ‘frailtyEM_manual.Rnw’
-
- SUMMARY: processing the following file failed:
- ‘frailtyEM_manual.Rnw’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-* checking Rd files ... NOTE
- ```
- checkRd: (-1) emfrail_control.Rd:49: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) emfrail_control.Rd:50: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) emfrail_control.Rd:51: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) emfrail_control.Rd:52: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) emfrail_control.Rd:53-54: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) emfrail_control.Rd:55-57: Lost braces in \itemize; meant \describe ?
- ```
+## In both
-* checking LazyData ... NOTE
+* checking C++ specification ... NOTE
```
- 'LazyData' is specified without a 'data' directory
+ Specified C++11: please drop specification unless essential
```
-# funcharts
+# forestPSD
-* Version: 1.7.0
-* GitHub: https://github.com/unina-sfere/funcharts
-* Source code: https://github.com/cran/funcharts
-* Date/Publication: 2025-03-17 17:30:02 UTC
-* Number of recursive dependencies: 126
+* Version: 1.0.0
+* GitHub: NA
+* Source code: https://github.com/cran/forestPSD
+* Date/Publication: 2024-11-11 16:50:05 UTC
+* Number of recursive dependencies: 44
-Run `revdepcheck::cloud_details(, "funcharts")` for more info
+Run `revdepcheck::cloud_details(, "forestPSD")` for more info
@@ -7114,62 +4434,36 @@ Run `revdepcheck::cloud_details(, "funcharts")` for more info
* checking examples ... ERROR
```
- Running examples in ‘funcharts-Ex.R’ failed
+ Running examples in ‘forestPSD-Ex.R’ failed
The error most likely occurred in:
- > ### Name: control_charts_pca_mfd_real_time
- > ### Title: Real-time T2 and SPE control charts for multivariate functional
- > ### data
- > ### Aliases: control_charts_pca_mfd_real_time
+ > ### Name: psdfun
+ > ### Title: Regression analysis for survival curves.
+ > ### Aliases: psdfun
>
> ### ** Examples
>
+ > data(Npop)
...
- >
- > cclist <- control_charts_pca_mfd_real_time(
- + pca_list = pca_list,
- + components_list = 1:3,
- + mfdobj_x_test = mfdobj_x2_list)
- > plot_control_charts_real_time(cclist, 1)
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
+ 16. │ └─l$compute_geom_2(d, theme = plot@theme)
+ 17. │ └─ggplot2 (local) compute_geom_2(..., self = self)
+ 18. │ └─self$geom$use_defaults(...)
+ 19. │ └─ggplot2 (local) use_defaults(..., self = self)
+ 20. │ └─ggplot2:::check_aesthetics(new_params, nrow(data))
+ 21. │ └─vctrs::list_sizes(x)
+ 22. └─vctrs:::stop_scalar_type(``(``), "x$label", ``)
+ 23. └─vctrs:::stop_vctrs(...)
+ 24. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
```
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(funcharts)
- Loading required package: robustbase
- >
- > test_check("funcharts")
- [1] "The Fisher omnibus combining function is considered."
- [1] "The Fisher omnibus combining function is considered."
- ...
- - e1:
- - e2:
- Backtrace:
- ▆
- 1. └─funcharts::plot_control_charts_real_time(cclist, 1) at test_phaseII.R:104:3
- 2. └─S7:::Ops.S7_object(...)
-
- [ FAIL 3 | WARN 0 | SKIP 1 | PASS 111 ]
- Error: Test failures
- Execution halted
- ```
-
## In both
-* checking installed package size ... NOTE
+* checking dependencies in R code ... NOTE
```
- installed size is 5.7Mb
- sub-directories of 1Mb or more:
- R 1.5Mb
- libs 3.4Mb
+ Namespaces in Imports field not imported from:
+ ‘ggplot2’ ‘reshape2’
+ All declared Imports should be used.
```
# FunnelPlotR
@@ -7328,47 +4622,6 @@ Run `revdepcheck::cloud_details(, "gapfill")` for more info
checkRd: (-1) ndvi.Rd:13: Lost braces in \itemize; meant \describe ?
```
-# gapminder
-
-
-
-* Version: 1.0.0
-* GitHub: https://github.com/jennybc/gapminder
-* Source code: https://github.com/cran/gapminder
-* Date/Publication: 2023-03-10 09:50:08 UTC
-* Number of recursive dependencies: 62
-
-Run `revdepcheck::cloud_details(, "gapminder")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘gapminder-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: country_colors
- > ### Title: Gapminder color schemes.
- > ### Aliases: country_colors continent_colors
- > ### Keywords: datasets
- >
- > ### ** Examples
- >
- ...
- and is now defunct.
- ℹ Please use the `show.legend` argument instead.
- Backtrace:
- ▆
- 1. └─ggplot2::geom_line(lwd = 1, show_guide = FALSE)
- 2. └─ggplot2::layer(...)
- 3. └─lifecycle::deprecate_stop("2.0.0", "layer(show_guide)", "layer(show.legend)")
- 4. └─lifecycle:::deprecate_stop0(msg)
- 5. └─rlang::cnd_signal(...)
- Execution halted
- ```
-
# genekitr
@@ -7414,10 +4667,10 @@ Run `revdepcheck::cloud_details(, "genekitr")` for more info
-* Version: 0.38.2
+* Version: 0.38.3
* GitHub: https://github.com/psobczyk/geneSLOPE
* Source code: https://github.com/cran/geneSLOPE
-* Date/Publication: 2023-08-16 09:12:37 UTC
+* Date/Publication: 2025-06-20 04:40:02 UTC
* Number of recursive dependencies: 76
Run `revdepcheck::cloud_details(, "geneSLOPE")` for more info
@@ -7466,28 +4719,6 @@ Run `revdepcheck::cloud_details(, "geofacet")` for more info
Note: found 646 marked UTF-8 strings
```
-# geoheatmap
-
-
-
-* Version: 0.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/geoheatmap
-* Date/Publication: 2024-09-05 15:40:02 UTC
-* Number of recursive dependencies: 102
-
-Run `revdepcheck::cloud_details(, "geoheatmap")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘geoheatmap.Rmd’ using rmarkdown
- ```
-
# geomtextpath
@@ -7809,7 +5040,7 @@ Run `revdepcheck::cloud_details(, "ggalign")` for more info
* GitHub: https://github.com/ggobi/ggally
* Source code: https://github.com/cran/GGally
* Date/Publication: 2024-02-14 00:53:32 UTC
-* Number of recursive dependencies: 143
+* Number of recursive dependencies: 142
Run `revdepcheck::cloud_details(, "GGally")` for more info
@@ -7865,78 +5096,6 @@ ERROR: lazy loading failed for package ‘GGally’
```
-# gganimate
-
-
-
-* Version: 1.0.9
-* GitHub: https://github.com/thomasp85/gganimate
-* Source code: https://github.com/cran/gganimate
-* Date/Publication: 2024-02-27 14:00:03 UTC
-* Number of recursive dependencies: 93
-
-Run `revdepcheck::cloud_details(, "gganimate")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(gganimate)
- Loading required package: ggplot2
- >
- > test_check("gganimate")
- [ FAIL 2 | WARN 4 | SKIP 1 | PASS 4 ]
-
- ...
- 22. └─self$extract_key(...)
- 23. └─ggplot2 (local) extract_key(...)
- 24. └─Guide$extract_key(scale, aesthetic, ...)
- 25. └─ggplot2 (local) extract_key(...)
- 26. └─scale$map(breaks)
- 27. └─ggplot2 (local) map(..., self = self)
-
- [ FAIL 2 | WARN 4 | SKIP 1 | PASS 4 ]
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘gganimate.Rmd’ using rmarkdown
- ```
-
-* checking S3 generic/method consistency ... WARNING
- ```
- ggplot_build:
- function(plot, ...)
- ggplot_build.gganim:
- function(plot)
-
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.ExitFactory:
- function(object, plot, object_name)
-
- ...
- function(object, plot, ...)
- ggplot_add.View:
- function(object, plot, object_name)
-
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.EaseAes:
- function(object, plot, object_name)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
- ```
-
# ggblend
@@ -8035,15 +5194,6 @@ Run `revdepcheck::cloud_details(, "ggbrain")` for more info
## Newly broken
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘ggbrain_aesthetics.Rmd’ using rmarkdown
- --- finished re-building ‘ggbrain_aesthetics.Rmd’
-
- --- re-building ‘ggbrain_introduction.Rmd’ using rmarkdown
- ```
-
* checking S3 generic/method consistency ... WARNING
```
ggplot_add:
@@ -8091,28 +5241,6 @@ Run `revdepcheck::cloud_details(, "ggbreak")` for more info
## Newly broken
-* checking examples ... ERROR
- ```
- Running examples in ‘ggbreak-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: scale_wrap
- > ### Title: scale-wrap
- > ### Aliases: scale_wrap
- >
- > ### ** Examples
- >
- > library(ggplot2)
- > library(ggbreak)
- > p <- ggplot(economics, aes(x=date, y = unemploy, colour = uempmed)) +
- + geom_line()
- > p + scale_wrap(n=4)
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
* checking re-building of vignette outputs ... ERROR
```
Error(s) in re-building vignettes:
@@ -8307,45 +5435,6 @@ Run `revdepcheck::cloud_details(, "ggdemetra")` for more info
See ‘/tmp/workdir/ggdemetra/new/ggdemetra.Rcheck/00install.out’ for details.
```
-# ggDoE
-
-
-
-* Version: 0.8
-* GitHub: https://github.com/toledo60/ggDoE
-* Source code: https://github.com/cran/ggDoE
-* Date/Publication: 2024-02-10 04:50:02 UTC
-* Number of recursive dependencies: 73
-
-Run `revdepcheck::cloud_details(, "ggDoE")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggDoE-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: gg_lm
- > ### Title: Regression Diagnostic Plots with ggplot2
- > ### Aliases: gg_lm
- >
- > ### ** Examples
- >
- > model <- lm(mpg ~ wt + am + gear, data = mtcars)
- > gg_lm(model)
- Warning: `fortify()` was deprecated in ggplot2 3.6.0.
- ℹ Please use `broom::augment()` instead.
- ℹ The deprecated feature was likely used in the ggplot2 package.
- Please report the issue at .
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
# ggDoubleHeat
@@ -8360,113 +5449,31 @@ Run `revdepcheck::cloud_details(, "ggDoubleHeat")` for more info
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggDoubleHeat-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: geom_heat_circle
- > ### Title: Heatcircle
- > ### Aliases: geom_heat_circle
- >
- > ### ** Examples
- >
- >
- ...
- + y = rep(c("d", "e", "f"), 3),
- + outside_values = rep(c(1,5,7),3),
- + inside_values = rep(c(2,3,4),3))
- >
- > ggplot(data, aes(x,y)) +
- + geom_heat_circle(outside = outside_values,
- + inside = inside_values)
- Error in scale_title(title) : object 'outside_values' not found
- Calls: ... extract_params -> -> make_title -> scale_title
- Execution halted
- ```
-
-# ggeasy
-
-
-
-* Version: 0.1.5
-* GitHub: https://github.com/jonocarroll/ggeasy
-* Source code: https://github.com/cran/ggeasy
-* Date/Publication: 2024-11-03 05:50:02 UTC
-* Number of recursive dependencies: 90
-
-Run `revdepcheck::cloud_details(, "ggeasy")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggeasy-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: easy_add_legend_title
- > ### Title: Easily add legend title(s)
- > ### Aliases: easy_add_legend_title
- >
- > ### ** Examples
- >
- >
- ...
- > # Add legend title to a specific aesthetic
- > ggplot(mtcars, aes(wt, mpg, colour = cyl, size = hp)) +
- + geom_point() + easy_add_legend_title(col = "Number of Cylinders")
- >
- > # Add legend title to all aesthetics
- > ggplot(mtcars, aes(wt, mpg, colour = cyl)) +
- + geom_point() + easy_add_legend_title("Number of Cylinders")
- Error: object is invalid:
- - labels cannot contain duplicate names (colour, linetype, shape, and size).
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(ggeasy)
- >
- > test_check("ggeasy")
- [ FAIL 6 | WARN 0 | SKIP 1 | PASS 151 ]
-
- ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
- ...
- 8. └─S7::validate(object, recursive = !parent_validated)
-
- [ FAIL 6 | WARN 0 | SKIP 1 | PASS 151 ]
- Deleting unused snapshots:
- • labs/labels-attrib.svg
- • labs/labels-manual.svg
- • labs/labels-mytitle.svg
- • labs/labels-y-col.svg
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘shortcuts.Rmd’ using rmarkdown
- ```
+## Newly broken
-* checking S3 generic/method consistency ... WARNING
+* checking examples ... ERROR
```
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.easy_labs:
- function(object, plot, object_name)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
+ Running examples in ‘ggDoubleHeat-Ex.R’ failed
+ The error most likely occurred in:
+
+ > ### Name: geom_heat_circle
+ > ### Title: Heatcircle
+ > ### Aliases: geom_heat_circle
+ >
+ > ### ** Examples
+ >
+ >
+ ...
+ + y = rep(c("d", "e", "f"), 3),
+ + outside_values = rep(c(1,5,7),3),
+ + inside_values = rep(c(2,3,4),3))
+ >
+ > ggplot(data, aes(x,y)) +
+ + geom_heat_circle(outside = outside_values,
+ + inside = inside_values)
+ Error in scale_title(title) : object 'outside_values' not found
+ Calls: ... extract_params -> -> make_title -> scale_title
+ Execution halted
```
# ggEDA
@@ -8569,47 +5576,6 @@ Run `revdepcheck::cloud_details(, "ggedit")` for more info
Execution halted
```
-# ggfields
-
-
-
-* Version: 0.0.6
-* GitHub: https://github.com/pepijn-devries/ggfields
-* Source code: https://github.com/cran/ggfields
-* Date/Publication: 2024-02-26 14:40:03 UTC
-* Number of recursive dependencies: 100
-
-Run `revdepcheck::cloud_details(, "ggfields")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggfields-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: angle_correction
- > ### Title: Calculate correction for angle in the plot coordinate system
- > ### Aliases: angle_correction
- >
- > ### ** Examples
- >
- > ## Create a data.frame with some xy-coordinates and all angles pointing North (0 degrees)
- ...
- + default_crs = 4326
- + )
- + )
- >
- > ## When plotting as lon-lat, the angle correction will be zero
- > angle_correction(d, params_mockup, ggplot2::coord_sf(default_crs = 4326))
- Error in panel_params$guides$get_guide(aesthetics) :
- attempt to apply non-function
- Calls: angle_correction ... train_panel_guides -> -> train_panel_guides
- Execution halted
- ```
-
# ggfixest
@@ -8724,54 +5690,6 @@ Run `revdepcheck::cloud_details(, "ggfocus")` for more info
'LazyData' is specified without a 'data' directory
```
-# ggforce
-
-
-
-* Version: 0.4.2
-* GitHub: https://github.com/thomasp85/ggforce
-* Source code: https://github.com/cran/ggforce
-* Date/Publication: 2024-02-19 11:00:02 UTC
-* Number of recursive dependencies: 67
-
-Run `revdepcheck::cloud_details(, "ggforce")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggforce-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: facet_matrix
- > ### Title: Facet by different data columns
- > ### Aliases: facet_matrix
- >
- > ### ** Examples
- >
- > # Standard use:
- > ggplot(mpg) +
- + geom_point(aes(x = .panel_x, y = .panel_y)) +
- + facet_matrix(vars(displ, cty, hwy))
- Error in get(x, envir = ns, inherits = FALSE) :
- object 'check_labeller' not found
- Calls: facet_matrix -> -> get
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 27.3Mb
- sub-directories of 1Mb or more:
- R 1.0Mb
- help 1.2Mb
- libs 25.0Mb
- ```
-
# ggformula
@@ -8861,47 +5779,6 @@ Run `revdepcheck::cloud_details(, "ggfortify")` for more info
Execution halted
```
-# ggfun
-
-
-
-* Version: 0.1.8
-* GitHub: https://github.com/YuLab-SMU/ggfun
-* Source code: https://github.com/cran/ggfun
-* Date/Publication: 2024-12-03 10:20:02 UTC
-* Number of recursive dependencies: 59
-
-Run `revdepcheck::cloud_details(, "ggfun")` for more info
-
-
-
-## Newly broken
-
-* checking S3 generic/method consistency ... WARNING
- ```
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.facet_set:
- function(object, plot, object_name)
-
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.scatter_rect:
- function(object, plot, object_name)
-
- ...
- function(object, plot, ...)
- ggplot_add.segmentC:
- function(object, plot, object_name)
-
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.volpoint:
- function(object, plot, object_name)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
- ```
-
# ggfx
@@ -8920,11 +5797,6 @@ Run `revdepcheck::cloud_details(, "ggfx")` for more info
* checking S3 generic/method consistency ... WARNING
```
- ggplot_gtable:
- function(plot)
- ggplot_gtable.filtered_gtable:
- function(data)
-
ggplot_build:
function(plot, ...)
ggplot_build.filtered_ggplot:
@@ -9034,189 +5906,32 @@ Run `revdepcheck::cloud_details(, "ggghost")` for more info
> ### Aliases: -.gg
>
> ### ** Examples
- >
- > ## create a ggghost object
- ...
- > ## remove the geom_smooth
- > z - geom_smooth()
- >
- > ## remove the labels
- > ## NOTE: argument must be present and able to be
- > ## evaluated in scope
- > z - labs(TRUE) # works
- Error: object is invalid:
- - every label must be named.
- Execution halted
- ```
-
-# gghalves
-
-
-
-* Version: 0.1.4
-* GitHub: https://github.com/erocoar/gghalves
-* Source code: https://github.com/cran/gghalves
-* Date/Publication: 2022-11-20 11:40:02 UTC
-* Number of recursive dependencies: 49
-
-Run `revdepcheck::cloud_details(, "gghalves")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘gghalves-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: geom_half_point
- > ### Title: Points with jitter for half geoms.
- > ### Aliases: geom_half_point
- >
- > ### ** Examples
- >
- > ggplot(iris, aes(x = Species, y = Petal.Width, fill = Species)) +
- ...
- 32. │ └─base::lapply(...)
- 33. │ └─ggplot2 (local) FUN(X[[i]], ...)
- 34. │ └─ggplot2 (local) apply_fun(cur_data)
- 35. │ └─ggplot2 (local) fun(x, ...)
- 36. └─base::.handleSimpleError(...)
- 37. └─rlang (local) h(simpleError(msg, call))
- 38. └─handlers[[1L]](cnd)
- 39. └─cli::cli_abort(...)
- 40. └─rlang::abort(...)
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- ...
- --- re-building ‘gghalves.Rmd’ using rmarkdown
-
- Quitting from gghalves.Rmd:39-42 [unnamed-chunk-2]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- NULL
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'gghalves.Rmd' failed with diagnostics:
- ...
- ℹ Error occurred in the 1st layer.
- Caused by error in `fun()`:
- ! argument "layout" is missing, with no default
- --- failed re-building ‘gghalves.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘gghalves.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘grDevices’ ‘gtable’
- All declared Imports should be used.
- ```
-
-# gghighlight
-
-
-
-* Version: 0.4.1
-* GitHub: https://github.com/yutannihilation/gghighlight
-* Source code: https://github.com/cran/gghighlight
-* Date/Publication: 2023-12-16 01:00:02 UTC
-* Number of recursive dependencies: 82
-
-Run `revdepcheck::cloud_details(, "gghighlight")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘gghighlight-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: gghighlight
- > ### Title: Highlight Data With Predicate
- > ### Aliases: gghighlight
- >
- > ### ** Examples
- >
- > d <- data.frame(
- ...
- 15. │ ├─purrr:::with_indexed_errors(...)
- 16. │ │ └─base::withCallingHandlers(...)
- 17. │ ├─purrr:::call_with_cleanup(...)
- 18. │ └─gghighlight (local) .f(.x[[i]], .y[[i]], ...)
- 19. │ └─gghighlight:::get_default_aes_param(nm, layer$geom, layer$mapping)
- 20. └─base::.handleSimpleError(...)
- 21. └─purrr (local) h(simpleError(msg, call))
- 22. └─cli::cli_abort(...)
- 23. └─rlang::abort(...)
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(gghighlight)
- Loading required package: ggplot2
- >
- > test_check("gghighlight")
- label_key: type
- label_key: type
- ...
- 25. └─cli::cli_abort(...)
- 26. └─rlang::abort(...)
-
- [ FAIL 7 | WARN 24 | SKIP 0 | PASS 159 ]
- Deleting unused snapshots:
- • vdiffr/simple-bar-chart-with-facet.svg
- • vdiffr/simple-line-chart.svg
- • vdiffr/simple-point-chart.svg
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘gghighlight.Rmd’ using rmarkdown
- ```
-
-* checking S3 generic/method consistency ... WARNING
- ```
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.gg_highlighter:
- function(object, plot, object_name)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
+ >
+ > ## create a ggghost object
+ ...
+ > ## remove the geom_smooth
+ > z - geom_smooth()
+ >
+ > ## remove the labels
+ > ## NOTE: argument must be present and able to be
+ > ## evaluated in scope
+ > z - labs(TRUE) # works
+ Error: object is invalid:
+ - every label must be named.
+ Execution halted
```
-# gghourglass
+# gghalves
-* Version: 0.0.2
-* GitHub: https://github.com/pepijn-devries/gghourglass
-* Source code: https://github.com/cran/gghourglass
-* Date/Publication: 2025-04-05 14:20:02 UTC
-* Number of recursive dependencies: 96
+* Version: 0.1.4
+* GitHub: https://github.com/erocoar/gghalves
+* Source code: https://github.com/cran/gghalves
+* Date/Publication: 2022-11-20 11:40:02 UTC
+* Number of recursive dependencies: 49
-Run `revdepcheck::cloud_details(, "gghourglass")` for more info
+Run `revdepcheck::cloud_details(, "gghalves")` for more info
@@ -9224,52 +5939,61 @@ Run `revdepcheck::cloud_details(, "gghourglass")` for more info
* checking examples ... ERROR
```
- Running examples in ‘gghourglass-Ex.R’ failed
+ Running examples in ‘gghalves-Ex.R’ failed
The error most likely occurred in:
- > ### Name: AnnotateLunarphase
- > ### Title: Annotate ggplot with lunar phases
- > ### Aliases: AnnotateLunarphase annotate_lunarphase
- > ### Keywords: datasets
+ > ### Name: geom_half_point
+ > ### Title: Points with jitter for half geoms.
+ > ### Aliases: geom_half_point
>
> ### ** Examples
>
+ > ggplot(iris, aes(x = Species, y = Petal.Width, fill = Species)) +
...
- 19. │ └─vctrs (local) ``()
- 20. │ ├─x[i = i]
- 21. │ └─grid:::`[.unit`(x = x, i = i)
- 22. │ └─base::stop(...)
- 23. └─base::.handleSimpleError(...)
- 24. └─rlang (local) h(simpleError(msg, call))
- 25. └─handlers[[1L]](cnd)
- 26. └─cli::cli_abort(...)
- 27. └─rlang::abort(...)
+ 32. │ └─base::lapply(...)
+ 33. │ └─ggplot2 (local) FUN(X[[i]], ...)
+ 34. │ └─ggplot2 (local) apply_fun(cur_data)
+ 35. │ └─ggplot2 (local) fun(x, ...)
+ 36. └─base::.handleSimpleError(...)
+ 37. └─rlang (local) h(simpleError(msg, call))
+ 38. └─handlers[[1L]](cnd)
+ 39. └─cli::cli_abort(...)
+ 40. └─rlang::abort(...)
Execution halted
```
-* checking tests ... ERROR
+* checking re-building of vignette outputs ... ERROR
```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(gghourglass)
- >
- > test_check("gghourglass")
- NULL
- [ FAIL 1 | WARN 2 | SKIP 4 | PASS 3 ]
-
+ Error(s) in re-building vignettes:
+ ...
+ --- re-building ‘gghalves.Rmd’ using rmarkdown
+
+ Quitting from gghalves.Rmd:39-42 [unnamed-chunk-2]
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ NULL
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ Error: processing vignette 'gghalves.Rmd' failed with diagnostics:
...
- 26. │ └─base::stop(...)
- 27. └─base::.handleSimpleError(...)
- 28. └─rlang (local) h(simpleError(msg, call))
- 29. └─handlers[[1L]](cnd)
- 30. └─cli::cli_abort(...)
- 31. └─rlang::abort(...)
-
- [ FAIL 1 | WARN 2 | SKIP 4 | PASS 3 ]
- Error: Test failures
- Execution halted
+ ℹ Error occurred in the 1st layer.
+ Caused by error in `fun()`:
+ ! argument "layout" is missing, with no default
+ --- failed re-building ‘gghalves.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘gghalves.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
+ ```
+
+## In both
+
+* checking dependencies in R code ... NOTE
+ ```
+ Namespaces in Imports field not imported from:
+ ‘grDevices’ ‘gtable’
+ All declared Imports should be used.
```
# ggimage
@@ -9382,7 +6106,7 @@ Run `revdepcheck::cloud_details(, "ggiraph")` for more info
* 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: 107
+* Number of recursive dependencies: 106
Run `revdepcheck::cloud_details(, "ggiraphExtra")` for more info
@@ -9421,47 +6145,6 @@ Run `revdepcheck::cloud_details(, "ggiraphExtra")` for more info
--- re-building ‘ggPredict.Rmd’ using rmarkdown
```
-# gglogger
-
-
-
-* Version: 0.1.5
-* GitHub: https://github.com/pwwang/gglogger
-* Source code: https://github.com/cran/gglogger
-* Date/Publication: 2024-10-25 09:10:02 UTC
-* Number of recursive dependencies: 42
-
-Run `revdepcheck::cloud_details(, "gglogger")` 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
- ...
- y[1]: displ, y = hwy))\n"
- ── Failure ('test-gglogger.R:124:5'): gglogger stringify works ─────────────────
- `code` not equal to "ggplot2::ggplot(ggplot2::mpg) +\n geom_point(aes(x = displ, y = hwy))".
- 1/1 mismatches
- x[1]: "ggplot2::ggplot(ggplot2::mpg)"
- y[1]: "ggplot2::ggplot(ggplot2::mpg) +\n geom_point(aes(x = displ, y = hwy))"
-
- [ FAIL 16 | WARN 0 | SKIP 0 | PASS 38 ]
- Error: Test failures
- Execution halted
- ```
-
# ggmap
@@ -9494,28 +6177,6 @@ Run `revdepcheck::cloud_details(, "ggmap")` for more info
data 7.0Mb
```
-# ggmice
-
-
-
-* Version: 0.1.0
-* GitHub: https://github.com/amices/ggmice
-* Source code: https://github.com/cran/ggmice
-* Date/Publication: 2023-08-07 14:20:02 UTC
-* Number of recursive dependencies: 119
-
-Run `revdepcheck::cloud_details(, "ggmice")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘ggmice.Rmd’ using rmarkdown
- ```
-
# ggmosaic
@@ -9660,57 +6321,6 @@ ERROR: lazy loading failed for package ‘ggmulti’
```
-# ggnewscale
-
-
-
-* Version: 0.5.1
-* GitHub: https://github.com/eliocamp/ggnewscale
-* Source code: https://github.com/cran/ggnewscale
-* Date/Publication: 2025-02-24 09:00:02 UTC
-* Number of recursive dependencies: 58
-
-Run `revdepcheck::cloud_details(, "ggnewscale")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(ggnewscale)
- >
- > test_check("ggnewscale")
- `new_stat_bin2d()` using `bins = 30`. Pick better value `binwidth`.
- `new_stat_bin2d()` using `bins = 30`. Pick better value `binwidth`.
- `new_stat_bin2d()` using `bins = 30`. Pick better value `binwidth`.
- ...
- 16. └─scales:::as_discrete_pal.default(elem)
- 17. └─cli::cli_abort("Cannot convert {.arg x} to a discrete palette.")
- 18. └─rlang::abort(...)
-
- [ FAIL 1 | WARN 0 | SKIP 5 | PASS 3 ]
- Deleting unused snapshots:
- • newscale/guides-outisde-of-scales.svg
- • newscale/respects-override-aes-2.svg
- Error: Test failures
- Execution halted
- ```
-
-* checking S3 generic/method consistency ... WARNING
- ```
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.new_aes:
- function(object, plot, object_name)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
- ```
-
# ggpackets
@@ -9778,114 +6388,7 @@ Run `revdepcheck::cloud_details(, "ggpackets")` for more info
* Date/Publication: 2024-03-09 22:00:02 UTC
* Number of recursive dependencies: 47
-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
- ...
- ▆
- 1. ├─ggplot2::ggplot_build(test_mtcars_plot) at test-ggparallel.R:12:3
- 2. ├─ggplot2:::ggplot_build.default(test_mtcars_plot)
- 3. │ └─ggplot2::build_ggplot(plot)
- 4. │ └─S7::S7_dispatch()
- 5. └─S7:::method_lookup_error("build_ggplot", ``)
-
- [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
- Error: Test failures
- Execution halted
- ```
-
-# ggpath
-
-
-
-* Version: 1.0.2
-* GitHub: https://github.com/mrcaseb/ggpath
-* Source code: https://github.com/cran/ggpath
-* Date/Publication: 2024-08-20 09:30:02 UTC
-* Number of recursive dependencies: 64
-
-Run `revdepcheck::cloud_details(, "ggpath")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggpath-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: element_path
- > ### Title: Theme Elements for Image Grobs
- > ### Aliases: element_path element_raster
- >
- > ### ** Examples
- >
- > library(ggplot2)
- ...
- + theme(
- + plot.caption = element_path(hjust = 1, size = 0.6),
- + axis.text.y = element_path(size = 1),
- + axis.title.x = element_path(),
- + axis.title.y = element_path(vjust = 0.9),
- + plot.title = element_path(hjust = 0, size = 2, alpha = 0.5),
- + plot.subtitle = element_path(hjust = 0.9, angle = 45),
- + )
- Error: `object` must be an , not a S3
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(ggpath)
- >
- > test_check("ggpath")
- [ FAIL 1 | WARN 0 | SKIP 5 | PASS 3 ]
-
- ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
- ...
- • geom_lines/p1.svg
- • geom_lines/p2.svg
- • geom_lines/p3.svg
- • geom_lines/p4.svg
- • geom_lines/p5.svg
- • theme-elements/p1.svg
- • theme-elements/p2.svg
- • theme-elements/p3.svg
- Error: Test failures
- Execution halted
- ```
-
-# ggpedigree
-
-
-
-* Version: 0.7.0
-* GitHub: https://github.com/R-Computing-Lab/ggpedigree
-* Source code: https://github.com/cran/ggpedigree
-* Date/Publication: 2025-06-10 00:10:02 UTC
-* Number of recursive dependencies: 146
-
-Run `revdepcheck::cloud_details(, "ggpedigree")` for more info
+Run `revdepcheck::cloud_details(, "ggparallel")` for more info
@@ -9904,29 +6407,57 @@ Run `revdepcheck::cloud_details(, "ggpedigree")` for more info
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
...
- ── Failure ('test-ggPedigreeInteractive.R:279:3'): ggPedigreeInteractive handles inbreeding ──
- `p_widget_nozyg` inherits from 'ggplot2::ggplot'/'ggplot'/'ggplot2::gg'/'S7_object'/'gg' not 'htmlwidget'.
- ── Failure ('test-ggPedigreeInteractive.R:294:3'): ggPedigreeInteractive handles inbreeding ──
- `p_nozyg` inherits from 'ggplot2::ggplot'/'ggplot'/'ggplot2::gg'/'S7_object'/'gg' not 'plotly'.
- ── Failure ('test-ggPedigreeInteractive.R:295:3'): ggPedigreeInteractive handles inbreeding ──
- `p_nozyg` inherits from 'ggplot2::ggplot'/'ggplot'/'ggplot2::gg'/'S7_object'/'gg' not 'htmlwidget'.
+ ▆
+ 1. ├─ggplot2::ggplot_build(test_mtcars_plot) at test-ggparallel.R:12:3
+ 2. ├─ggplot2:::ggplot_build.default(test_mtcars_plot)
+ 3. │ └─ggplot2::build_ggplot(plot)
+ 4. │ └─S7::S7_dispatch()
+ 5. └─S7:::method_lookup_error("build_ggplot", ``)
- [ FAIL 16 | WARN 14 | SKIP 0 | PASS 281 ]
+ [ FAIL 1 | WARN 0 | SKIP 0 | PASS 0 ]
Error: Test failures
Execution halted
```
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘v00_plots.Rmd’ using rmarkdown
- ```
+# ggpath
-## In both
+
-* checking package dependencies ... NOTE
+* Version: 1.0.2
+* GitHub: https://github.com/mrcaseb/ggpath
+* Source code: https://github.com/cran/ggpath
+* Date/Publication: 2024-08-20 09:30:02 UTC
+* Number of recursive dependencies: 64
+
+Run `revdepcheck::cloud_details(, "ggpath")` for more info
+
+
+
+## Newly broken
+
+* checking tests ... ERROR
```
- Package suggested but not available for checking: ‘OpenMx’
+ Running ‘testthat.R’
+ Running the tests in ‘tests/testthat.R’ failed.
+ Complete output:
+ > library(testthat)
+ > library(ggpath)
+ >
+ > test_check("ggpath")
+ [ FAIL 1 | WARN 0 | SKIP 5 | PASS 3 ]
+
+ ══ Skipped tests (5) ═══════════════════════════════════════════════════════════
+ ...
+ • geom_lines/p1.svg
+ • geom_lines/p2.svg
+ • geom_lines/p3.svg
+ • geom_lines/p4.svg
+ • geom_lines/p5.svg
+ • theme-elements/p1.svg
+ • theme-elements/p2.svg
+ • theme-elements/p3.svg
+ Error: Test failures
+ Execution halted
```
# ggplot2.utils
@@ -10214,58 +6745,6 @@ Run `revdepcheck::cloud_details(, "ggpubr")` for more info
Execution halted
```
-# ggquickeda
-
-
-
-* Version: 0.3.1
-* GitHub: https://github.com/smouksassi/ggquickeda
-* Source code: https://github.com/cran/ggquickeda
-* Date/Publication: 2024-01-15 10:20:02 UTC
-* Number of recursive dependencies: 174
-
-Run `revdepcheck::cloud_details(, "ggquickeda")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggquickeda-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: ggcontinuousexpdist
- > ### Title: Create a continuous exposure fit plot
- > ### Aliases: ggcontinuousexpdist
- >
- > ### ** Examples
- >
- > # Example 1
- ...
- Joining with `by = join_by(loopvariable, DOSE, quant_25)`
- Joining with `by = join_by(loopvariable, DOSE, quant_75)`
- Joining with `by = join_by(loopvariable, DOSE, medexp)`
- > a / b +
- + plot_layout(guides = "collect") &
- + theme(legend.position = "top")
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘RPostgres’ ‘colourpicker’ ‘ggpmisc’
- ‘ggpubr’ ‘glue’ ‘gridExtra’ ‘markdown’ ‘patchwork’ ‘plotly’
- ‘quantreg’ ‘shinyFiles’ ‘shinyjqui’ ‘shinyjs’ ‘table1’ ‘zoo’
- All declared Imports should be used.
- ```
-
# ggraph
@@ -10274,7 +6753,7 @@ Run `revdepcheck::cloud_details(, "ggquickeda")` for more info
* GitHub: https://github.com/thomasp85/ggraph
* Source code: https://github.com/cran/ggraph
* Date/Publication: 2024-03-07 12:40:02 UTC
-* Number of recursive dependencies: 113
+* Number of recursive dependencies: 112
Run `revdepcheck::cloud_details(, "ggraph")` for more info
@@ -10334,47 +6813,6 @@ Run `revdepcheck::cloud_details(, "ggraph")` for more info
libs 2.8Mb
```
-# ggredist
-
-
-
-* Version: 0.0.2
-* GitHub: https://github.com/alarm-redist/ggredist
-* Source code: https://github.com/cran/ggredist
-* Date/Publication: 2022-11-23 11:20:02 UTC
-* Number of recursive dependencies: 64
-
-Run `revdepcheck::cloud_details(, "ggredist")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘ggredist-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: geom_district_text
- > ### Title: Label Map Regions
- > ### Aliases: geom_district_text geom_district_label
- > ### stat_district_coordinates StatDistrictCoordinates GeomDistrictText
- > ### Keywords: datasets
- >
- > ### ** Examples
- ...
- 25. │ └─coord$transform(data, panel_params)
- 26. │ └─ggplot2 (local) transform(..., self = self)
- 27. │ └─ggplot2:::sf_rescale01(data[[geom_column(data)]], x_range, y_range)
- 28. │ └─sf::st_normalize(x, c(x_range[1], y_range[1], x_range[2], y_range[2]))
- 29. └─base::.handleSimpleError(...)
- 30. └─rlang (local) h(simpleError(msg, call))
- 31. └─handlers[[1L]](cnd)
- 32. └─cli::cli_abort(...)
- 33. └─rlang::abort(...)
- Execution halted
- ```
-
# ggResidpanel
@@ -10396,20 +6834,23 @@ Run `revdepcheck::cloud_details(, "ggResidpanel")` for more info
Running examples in ‘ggResidpanel-Ex.R’ failed
The error most likely occurred in:
- > ### Name: resid_interact
- > ### Title: Panel of Interactive Versions of Diagnostic Residual Plots.
- > ### Aliases: resid_interact
+ > ### Name: resid_panel
+ > ### Title: Panel of Diagnostic Residual Plots.
+ > ### Aliases: resid_panel
>
> ### ** Examples
>
>
- > # Fit a model to the penguin data
- > penguin_model <- lme4::lmer(heartrate ~ depth + duration + (1|bird), data = penguins)
- >
- > # Create the default interactive panel
- > resid_interact(penguin_model)
- Error in pm[[2]] : subscript out of bounds
- Calls: resid_interact ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list
+ ...
+ 36. │ └─ggplot2 (local) FUN(X[[i]], ...)
+ 37. │ └─self$draw_group(group, panel_params, coord, ...)
+ 38. │ └─ggplot2 (local) draw_group(...)
+ 39. │ └─ggplot2 (local) draw_group(..., self = self)
+ 40. └─base::.handleSimpleError(...)
+ 41. └─rlang (local) h(simpleError(msg, call))
+ 42. └─handlers[[1L]](cnd)
+ 43. └─cli::cli_abort(...)
+ 44. └─rlang::abort(...)
Execution halted
```
@@ -10517,44 +6958,6 @@ Run `revdepcheck::cloud_details(, "ggRtsy")` for more info
Note: found 19 marked UTF-8 strings
```
-# ggseas
-
-
-
-* Version: 0.5.4
-* GitHub: https://github.com/ellisp/ggseas
-* Source code: https://github.com/cran/ggseas
-* Date/Publication: 2018-06-12 13:33:33 UTC
-* Number of recursive dependencies: 62
-
-Run `revdepcheck::cloud_details(, "ggseas")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(ggseas)
- Loading required package: ggplot2
- >
- > test_check("ggseas")
- [ FAIL 1 | WARN 1 | SKIP 0 | PASS 9 ]
-
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Failure ('test-tsdf.R:22:4'): ggplot can draw graphic with tsdf output ──────
- class(tmp2) not equal to c("gg", "ggplot").
- Lengths differ: 5 is not 2
-
- [ FAIL 1 | WARN 1 | SKIP 0 | PASS 9 ]
- Error: Test failures
- Execution halted
- ```
-
# ggseqplot
@@ -10576,23 +6979,23 @@ Run `revdepcheck::cloud_details(, "ggseqplot")` for more info
Running examples in ‘ggseqplot-Ex.R’ failed
The error most likely occurred in:
- > ### Name: ggseqrfplot
- > ### Title: Relative Frequency Sequence Plot
- > ### Aliases: ggseqrfplot
+ > ### Name: ggseqtrplot
+ > ### Title: Sequence Transition Rate Plot
+ > ### Aliases: ggseqtrplot
>
> ### ** Examples
>
- > # Load additional library for fine-tuning the plots
+ > # Use example data from TraMineR: biofam data set
...
+ 8 7 7 Divorced
+ [>] sum of weights: 330.07 - min/max: 0/6.02881860733032
+ [>] 300 sequences in the data set
+ [>] min/max sequence length: 16/16
>
- > # ... with ggseqrfplot
- > ggseqrfplot(biofam.seq, weighted = FALSE, diss = diss, k = 12, grp.meth="first")
- [>] Using k=12 frequency groups with grp.meth='first'
- [>] Pseudo/medoid-based-R2: 0.4620155
- [>] Pseudo/medoid-based-F statistic: 6.870317, p-value: 3.09994e-08
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
+ > # Basic transition rate plot (with adjusted x-axis labels)
+ > ggseqtrplot(biofam.seq, x_n.dodge = 2)
+ Error in ggseqtrplot(biofam.seq, x_n.dodge = 2) :
+ labsize must be a single number
Execution halted
```
@@ -10616,7 +7019,7 @@ Run `revdepcheck::cloud_details(, "ggseqplot")` for more info
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─ggseqplot::ggseqtrplot(biofam.seq)
- [ FAIL 3 | WARN 16 | SKIP 0 | PASS 117 ]
+ [ FAIL 1 | WARN 16 | SKIP 0 | PASS 131 ]
Error: Test failures
Execution halted
```
@@ -10933,7 +7336,7 @@ Run `revdepcheck::cloud_details(, "ggswissmaps")` for more info
* GitHub: NA
* Source code: https://github.com/cran/ggtangle
* Date/Publication: 2024-12-18 14:30:06 UTC
-* Number of recursive dependencies: 76
+* Number of recursive dependencies: 75
Run `revdepcheck::cloud_details(, "ggtangle")` for more info
@@ -11041,69 +7444,6 @@ ERROR: lazy loading failed for package ‘ggtern’
```
-# ggtext
-
-
-
-* Version: 0.1.2
-* GitHub: https://github.com/wilkelab/ggtext
-* Source code: https://github.com/cran/ggtext
-* Date/Publication: 2022-09-16 11:36:07 UTC
-* Number of recursive dependencies: 76
-
-Run `revdepcheck::cloud_details(, "ggtext")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘plotting_text.Rmd’ using rmarkdown
- ```
-
-# ggtibble
-
-
-
-* Version: 1.0.1
-* GitHub: NA
-* Source code: https://github.com/cran/ggtibble
-* Date/Publication: 2024-06-19 12:50:02 UTC
-* Number of recursive dependencies: 72
-
-Run `revdepcheck::cloud_details(, "ggtibble")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘spelling.R’
- 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
- ...
- 3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
- 4. ├─ggtibble::new_gglist(list(ggplot2::labs("foo")))
- 5. └─ggplot2::labs("foo")
- 6. └─ggplot2::class_labels(args)
- 7. └─S7::new_object(labels)
- 8. └─S7::validate(object, recursive = !parent_validated)
-
- [ FAIL 1 | WARN 0 | SKIP 0 | PASS 59 ]
- Error: Test failures
- Execution halted
- ```
-
# ggtime
@@ -11149,10 +7489,10 @@ Run `revdepcheck::cloud_details(, "ggtime")` for more info
-* Version: 1.5.2
+* Version: 1.5.4
* GitHub: https://github.com/gaospecial/ggVennDiagram
* Source code: https://github.com/cran/ggVennDiagram
-* Date/Publication: 2024-02-20 08:10:02 UTC
+* Date/Publication: 2025-06-21 11:10:02 UTC
* Number of recursive dependencies: 94
Run `revdepcheck::cloud_details(, "ggVennDiagram")` for more info
@@ -11302,113 +7642,6 @@ Run `revdepcheck::cloud_details(, "graphPAF")` for more info
Execution halted
```
-# gratia
-
-
-
-* Version: 0.10.0
-* GitHub: https://github.com/gavinsimpson/gratia
-* Source code: https://github.com/cran/gratia
-* Date/Publication: 2024-12-19 19:10:02 UTC
-* Number of recursive dependencies: 153
-
-Run `revdepcheck::cloud_details(, "gratia")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘gratia-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: appraise
- > ### Title: Model diagnostic plots
- > ### Aliases: appraise appraise.gam appraise.lm
- >
- > ### ** Examples
- >
- > load_mgcv()
- ...
- > ## change the ggplot theme for all panels
- > library("ggplot2")
- > appraise(mod, seed = 42,
- + point_col = "steelblue", point_alpha = 0.4,
- + line_col = "black"
- + ) & theme_minimal()
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘test-all.R’
- Running the tests in ‘tests/test-all.R’ failed.
- Complete output:
- > ## Test `gratia` using the `testthat` package
- >
- > ## Setup
- > library("testthat")
- > library("gratia")
- >
- > ## Runs the tests in tests/testthat
- ...
- • penalty/draw-penalty-single-smooths-user-continuous-fill.svg
- • rootograms/draw-gaussian-rootogram.svg
- • rootograms/draw-neg-bin-rootogram.svg
- • rootograms/draw-neg-bin-sqrt-rootogram.svg
- • rootograms/draw-neg-bin-standing-rootogram.svg
- • rootograms/draw-neg-bin-suspended-rootogram.svg
- • soap-films/draw-gam-so-soap-film.svg
- • soap-films/draw-smooth-estimates-so-soap-film.svg
- Error: Test failures
- Execution halted
- ```
-
-# Greymodels
-
-
-
-* Version: 2.0.1
-* GitHub: https://github.com/havishaJ/Greymodels
-* Source code: https://github.com/cran/Greymodels
-* Date/Publication: 2022-12-05 12:42:35 UTC
-* Number of recursive dependencies: 86
-
-Run `revdepcheck::cloud_details(, "Greymodels")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘Greymodels-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: Plots
- > ### Title: plots
- > ### Aliases: plots plotrm plotsmv1 plotsmv2 plotsigndgm plots_mdbgm12
- >
- > ### ** Examples
- >
- > # Plots - EPGM (1, 1) model
- ...
- + geom_point(data = set4, aes(x = CI, y = y), shape = 23, color = "black") +
- + geom_line(data = xy1, aes(x = x, y = y,color = "Raw Data")) +
- + geom_line(data = xy2, aes(x = x, y = y,color = "Fitted&Forecasts")) +
- + geom_line(data = set3, aes(x = CI, y = y,color = "LowerBound"), linetype=2) +
- + geom_line(data = set4, aes(x = CI, y = y,color = "UpperBound"), linetype=2) +
- + scale_color_manual(name = "Label",values = colors)
- > r <- ggplotly(p)
- Error in pm[[2]] : subscript out of bounds
- Calls: ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# GRShiny
@@ -11551,50 +7784,24 @@ Run `revdepcheck::cloud_details(, "gtExtras")` for more info
Execution halted
```
-# guideR
+# handwriterRF
-* Version: 0.4.0
-* GitHub: https://github.com/larmarange/guideR
-* Source code: https://github.com/cran/guideR
-* Date/Publication: 2025-04-22 12:00:02 UTC
-* Number of recursive dependencies: 154
-
-Run `revdepcheck::cloud_details(, "guideR")` for more info
-
-
+* Version: 1.1.1
+* GitHub: https://github.com/CSAFE-ISU/handwriterRF
+* Source code: https://github.com/cran/handwriterRF
+* Date/Publication: 2025-01-29 00:20:01 UTC
+* Number of recursive dependencies: 123
-## Newly broken
+Run `revdepcheck::cloud_details(, "handwriterRF")` for more info
-* checking examples ... ERROR
- ```
- Running examples in ‘guideR-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_inertia_from_tree
- > ### Title: Plot inertia, absolute loss and relative loss from a
- > ### classification tree
- > ### Aliases: plot_inertia_from_tree get_inertia_from_tree
- > ### Keywords: tree
- >
- > ### ** Examples
- ...
- 11 11 38.5 -2.96 -0.0713
- 12 12 36.8 -1.68 -0.0436
- 13 13 36.7 -0.113 -0.00307
- 14 14 32.7 -4.02 -0.109
- 15 15 31.6 -1.10 -0.0336
- > plot_inertia_from_tree(hc)
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
+
+
+## Newly broken
* checking tests ... ERROR
```
- Running ‘spelling.R’
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
@@ -11604,17 +7811,18 @@ Run `revdepcheck::cloud_details(, "guideR")` for more info
> # 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
...
- ── Failure ('test-plot_inertia_from_tree.R:6:3'): plot_inertia_from_tree() does not produce an error ──
- Expected `plot_inertia_from_tree(hc)` to run without any errors.
- i Actually got a with text:
- Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
-
- [ FAIL 1 | WARN 34 | SKIP 4 | PASS 60 ]
- Error: Test failures
- Execution halted
+ Calculating similarity score...
+ Calculating distance between samples...
+ Calculating similarity score...
+ Calculating distance between samples...
+ Calculating similarity score...
+ Calculating SLR...
+ Calculating distance between samples...
+ Calculating similarity score...
+ Calculating SLR...
+ Killed
```
# harmony
@@ -11720,160 +7928,6 @@ Run `revdepcheck::cloud_details(, "hatchR")` for more info
doc 1.9Mb
```
-# healthyR
-
-
-
-* Version: 0.2.2
-* GitHub: https://github.com/spsanderson/healthyR
-* Source code: https://github.com/cran/healthyR
-* Date/Publication: 2024-07-01 13:20:02 UTC
-* Number of recursive dependencies: 145
-
-Run `revdepcheck::cloud_details(, "healthyR")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘getting-started.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.6Mb
- sub-directories of 1Mb or more:
- data 2.5Mb
- doc 3.7Mb
- ```
-
-# healthyR.ai
-
-
-
-* Version: 0.1.1
-* GitHub: https://github.com/spsanderson/healthyR.ai
-* Source code: https://github.com/cran/healthyR.ai
-* Date/Publication: 2025-04-24 11:40:17 UTC
-* Number of recursive dependencies: 203
-
-Run `revdepcheck::cloud_details(, "healthyR.ai")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘healthyR.ai-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: pca_your_recipe
- > ### Title: Perform PCA
- > ### Aliases: pca_your_recipe
- >
- > ### ** Examples
- >
- > suppressPackageStartupMessages(library(timetk))
- ...
- + step_rm(matches("(iso$)|(xts$)|(hour)|(min)|(sec)|(am.pm)"))
- >
- > output_list <- pca_your_recipe(rec_obj, .data = data_tbl)
- Warning: ! The following columns have zero variance so scaling cannot be used:
- date_col_day, date_col_mday, date_col_mweek, and date_col_mday7.
- ℹ Consider using ?step_zv (`?recipes::step_zv()`) to remove those columns
- before normalizing.
- Error in pm[[2]] : subscript out of bounds
- Calls: pca_your_recipe -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘auto-kmeans.Rmd’ using rmarkdown
- --- finished re-building ‘auto-kmeans.Rmd’
-
- --- re-building ‘getting-started.Rmd’ using rmarkdown
-
- Quitting from getting-started.Rmd:106-113 [pca_your_rec]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ...
- 2. ├─plotly::ggplotly(loadings_plt)
- 3. └─plotly:::ggplotly.ggplot(loadings_plt)
- 4. └─plotly::gg2list(...)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘getting-started.Rmd’
-
- --- re-building ‘kmeans-umap.Rmd’ using rmarkdown
- ```
-
-# healthyR.ts
-
-
-
-* Version: 0.3.1
-* GitHub: https://github.com/spsanderson/healthyR.ts
-* Source code: https://github.com/cran/healthyR.ts
-* Date/Publication: 2024-10-11 23:00:03 UTC
-* Number of recursive dependencies: 209
-
-Run `revdepcheck::cloud_details(, "healthyR.ts")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘healthyR.ts-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: tidy_fft
- > ### Title: Tidy Style FFT
- > ### Aliases: tidy_fft
- >
- > ### ** Examples
- >
- > suppressPackageStartupMessages(library(dplyr))
- ...
- > a <- tidy_fft(
- + .data = data_tbl,
- + .value_col = value,
- + .date_col = date_col,
- + .harmonics = 3,
- + .frequency = 12
- + )
- Error in pm[[2]] : subscript out of bounds
- Calls: tidy_fft -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘getting-started.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.3Mb
- sub-directories of 1Mb or more:
- doc 5.3Mb
- ```
-
# heatmaply
@@ -11903,43 +7957,18 @@ Run `revdepcheck::cloud_details(, "heatmaply")` for more info
Attaching package: 'plotly'
...
- 4. │ │ └─base::withCallingHandlers(...)
- 5. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
- 6. ├─heatmaply:::predict_colors(ggplotly(g), plot_method = "ggplot")
- 7. ├─plotly::ggplotly(g)
- 8. └─plotly:::ggplotly.ggplot(g)
- 9. └─plotly::gg2list(...)
+ 11. ├─ggplot2::theme(...)
+ 12. │ └─ggplot2:::find_args(..., complete = NULL, validate = NULL)
+ 13. │ └─base::mget(args, envir = env)
+ 14. └─ggplot2::element_text(...)
+ 15. └─S7::new_object(...)
+ 16. └─S7::validate(object, recursive = !parent_validated)
- [ FAIL 58 | WARN 0 | SKIP 0 | PASS 193 ]
+ [ FAIL 1 | WARN 1 | SKIP 0 | PASS 264 ]
Error: Test failures
Execution halted
```
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘heatmaply.Rmd’ using rmarkdown
-
- Quitting from heatmaply.Rmd:108-111 [unnamed-chunk-5]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘heatmaply.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘heatmaply.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
## In both
* checking installed package size ... NOTE
@@ -12014,62 +8043,6 @@ Run `revdepcheck::cloud_details(, "hesim")` for more info
libs 30.8Mb
```
-# hmsidwR
-
-
-
-* Version: 1.1.2
-* GitHub: https://github.com/Fgazzelloni/hmsidwR
-* Source code: https://github.com/cran/hmsidwR
-* Date/Publication: 2024-11-13 15:00:02 UTC
-* Number of recursive dependencies: 175
-
-Run `revdepcheck::cloud_details(, "hmsidwR")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- ...
- --- re-building ‘hmsidwR.Rmd’ using rmarkdown
-
- Quitting from hmsidwR.Rmd:51-84 [unnamed-chunk-6]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- ...
-
- Error: processing vignette 'hmsidwR.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘hmsidwR.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘hmsidwR.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.2Mb
- sub-directories of 1Mb or more:
- data 2.0Mb
- doc 4.0Mb
- ```
-
-* checking data for non-ASCII characters ... NOTE
- ```
- Note: found 1686 marked UTF-8 strings
- ```
-
# hrbrthemes
@@ -12111,47 +8084,6 @@ Run `revdepcheck::cloud_details(, "hrbrthemes")` for more info
Execution halted
```
-# HVT
-
-
-
-* Version: 25.2.4
-* GitHub: https://github.com/Mu-Sigma/HVT
-* Source code: https://github.com/cran/HVT
-* Date/Publication: 2025-06-10 12:40:21 UTC
-* Number of recursive dependencies: 208
-
-Run `revdepcheck::cloud_details(, "HVT")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘HVT-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: clustHVT
- > ### Title: Performing Hierarchical Clustering Analysis
- > ### Aliases: clustHVT
- > ### Keywords: Clustering_Analysis
- >
- > ### ** Examples
- >
- ...
- > scoring <- scoreHVT(dataset, hvt.results, analysis.plots = TRUE, names.column = dataset[,1])
- Scale for colour is already present.
- Adding another scale for colour, which will replace the existing scale.
- Scale for x is already present.
- Adding another scale for x, which will replace the existing scale.
- Scale for y is already present.
- Adding another scale for y, which will replace the existing scale.
- Error in pm[[2]] : subscript out of bounds
- Calls: scoreHVT
- Execution halted
- ```
-
# hyperoverlap
@@ -12184,39 +8116,6 @@ Run `revdepcheck::cloud_details(, "hyperoverlap")` for more info
doc 6.3Mb
```
-# hypervolume
-
-
-
-* Version: 3.1.5
-* GitHub: https://github.com/bblonder/hypervolume
-* Source code: https://github.com/cran/hypervolume
-* Date/Publication: 2025-01-17 20:50:16 UTC
-* Number of recursive dependencies: 142
-
-Run `revdepcheck::cloud_details(, "hypervolume")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘hypervolume’ can be installed ... WARNING
- ```
- Found the following significant warnings:
- Warning: replacing previous import ‘e1071::element’ by ‘ggplot2::element’ when loading ‘hypervolume’
- See ‘/tmp/workdir/hypervolume/new/hypervolume.Rcheck/00install.out’ for details.
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.4Mb
- sub-directories of 1Mb or more:
- doc 2.8Mb
- libs 2.4Mb
- ```
-
# hypsoLoop
@@ -12362,101 +8261,29 @@ Run `revdepcheck::cloud_details(, "imputeTS")` for more info
--- re-building ‘imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx’ using tex
Error: processing vignette 'imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx' failed with diagnostics:
Running 'texi2dvi' on 'imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx' failed.
- LaTeX errors:
- ! LaTeX Error: File `etex.sty' not found.
-
- ...
-
- ! Emergency stop.
-
-
- l.5 \usepackage
- [utf8]{inputenc}^^M
- ! ==> Fatal error occurred, no output PDF file produced!
- --- failed re-building ‘imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx’
-
- --- re-building ‘gallery_visualizations.Rmd’ using rmarkdown
- ```
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.7Mb
- sub-directories of 1Mb or more:
- data 2.0Mb
- doc 1.1Mb
- libs 1.9Mb
- ```
-
-# incidence
-
-
-
-* Version: 1.7.5
-* GitHub: https://github.com/reconhub/incidence
-* Source code: https://github.com/cran/incidence
-* Date/Publication: 2024-05-31 10:10:02 UTC
-* Number of recursive dependencies: 65
-
-Run `revdepcheck::cloud_details(, "incidence")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘incidence-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: get_fit
- > ### Title: Accessors for 'incidence_fit' objects
- > ### Aliases: get_fit get_fit.incidence_fit get_fit.incidence_fit_list
- > ### get_info get_info.incidence_fit get_info.incidence_fit_list
- >
- > ### ** Examples
- >
- ...
- + })}
- Loading required package: outbreaks
- > dat <- ebola_sim$linelist$date_of_onset
- > sex <- ebola_sim$linelist$gender
- > i.sex <- incidence(dat, interval = 7, group = sex)
- > fits <- fit_optim_split(i.sex, separate_split = TRUE)
- Error in names(out$plot) <- names(res) :
- invalid to use names()<- on an S4 object of class 'ggplot2::ggplot'
- Calls: withAutoprint ... source -> withVisible -> eval -> eval -> fit_optim_split
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(incidence)
- >
- > test_check("incidence")
- [ FAIL 1 | WARN 0 | SKIP 18 | PASS 213 ]
-
- ══ Skipped tests (18) ══════════════════════════════════════════════════════════
+ LaTeX errors:
+ ! LaTeX Error: File `etex.sty' not found.
+
...
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Error ('test-accessors.R:156:1'): (code run outside of `test_that()`) ───────
- Error in `names(out$plot) <- names(res)`: invalid to use names()<- on an S4 object of class 'ggplot2::ggplot'
- Backtrace:
- ▆
- 1. └─incidence::fit_optim_split(i.sex.o) at test-accessors.R:156:1
-
- [ FAIL 1 | WARN 0 | SKIP 18 | PASS 213 ]
- Error: Test failures
- Execution halted
+
+ ! Emergency stop.
+
+
+ l.5 \usepackage
+ [utf8]{inputenc}^^M
+ ! ==> Fatal error occurred, no output PDF file produced!
+ --- failed re-building ‘imputeTS-Time-Series-Missing-Value-Imputation-in-R.ltx’
+
+ --- re-building ‘gallery_visualizations.Rmd’ using rmarkdown
```
-* checking re-building of vignette outputs ... ERROR
+* checking installed package size ... NOTE
```
- Error(s) in re-building vignettes:
- --- re-building ‘conversions.Rmd’ using rmarkdown
+ installed size is 5.7Mb
+ sub-directories of 1Mb or more:
+ data 2.0Mb
+ doc 1.1Mb
+ libs 1.9Mb
```
# infer
@@ -12510,57 +8337,6 @@ Run `revdepcheck::cloud_details(, "infer")` for more info
Extensions’ manual.
```
-# inferCSN
-
-
-
-* Version: 1.1.7
-* GitHub: https://github.com/mengxu98/inferCSN
-* Source code: https://github.com/cran/inferCSN
-* Date/Publication: 2025-03-30 17:00:02 UTC
-* Number of recursive dependencies: 186
-
-Run `revdepcheck::cloud_details(, "inferCSN")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘inferCSN-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_dynamic_networks
- > ### Title: Plot dynamic networks
- > ### Aliases: plot_dynamic_networks
- >
- > ### ** Examples
- >
- > data("example_matrix")
- ...
- + )
- >
- > plot_dynamic_networks(
- + network,
- + celltypes_order = celltypes_order,
- + plot_type = "ggplotly"
- + )
- Error in pm[[2]] : subscript out of bounds
- Calls: plot_dynamic_networks -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 27.7Mb
- sub-directories of 1Mb or more:
- data 2.0Mb
- libs 25.1Mb
- ```
-
# inTextSummaryTable
@@ -12636,65 +8412,6 @@ Run `revdepcheck::cloud_details(, "inTextSummaryTable")` for more info
doc 9.7Mb
```
-# inventorize
-
-
-
-* Version: 1.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/inventorize
-* Date/Publication: 2025-05-28 13:20:02 UTC
-* Number of recursive dependencies: 68
-
-Run `revdepcheck::cloud_details(, "inventorize")` for more info
-
-
-
-## Newly broken
-
-* checking whether package ‘inventorize’ can be installed ... ERROR
- ```
- Installation failed.
- See ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/00install.out’ for details.
- ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘inventorize’ ...
-** package ‘inventorize’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** byte-compile and prepare package for lazy loading
-Error in pm[[2]] : subscript out of bounds
-Error: unable to load R code in package ‘inventorize’
-Execution halted
-ERROR: lazy loading failed for package ‘inventorize’
-* removing ‘/tmp/workdir/inventorize/new/inventorize.Rcheck/inventorize’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘inventorize’ ...
-** package ‘inventorize’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** byte-compile and prepare package for lazy loading
-Warning in qgamma(service_level, alpha, beta) : NaNs produced
-** 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 (inventorize)
-
-
-```
# iNZightTS
@@ -12720,18 +8437,18 @@ Run `revdepcheck::cloud_details(, "iNZightTS")` for more info
> library(iNZightTS)
>
> test_check("iNZightTS")
- [ FAIL 6 | WARN 3 | SKIP 0 | PASS 91 ]
+ [ FAIL 1 | WARN 3 | SKIP 0 | PASS 107 ]
══ Failed tests ════════════════════════════════════════════════════════════════
...
- ▆
- 1. ├─base::plot(tm, names(tm)[-1], xlim = c(2000, 2011)) at test_subset.R:44:5
- 2. └─iNZightTS:::plot.inz_ts(tm, names(tm)[-1], xlim = c(2000, 2011))
- 3. ├─(function(.) structure(., use.plotly = ggplotable(.)))(...)
- 4. │ └─base::structure(., use.plotly = ggplotable(.))
- 5. └─S7:::Ops.S7_object(...)
+ 9. └─ggplot2::coord_fixed(...)
+ 10. └─ggplot2::coord_cartesian(ratio = ratio)
+ 11. └─ggplot2:::check_number_decimal(...)
+ 12. └─ggplot2:::.stop_not_number(...)
+ 13. └─ggplot2:::stop_input_type(...)
+ 14. └─rlang::abort(message, ..., call = call, arg = arg)
- [ FAIL 6 | WARN 3 | SKIP 0 | PASS 91 ]
+ [ FAIL 1 | WARN 3 | SKIP 0 | PASS 107 ]
Error: Test failures
Execution halted
```
@@ -12848,10 +8565,10 @@ Run `revdepcheck::cloud_details(, "isoorbi")` for more info
-* Version: 0.5.11
+* Version: 0.5.13
* GitHub: https://github.com/jinseob2kim/jstable
* Source code: https://github.com/cran/jskm
-* Date/Publication: 2025-03-20 03:10:02 UTC
+* Date/Publication: 2025-06-12 15:20:06 UTC
* Number of recursive dependencies: 108
Run `revdepcheck::cloud_details(, "jskm")` for more info
@@ -12866,136 +8583,6 @@ Run `revdepcheck::cloud_details(, "jskm")` for more info
--- re-building ‘jskm.Rmd’ using rmarkdown
```
-# karel
-
-
-
-* Version: 0.1.1
-* GitHub: https://github.com/mpru/karel
-* Source code: https://github.com/cran/karel
-* Date/Publication: 2022-03-26 21:50:02 UTC
-* Number of recursive dependencies: 86
-
-Run `revdepcheck::cloud_details(, "karel")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘karel-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: acciones
- > ### Title: Acciones que Karel puede realizar
- > ### Aliases: acciones avanzar girar_izquierda poner_coso juntar_coso
- > ### girar_derecha darse_vuelta
- >
- > ### ** Examples
- >
- ...
- 1. └─karel::ejecutar_acciones()
- 2. ├─base::suppressWarnings(...)
- 3. │ └─base::withCallingHandlers(...)
- 4. ├─gganimate::animate(...)
- 5. └─gganimate:::animate.gganim(...)
- 6. └─args$renderer(frames_vars$frame_source, args$fps)
- 7. └─gganimate:::png_dim(frames[1])
- 8. └─cli::cli_abort("Provided file ({file}) does not exist")
- 9. └─rlang::abort(...)
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(karel)
- >
- > test_check("karel")
- [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ]
-
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ...
- 5. ├─gganimate::animate(...)
- 6. └─gganimate:::animate.gganim(...)
- 7. └─args$renderer(frames_vars$frame_source, args$fps)
- 8. └─gganimate:::png_dim(frames[1])
- 9. └─cli::cli_abort("Provided file ({file}) does not exist")
- 10. └─rlang::abort(...)
-
- [ FAIL 2 | WARN 2 | SKIP 0 | PASS 78 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespace in Imports field not imported from: ‘gifski’
- All declared Imports should be used.
- ```
-
-# kDGLM
-
-
-
-* Version: 1.2.7
-* GitHub: https://github.com/silvaneojunior/kDGLM
-* Source code: https://github.com/cran/kDGLM
-* Date/Publication: 2025-03-20 01:00:03 UTC
-* Number of recursive dependencies: 132
-
-Run `revdepcheck::cloud_details(, "kDGLM")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘kDGLM-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: forecast.fitted_dlm
- > ### Title: Auxiliary function for forecasting
- > ### Aliases: forecast.fitted_dlm
- >
- > ### ** Examples
- >
- >
- ...
- Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
- ℹ Please use tidy evaluation idioms with `aes()`.
- ℹ See also `vignette("ggplot2-in-packages")` for more information.
- ℹ The deprecated feature was likely used in the kDGLM package.
- Please report the issue at .
- Scale for y is already present.
- Adding another scale for y, which will replace the existing scale.
- Error in pm[[2]] : subscript out of bounds
- Calls: forecast ... lapply -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘example1.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 10.9Mb
- sub-directories of 1Mb or more:
- doc 9.9Mb
- ```
-
# lares
@@ -13037,74 +8624,6 @@ Run `revdepcheck::cloud_details(, "lares")` for more info
Execution halted
```
-# latentcor
-
-
-
-* Version: 2.0.1
-* GitHub: NA
-* Source code: https://github.com/cran/latentcor
-* Date/Publication: 2022-09-05 20:50:02 UTC
-* Number of recursive dependencies: 141
-
-Run `revdepcheck::cloud_details(, "latentcor")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘latentcor-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: latentcor
- > ### Title: Estimate latent correlation for mixed types.
- > ### Aliases: latentcor
- >
- > ### ** Examples
- >
- > # Example 1 - truncated data type, same type for all variables
- ...
- > R_approx = latentcor(X = X, types = "tru", method = "approx")$R
- > proc.time() - start_time
- user system elapsed
- 0.025 0.000 0.024
- > # Heatmap for latent correlation matrix.
- > Heatmap_R_approx = latentcor(X = X, types = "tru", method = "approx",
- + showplot = TRUE)$plotR
- Error in pm[[2]] : subscript out of bounds
- Calls: latentcor ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking Rd files ... NOTE
- ```
- checkRd: (-1) evaluation.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:46: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) evaluation.Rd:47: Lost braces in \itemize; \value handles \item{}{} directly
- ...
- checkRd: (-1) gen_data.Rd:35: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) gen_data.Rd:36-37: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) get_types.Rd:17: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) interpolation.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) interpolation.Rd:24: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) latentcor.Rd:38: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) latentcor.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) latentcor.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) latentcor.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) latentcor.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly
- ```
-
# latrend
@@ -13113,56 +8632,9 @@ Run `revdepcheck::cloud_details(, "latentcor")` for more info
* GitHub: https://github.com/philips-software/latrend
* Source code: https://github.com/cran/latrend
* Date/Publication: 2024-05-15 11:50:02 UTC
-* Number of recursive dependencies: 237
-
-Run `revdepcheck::cloud_details(, "latrend")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘latrend-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: qqPlot
- > ### Title: Quantile-quantile plot
- > ### Aliases: qqPlot
- >
- > ### ** Examples
- >
- > data(latrendData)
- ...
- 26. │ └─ggplot2 (local) FUN(X[[i]], ...)
- 27. │ └─self$draw_group(group, panel_params, coord, ...)
- 28. │ └─ggplot2 (local) draw_group(...)
- 29. │ └─ggplot2 (local) draw_group(..., self = self)
- 30. └─base::.handleSimpleError(...)
- 31. └─rlang (local) h(simpleError(msg, call))
- 32. └─handlers[[1L]](cnd)
- 33. └─cli::cli_abort(...)
- 34. └─rlang::abort(...)
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘demo.Rmd’ using rmarkdown
- ```
-
-# lcars
-
-
-
-* Version: 0.4.0
-* GitHub: https://github.com/leonawicz/lcars
-* Source code: https://github.com/cran/lcars
-* Date/Publication: 2024-09-11 22:52:42 UTC
-* Number of recursive dependencies: 84
+* Number of recursive dependencies: 237
-Run `revdepcheck::cloud_details(, "lcars")` for more info
+Run `revdepcheck::cloud_details(, "latrend")` for more info
@@ -13170,52 +8642,33 @@ Run `revdepcheck::cloud_details(, "lcars")` for more info
* checking examples ... ERROR
```
- Running examples in ‘lcars-Ex.R’ failed
+ Running examples in ‘latrend-Ex.R’ failed
The error most likely occurred in:
- > ### Name: lcars_border
- > ### Title: LCARS border plot
- > ### Aliases: lcars_border
+ > ### Name: qqPlot
+ > ### Title: Quantile-quantile plot
+ > ### Aliases: qqPlot
>
> ### ** Examples
>
- > lcars_border()
+ > data(latrendData)
...
- >
- > len_frac <- c(0.3, 0.5, 0.2, 0.4, 0.3, 0.2, 0.1, 0.3)
- > n_seg <- c(1, 2, 0, 8)
- >
- > library(ggplot2)
- > g <- ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
- + geom_point() + facet_wrap(~Species, 2) + theme_lcars_light()
- Error: object properties are invalid:
- - @family must be or , not
+ 26. │ └─ggplot2 (local) FUN(X[[i]], ...)
+ 27. │ └─self$draw_group(group, panel_params, coord, ...)
+ 28. │ └─ggplot2 (local) draw_group(...)
+ 29. │ └─ggplot2 (local) draw_group(..., self = self)
+ 30. └─base::.handleSimpleError(...)
+ 31. └─rlang (local) h(simpleError(msg, call))
+ 32. └─handlers[[1L]](cnd)
+ 33. └─cli::cli_abort(...)
+ 34. └─rlang::abort(...)
Execution halted
```
* checking re-building of vignette outputs ... ERROR
```
Error(s) in re-building vignettes:
- --- re-building ‘lcars.Rmd’ using rmarkdown
-
- Quitting from lcars.Rmd:20-54 [ex-1]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error:
- ! object properties are invalid:
- - @family must be or , not
- ---
- ...
- Error: processing vignette 'lcars.Rmd' failed with diagnostics:
- object properties are invalid:
- - @family must be or , not
- --- failed re-building ‘lcars.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘lcars.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
+ --- re-building ‘demo.Rmd’ using rmarkdown
```
# legendry
@@ -13378,11 +8831,6 @@ Run `revdepcheck::cloud_details(, "lemon")` for more info
function(object, plot, ...)
ggplot_add.axis_annotation:
function(object, plot, object_name)
-
- ggplot_gtable:
- function(plot)
- ggplot_gtable.built_lemon:
- function(data)
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
```
@@ -13408,37 +8856,42 @@ Run `revdepcheck::cloud_details(, "lfproQC")` for more info
Running examples in ‘lfproQC-Ex.R’ failed
The error most likely occurred in:
- > ### Name: Boxplot_data
- > ### Title: Creating Boxplot for a dataset
- > ### Aliases: Boxplot_data
+ > ### Name: QQplot_data
+ > ### Title: Creating QQ-Plot for a dataset
+ > ### Aliases: QQplot_data
>
> ### ** Examples
>
- > Boxplot_data(yeast_data)
- Using Majority protein IDs as id variables
- Warning: Removed 269 rows containing non-finite outside the scale range
- (`stat_boxplot()`).
- Error in pm[[2]] : subscript out of bounds
- Calls: Boxplot_data -> -> ggplotly.ggplot -> gg2list
+ > qqplot <- QQplot_data(rlr_knn_yeast_data)
+ ...
+ 11. ├─tidyr:::wrap_error_names(...)
+ 12. │ └─base::withCallingHandlers(...)
+ 13. └─vctrs::vec_cbind(...)
+ 14. └─vctrs (local) ``()
+ 15. └─vctrs:::validate_unique(names = names, arg = arg, call = call)
+ 16. └─vctrs:::stop_names_must_be_unique(names, arg, call = call)
+ 17. └─vctrs:::stop_names(...)
+ 18. └─vctrs:::stop_vctrs(...)
+ 19. └─rlang::abort(message, class = c(class, "vctrs_error"), ..., call = call)
Execution halted
```
* checking re-building of vignette outputs ... ERROR
```
Error(s) in re-building vignettes:
+ ...
--- re-building ‘user_guide.Rmd’ using rmarkdown
- Quitting from user_guide.Rmd:54-56 [unnamed-chunk-8]
+ Quitting from user_guide.Rmd:74-76 [unnamed-chunk-12]
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ NULL
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
Error: processing vignette 'user_guide.Rmd' failed with diagnostics:
- subscript out of bounds
+ ...
+ ✖ These names are duplicated:
+ * "variable" at locations 4 and 14.
+ ℹ Use argument `names_repair` to specify repair strategy.
--- failed re-building ‘user_guide.Rmd’
SUMMARY: processing the following file failed:
@@ -13484,7 +8937,7 @@ Run `revdepcheck::cloud_details(, "lgpr")` for more info
`c2` not equal to c("gg", "ggplot").
Lengths differ: 5 is not 2
- [ FAIL 2 | WARN 2 | SKIP 0 | PASS 446 ]
+ [ FAIL 2 | WARN 1 | SKIP 0 | PASS 446 ]
Error: Test failures
Execution halted
```
@@ -13511,34 +8964,6 @@ Run `revdepcheck::cloud_details(, "lgpr")` for more info
GNU make is a SystemRequirements.
```
-# lionfish
-
-
-
-* Version: 1.0.27
-* GitHub: NA
-* Source code: https://github.com/cran/lionfish
-* Date/Publication: 2025-03-13 20:50:02 UTC
-* Number of recursive dependencies: 125
-
-Run `revdepcheck::cloud_details(, "lionfish")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘Bioprocess-Optimization.Rmd’ using knitr
- --- finished re-building ‘Bioprocess-Optimization.Rmd’
-
- --- re-building ‘General-interactivity.Rmd’ using knitr
- --- finished re-building ‘General-interactivity.Rmd’
-
- --- re-building ‘Market-segmentation.Rmd’ using knitr
- ```
-
# listdown
@@ -13669,80 +9094,6 @@ Run `revdepcheck::cloud_details(, "LMD")` for more info
--- re-building ‘Getting_Started_with_LMD.Rmd’ using rmarkdown
```
-# lnmixsurv
-
-
-
-* Version: 3.1.6
-* GitHub: NA
-* Source code: https://github.com/cran/lnmixsurv
-* Date/Publication: 2024-09-03 15:20:08 UTC
-* Number of recursive dependencies: 195
-
-Run `revdepcheck::cloud_details(, "lnmixsurv")` 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
- ...
-
- Error in `pm[[2]]`: subscript out of bounds
- Backtrace:
- ▆
- 1. └─testthat::expect_snapshot(plot(mod1)) at test-survival_ln_mixture_em-methods.R:25:3
- 2. └─rlang::cnd_signal(state$error)
-
- [ FAIL 1 | WARN 0 | SKIP 7 | PASS 50 ]
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘compare.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 10.2Mb
- sub-directories of 1Mb or more:
- doc 4.0Mb
- libs 5.8Mb
- ```
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘purrr’ ‘readr’
- All declared Imports should be used.
- ```
-
-* checking Rd cross-references ... NOTE
- ```
- Package unavailable to check Rd xrefs: ‘rstanarm’
- ```
-
-* checking for GNU extensions in Makefiles ... NOTE
- ```
- GNU make is a SystemRequirements.
- ```
-
# longevity
@@ -13751,7 +9102,7 @@ Run `revdepcheck::cloud_details(, "lnmixsurv")` for more info
* GitHub: https://github.com/lbelzile/longevity
* Source code: https://github.com/cran/longevity
* Date/Publication: 2025-05-12 02:10:02 UTC
-* Number of recursive dependencies: 52
+* Number of recursive dependencies: 58
Run `revdepcheck::cloud_details(, "longevity")` for more info
@@ -13819,54 +9170,6 @@ Run `revdepcheck::cloud_details(, "longevity")` for more info
libs 2.3Mb
```
-# LSX
-
-
-
-* Version: 1.4.4
-* GitHub: https://github.com/koheiw/LSX
-* Source code: https://github.com/cran/LSX
-* Date/Publication: 2025-05-23 09:02:06 UTC
-* Number of recursive dependencies: 90
-
-Run `revdepcheck::cloud_details(, "LSX")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘spelling.R’
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > require(testthat)
- Loading required package: testthat
- > require(quanteda)
- Loading required package: quanteda
- Package version: 4.3.0
- Unicode version: 15.1
- ...
- ── Failure ('test-textplot.R:84:5'): textplot_components() works ───────────────
- class(textplot_components(lss_svd, 3, scale = "relative")) not equal to c("gg", "ggplot").
- Lengths differ: 5 is not 2
- ── Failure ('test-textplot.R:109:5'): textplot_terms works even when frequency has zeros (#85) ──
- class(textplot_terms(lss)) not equal to c("gg", "ggplot").
- Lengths differ: 5 is not 2
-
- [ FAIL 24 | WARN 0 | SKIP 10 | PASS 221 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking data for non-ASCII characters ... NOTE
- ```
- Note: found 2096 marked UTF-8 strings
- ```
-
# ltertools
@@ -13908,47 +9211,6 @@ Run `revdepcheck::cloud_details(, "ltertools")` for more info
Execution halted
```
-# manydata
-
-
-
-* Version: 1.0.2
-* GitHub: https://github.com/globalgov/manydata
-* Source code: https://github.com/cran/manydata
-* Date/Publication: 2025-06-03 08:40:02 UTC
-* Number of recursive dependencies: 115
-
-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)
- Loading required package: cli
- Loading required package: dplyr
-
- Attaching package: 'dplyr'
-
- ...
- ── Failure ('test_compare.R:6:3'): plot for compare_categories returns the correct output format ──
- `db` has length 1, not length 11.
- ── Failure ('test_compare.R:48:3'): compare_overlap() and return the correct output format ──
- `pl` has type 'object', not 'list'.
- ── Failure ('test_compare.R:60:3'): compare_missing() and plot_missing() returns the correct output format ──
- `pl` has type 'object', not 'list'.
-
- [ FAIL 5 | WARN 1 | SKIP 3 | PASS 122 ]
- Error: Test failures
- Execution halted
- ```
-
# manymodelr
@@ -13980,7 +9242,7 @@ Run `revdepcheck::cloud_details(, "manymodelr")` for more info
* GitHub: https://github.com/stocnet/manynet
* Source code: https://github.com/cran/manynet
* Date/Publication: 2024-11-05 20:50:02 UTC
-* Number of recursive dependencies: 142
+* Number of recursive dependencies: 135
Run `revdepcheck::cloud_details(, "manynet")` for more info
@@ -14079,23 +9341,23 @@ Run `revdepcheck::cloud_details(, "marquee")` for more info
Running examples in ‘marquee-Ex.R’ failed
The error most likely occurred in:
- > ### Name: element_marquee
- > ### Title: ggplot2 theme element supporting marquee syntax
- > ### Aliases: element_marquee
+ > ### Name: guide_marquee
+ > ### Title: Marquee subtitle guide
+ > ### Aliases: guide_marquee
>
> ### ** Examples
>
> ## Don't show:
...
- + What more could you _possibly_ want?") +
- + theme(title = element_marquee())
- + ## Don't show:
- + }) # examplesIf
- > library(ggplot2)
- > p <- ggplot(mtcars) + geom_point(aes(mpg, disp)) + labs(title = "A {.red *marquee*} title\n* Look at this bullet list\n\n* great, huh?") +
- + theme_gray(base_size = 6) + theme(title = element_marquee())
- > plot(p)
- Error: `object` must be an , not a S3
+ Warning in split.default(glyphs, rep(seq_len(n_breaks), each = n_layers)) :
+ data length is not a multiple of split variable
+ Warning in max(unlist(width)) :
+ no non-missing arguments to max; returning -Inf
+ Warning in max(unlist(height)) :
+ no non-missing arguments to max; returning -Inf
+ Error in gridGTreeCoords(unname(lapply(x$children[x$childrenOrder], grobCoords, :
+ Invalid gTree coordinates
+ Calls: ... lapply -> FUN -> grobCoords.gTree -> gridGTreeCoords
Execution halted
```
@@ -14113,156 +9375,41 @@ Run `revdepcheck::cloud_details(, "marquee")` for more info
-* Version: 1.0.5
-* GitHub: NA
-* Source code: https://github.com/cran/MaxWiK
-* Date/Publication: 2024-11-25 11:40:13 UTC
-* Number of recursive dependencies: 54
-
-Run `revdepcheck::cloud_details(, "MaxWiK")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘User-Guide.Rmd’ using rmarkdown
- # Input data
-
- ## Data format
-
- The data format of input should be numerical only in the form of data frame, for example:
-
-
- ``` r
- ...
-
- Error: processing vignette 'User-Guide.Rmd' failed with diagnostics:
- `object` must be an , not a S3
- --- failed re-building ‘User-Guide.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘User-Guide.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-# MBMethPred
-
-
-
-* Version: 0.1.4.2
-* GitHub: https://github.com/sharifrahmanie/MBMethPred
-* Source code: https://github.com/cran/MBMethPred
-* Date/Publication: 2023-09-18 14:10:09 UTC
-* Number of recursive dependencies: 138
-
-Run `revdepcheck::cloud_details(, "MBMethPred")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(MBMethPred)
- >
- > test_check("MBMethPred")
- y_pred
- y_true Group3 SHH Group4
- Group3 1 0 0
- ...
-
- [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
-
- ══ Failed tests ════════════════════════════════════════════════════════════════
- ── Failure ('test-BoxPlot.R:8:3'): MakeBoxPlot returns correct type ────────────
- BoxPlot(File = data) has type 'object', not 'list'.
-
- [ FAIL 1 | WARN 0 | SKIP 0 | PASS 11 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 10.2Mb
- sub-directories of 1Mb or more:
- R 3.0Mb
- data 7.0Mb
- ```
-
-# mcp
-
-
-
-* Version: 0.3.4
-* GitHub: https://github.com/lindeloev/mcp
-* Source code: https://github.com/cran/mcp
-* Date/Publication: 2024-03-17 20:10:02 UTC
-* Number of recursive dependencies: 96
+* Version: 1.0.5
+* GitHub: NA
+* Source code: https://github.com/cran/MaxWiK
+* Date/Publication: 2024-11-25 11:40:13 UTC
+* Number of recursive dependencies: 54
-Run `revdepcheck::cloud_details(, "mcp")` for more info
+Run `revdepcheck::cloud_details(, "MaxWiK")` for more info
## Newly broken
-* checking examples ... ERROR
+* checking re-building of vignette outputs ... ERROR
```
- Running examples in ‘mcp-Ex.R’ failed
- The error most likely occurred in:
+ Error(s) in re-building vignettes:
+ --- re-building ‘User-Guide.Rmd’ using rmarkdown
+ # Input data
- > ### Name: plot_pars
- > ### Title: Plot individual parameters
- > ### Aliases: plot_pars
- >
- > ### ** Examples
- >
- > # Typical usage. demo_fit is an mcpfit object.
- > plot_pars(demo_fit)
- Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
- ℹ Please use `linewidth` instead.
- ℹ The deprecated feature was likely used in the bayesplot package.
- Please report the issue at .
- Error: Can't find method for generic `&(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(mcp)
- >
- > test_check("mcp")
- [ FAIL 24 | WARN 2 | SKIP 6 | PASS 749 ]
-
- ══ Skipped tests (6) ═══════════════════════════════════════════════════════════
+ ## Data format
+
+ The data format of input should be numerical only in the form of data frame, for example:
+
+
+ ``` r
...
- Backtrace:
- ▆
- 1. └─mcp:::test_runs(model, ...) at tests/testthat/helper-runs.R:338:7
- 2. └─mcp:::test_plot_pars(fit) at tests/testthat/helper-runs.R:112:7
- 3. └─mcp::plot_pars(fit, type = "dens_overlay") at tests/testthat/helper-runs.R:171:3
- 4. └─S7:::Ops.S7_object(...)
-
- [ FAIL 24 | WARN 2 | SKIP 6 | PASS 749 ]
- Error: Test failures
- Execution halted
+
+ Error: processing vignette 'User-Guide.Rmd' failed with diagnostics:
+ Can't find method for `draw_element(S3)`.
+ --- failed re-building ‘User-Guide.Rmd’
+
+ SUMMARY: processing the following file failed:
+ ‘User-Guide.Rmd’
+
+ Error: Vignette re-building failed.
+ Execution halted
```
# mcStats
@@ -14335,52 +9482,6 @@ Run `revdepcheck::cloud_details(, "meme")` for more info
--- re-building ‘meme.Rmd’ using rmarkdown
```
-# MendelianRandomization
-
-
-
-* Version: 0.10.0
-* GitHub: NA
-* Source code: https://github.com/cran/MendelianRandomization
-* Date/Publication: 2024-04-12 10:10:02 UTC
-* Number of recursive dependencies: 85
-
-Run `revdepcheck::cloud_details(, "MendelianRandomization")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘MendelianRandomization-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: mr_plot
- > ### Title: Draw a scatter plot of the genetic associations and/or causal
- > ### estimates
- > ### Aliases: mr_plot mr_plot,MRInput-method mr_plot,MRAll-method
- > ### mr_plot,MRMVInput-method
- >
- > ### ** Examples
- >
- > mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
- + line="egger", orientate = TRUE)
- Error in pm[[2]] : subscript out of bounds
- Calls: mr_plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.9Mb
- sub-directories of 1Mb or more:
- R 1.0Mb
- libs 4.2Mb
- ```
-
# metagam
@@ -14403,47 +9504,6 @@ Run `revdepcheck::cloud_details(, "metagam")` for more info
--- re-building ‘dominance.Rmd’ using rmarkdown
```
-# MetAlyzer
-
-
-
-* Version: 1.1.0
-* GitHub: https://github.com/nilsmechtel/MetAlyzer
-* Source code: https://github.com/cran/MetAlyzer
-* Date/Publication: 2024-12-06 14:00:02 UTC
-* Number of recursive dependencies: 94
-
-Run `revdepcheck::cloud_details(, "MetAlyzer")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘MetAlyzer-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plotly_scatter
- > ### Title: Plotly Log2FC Scatter Plot
- > ### Aliases: plotly_scatter
- >
- > ### ** Examples
- >
- >
- ...
- Warning: Partial NA coefficients for 2 probe(s)
- >
- > p_scatter <- plotly_scatter(metalyzer_se)
- Warning in geom_rect(data = rects_df, inherit.aes = FALSE, aes(xmin = .data$Start, :
- Ignoring unknown aesthetics: text
- Warning in geom_point(size = 0.5, aes(text = paste0(.data$Metabolite, "\nClass: ", :
- Ignoring unknown aesthetics: text
- Error in pm[[2]] : subscript out of bounds
- Calls: plotly_scatter -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# MetaNet
@@ -14485,47 +9545,6 @@ Run `revdepcheck::cloud_details(, "MetaNet")` for more info
Execution halted
```
-# metaquant
-
-
-
-* Version: 0.1.1
-* GitHub: NA
-* Source code: https://github.com/cran/metaquant
-* Date/Publication: 2025-02-11 17:00:02 UTC
-* Number of recursive dependencies: 75
-
-Run `revdepcheck::cloud_details(, "metaquant")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘metaquant-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plotdist
- > ### Title: Visualising Densities using Quantiles
- > ### Aliases: plotdist
- >
- > ### ** Examples
- >
- > #Example dataset of 3-point summaries (min, med, max) for 2 groups
- ...
- + display.legend = TRUE,
- + pooled.dist = TRUE
- + )
- Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
- ℹ Please use `linewidth` instead.
- ℹ The deprecated feature was likely used in the metaquant package.
- Please report the issue to the authors.
- Error in pm[[2]] : subscript out of bounds
- Calls: plotdist -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# metR
@@ -14691,72 +9710,6 @@ Run `revdepcheck::cloud_details(, "MIC")` for more info
Execution halted
```
-# migraph
-
-
-
-* Version: 1.4.5
-* GitHub: https://github.com/stocnet/migraph
-* Source code: https://github.com/cran/migraph
-* Date/Publication: 2024-12-02 10:00:10 UTC
-* Number of recursive dependencies: 95
-
-Run `revdepcheck::cloud_details(, "migraph")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘migraph-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: regression
- > ### Title: Linear and logistic regression for network data
- > ### Aliases: regression net_regression
- >
- > ### ** Examples
- >
- > networkers <- ison_networkers %>% to_subgraph(Discipline == "Sociology")
- ...
- 4 sim Citations 39.4 3.13 0.1
- > glance(model1)
- # A tibble: 1 × 8
- r.squared adj.r.squared sigma statistic p.value df df.residual nobs
-
- 1 0.0674 0.0570 48.9 6.46 0.000309 3 268 272
- > plot(model1)
- Error in loadNamespace(x) : there is no package called ‘patchwork’
- Calls: plot ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(manynet)
- > library(migraph)
- >
- > test_check("migraph")
- Starting 2 test processes
- [ FAIL 2 | WARN 1 | SKIP 0 | PASS 34 ]
- ...
- 2. ├─migraph:::plot.network_test(cugtest)
- 3. │ └─manynet:::`+.ggplot`(...)
- 4. └─base::loadNamespace(x)
- 5. └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
- 6. └─base (local) withOneRestart(expr, restarts[[1L]])
- 7. └─base (local) doWithOneRestart(return(expr), restart)
-
- [ FAIL 2 | WARN 1 | SKIP 0 | PASS 34 ]
- Error: Test failures
- Execution halted
- ```
-
# mikropml
@@ -14840,23 +9793,23 @@ Run `revdepcheck::cloud_details(, "MiMIR")` for more info
Running examples in ‘MiMIR-Ex.R’ failed
The error most likely occurred in:
- > ### Name: LOBOV_accuracies
- > ### Title: LOBOV_accuracies
- > ### Aliases: LOBOV_accuracies
+ > ### Name: MetaboWAS
+ > ### Title: MetaboWAS
+ > ### Aliases: MetaboWAS
>
> ### ** Examples
>
- > require(pROC)
- ...
- 56 metabolites x 500 samples
- | Pruning samples on5SD:
- 56 metabolites x 500 samples
- | Performing scaling ... DONE!
- | Imputation ... DONE!
- > p_avail<-colnames(b_p)[c(1:5)]
- > LOBOV_accuracies(sur$surrogates, b_p, p_avail, MiMIR::acc_LOBOV)
- Error in pm[[2]] : subscript out of bounds
- Calls: LOBOV_accuracies -> -> ggplotly.ggplot -> gg2list
+ > require(MiMIR)
+ ...
+ Backtrace:
+ ▆
+ 1. └─MiMIR::MetaboWAS(...)
+ 2. └─ggplot2::scale_y_continuous(expand = c(0, 0), limits = c(0, ylim))
+ 3. └─ggplot2::continuous_scale(...)
+ 4. └─ggplot2:::check_continuous_limits(limits, call = call)
+ 5. └─ggplot2:::check_length(limits, 2L, arg = arg, call = call)
+ 6. └─cli::cli_abort(msg, call = call, arg = arg)
+ 7. └─rlang::abort(...)
Execution halted
```
@@ -14885,7 +9838,7 @@ Run `revdepcheck::cloud_details(, "miRetrieve")` for more info
> library(miRetrieve)
>
> test_check("miRetrieve")
- [ FAIL 7 | WARN 15 | SKIP 0 | PASS 196 ]
+ [ FAIL 6 | WARN 15 | SKIP 0 | PASS 204 ]
══ Failed tests ════════════════════════════════════════════════════════════════
...
@@ -14896,7 +9849,7 @@ Run `revdepcheck::cloud_details(, "miRetrieve")` for more info
x[1]: "object"
y[1]: "list"
- [ FAIL 7 | WARN 15 | SKIP 0 | PASS 196 ]
+ [ FAIL 6 | WARN 15 | SKIP 0 | PASS 204 ]
Error: Test failures
Execution halted
```
@@ -14905,10 +9858,10 @@ Run `revdepcheck::cloud_details(, "miRetrieve")` for more info
-* Version: 0.14.2
+* Version: 0.14.3
* GitHub: https://github.com/adrientaudiere/MiscMetabar
* Source code: https://github.com/cran/MiscMetabar
-* Date/Publication: 2025-03-20 15:20:02 UTC
+* Date/Publication: 2025-06-21 14:00:02 UTC
* Number of recursive dependencies: 420
Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info
@@ -14962,7 +9915,7 @@ Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info
── Failure ('test_figures_beta_div.R:258:5'): upset_pq works with data_fungi dataset ──
`suppressMessages(upset_pq(data_fungi_mini, "Height"))` produced warnings.
- [ FAIL 2 | WARN 4 | SKIP 74 | PASS 80 ]
+ [ FAIL 2 | WARN 2 | SKIP 74 | PASS 81 ]
Error: Test failures
Execution halted
```
@@ -14983,69 +9936,6 @@ Run `revdepcheck::cloud_details(, "MiscMetabar")` for more info
extdata 1.2Mb
```
-# miscset
-
-
-
-* Version: 1.1.0
-* GitHub: https://github.com/setempler/miscset
-* Source code: https://github.com/cran/miscset
-* Date/Publication: 2017-02-24 16:46:57
-* Number of recursive dependencies: 109
-
-Run `revdepcheck::cloud_details(, "miscset")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘miscset.Rmd’ using rmarkdown
- ```
-
-# misspi
-
-
-
-* Version: 0.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/misspi
-* Date/Publication: 2023-10-17 09:50:02 UTC
-* Number of recursive dependencies: 85
-
-Run `revdepcheck::cloud_details(, "misspi")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘misspi-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: evaliq
- > ### Title: Evaluate the Imputation Quality
- > ### Aliases: evaliq
- >
- > ### ** Examples
- >
- > # A very quick example
- ...
- > # Default plot
- > er.eval <- evaliq(x.true[na.idx], x.est[na.idx])
- `geom_smooth()` using formula = 'y ~ x'
- >
- > # Interactive plot
- > er.eval <- evaliq(x.true[na.idx], x.est[na.idx], interactive = TRUE)
- `geom_smooth()` using formula = 'y ~ x'
- Error in pm[[2]] : subscript out of bounds
- Calls: evaliq -> print -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# mistral
@@ -15097,77 +9987,27 @@ Run `revdepcheck::cloud_details(, "misty")` for more info
> ### ** Examples
>
> # Example 1: Compute a summary of missing data patterns
- ...
- 26. └─ggplot2 (local) extract_key(...)
- 27. └─Guide$extract_key(scale, aesthetic, ...)
- 28. └─ggplot2 (local) extract_key(...)
- 29. └─scale$get_labels(breaks)
- 30. └─ggplot2 (local) get_labels(..., self = self)
- 31. └─self$scale$get_labels(breaks)
- 32. └─ggplot2 (local) get_labels(..., self = self)
- 33. └─cli::cli_abort(...)
- 34. └─rlang::abort(...)
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.6Mb
- sub-directories of 1Mb or more:
- R 4.0Mb
- help 1.5Mb
- ```
-
-# mizer
-
-
-
-* Version: 2.5.3
-* GitHub: https://github.com/sizespectrum/mizer
-* Source code: https://github.com/cran/mizer
-* Date/Publication: 2024-10-17 07:10:09 UTC
-* Number of recursive dependencies: 107
-
-Run `revdepcheck::cloud_details(, "mizer")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘spelling.R’
- 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
- ...
- • plots/plot-feeding-level.svg
- • plots/plot-single-growth-curve.svg
- • plots/plot-spectra.svg
- • plots/plot-yield-by-gear.svg
- • plots/plot-yield.svg
- • plots/plotfishing-mortality.svg
- • plots/plotfmort-truncated.svg
- • plots/plotpredation-mortality.svg
- Error: Test failures
- Execution halted
+ ...
+ 26. └─ggplot2 (local) extract_key(...)
+ 27. └─Guide$extract_key(scale, aesthetic, ...)
+ 28. └─ggplot2 (local) extract_key(...)
+ 29. └─scale$get_labels(breaks)
+ 30. └─ggplot2 (local) get_labels(..., self = self)
+ 31. └─self$scale$get_labels(breaks)
+ 32. └─ggplot2 (local) get_labels(..., self = self)
+ 33. └─cli::cli_abort(...)
+ 34. └─rlang::abort(...)
+ Execution halted
```
## In both
* checking installed package size ... NOTE
```
- installed size is 5.5Mb
+ installed size is 5.6Mb
sub-directories of 1Mb or more:
- help 1.8Mb
+ R 4.0Mb
+ help 1.5Mb
```
# MKpower
@@ -15211,56 +10051,6 @@ Run `revdepcheck::cloud_details(, "MKpower")` for more info
Execution halted
```
-# mlr3spatiotempcv
-
-
-
-* Version: 2.3.2
-* GitHub: https://github.com/mlr-org/mlr3spatiotempcv
-* Source code: https://github.com/cran/mlr3spatiotempcv
-* Date/Publication: 2024-11-29 13:10:02 UTC
-* Number of recursive dependencies: 165
-
-Run `revdepcheck::cloud_details(, "mlr3spatiotempcv")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > if (requireNamespace("testthat", quietly = TRUE)) {
- + library("checkmate")
- + library("testthat")
- + library("mlr3spatiotempcv")
- + test_check("mlr3spatiotempcv")
- + }
- Loading required package: mlr3
- ...
- • 2-autoplot/sptcvcstf-2d-time-var-fold-1-rep-2.svg
- • 2-autoplot/sptcvcstf-2d-time-var-fold-1-sample-fold-n.svg
- • 2-autoplot/sptcvcstf-2d-time-var-fold-1.svg
- • 2-autoplot/sptcvcstf-2d-time-var-sample-fold-n.svg
- • 2-autoplot/sptcvcstf-3d-time-var-fold-1-2-sample-fold-n.svg
- • 2-autoplot/sptcvcstf-3d-time-var-fold-1-2.svg
- • 2-autoplot/sptcvcstf-3d-time-var-fold-1-sample-fold-n.svg
- • autoplot_buffer/spcvbuffer-fold-1-2.svg
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.9Mb
- sub-directories of 1Mb or more:
- data 3.5Mb
- ```
-
# modeldb
@@ -15302,56 +10092,6 @@ Run `revdepcheck::cloud_details(, "modeldb")` for more info
Execution halted
```
-# modeltime.resample
-
-
-
-* Version: 0.2.3
-* GitHub: https://github.com/business-science/modeltime.resample
-* Source code: https://github.com/cran/modeltime.resample
-* Date/Publication: 2023-04-12 15:50:02 UTC
-* Number of recursive dependencies: 234
-
-Run `revdepcheck::cloud_details(, "modeltime.resample")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- >
- > # Machine Learning
- > library(tidymodels)
- ── Attaching packages ────────────────────────────────────── tidymodels 1.3.0 ──
- ✔ broom 1.0.8 ✔ recipes 1.3.1
- ✔ dials 1.4.0 ✔ rsample 1.3.0
- ...
- ▆
- 1. ├─m750_models_resample %>% ... at test-modeltime_fit_resamples.R:116:5
- 2. └─modeltime.resample::plot_modeltime_resamples(., .interactive = TRUE)
- 3. ├─plotly::ggplotly(g)
- 4. └─plotly:::ggplotly.ggplot(g)
- 5. └─plotly::gg2list(...)
-
- [ FAIL 1 | WARN 4 | SKIP 0 | PASS 16 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
- All declared Imports should be used.
- ```
-
# Momocs
@@ -15434,13 +10174,6 @@ Run `revdepcheck::cloud_details(, "mpactr")` for more info
Execution halted
```
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘downstream_analyses.Rmd’ using rmarkdown
- Warning: Duplicated chunk option(s) 'warning' in both chunk header and pipe comments of the chunk 'unnamed-chunk-18'.
- ```
-
## In both
* checking installed package size ... NOTE
@@ -15452,42 +10185,6 @@ Run `revdepcheck::cloud_details(, "mpactr")` for more info
libs 1.6Mb
```
-# MRZero
-
-
-
-* Version: 0.2.0
-* GitHub: NA
-* Source code: https://github.com/cran/MRZero
-* Date/Publication: 2024-04-14 09:30:03 UTC
-* Number of recursive dependencies: 79
-
-Run `revdepcheck::cloud_details(, "MRZero")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘MRZero-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: mr_plot
- > ### Title: Draw a scatter plot of the genetic associations and/or causal
- > ### estimates
- > ### Aliases: mr_plot mr_plot,MRInput-method mr_plot,MRAll-method
- > ### mr_plot,MRMVInput-method
- >
- > ### ** Examples
- >
- > mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
- + line="egger", orientate = TRUE)
- Error in pm[[2]] : subscript out of bounds
- Calls: mr_plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# mshap
@@ -15562,9 +10259,9 @@ Run `revdepcheck::cloud_details(, "mtdesign")` for more info
> library(mtdesign)
>
> test_check("mtdesign")
- testthat 2025-06-11 09:02:22 DEBUG test_check: Entry
- testthat 2025-06-11 09:02:22 DEBUG test_check: Entry
- testthat 2025-06-11 09:02:22 DEBUG test_check: Exit
+ testthat 2025-06-23 07:35:52 DEBUG test_check: Entry
+ testthat 2025-06-23 07:35:52 DEBUG test_check: Entry
+ testthat 2025-06-23 07:35:52 DEBUG test_check: Exit
...
`expected[2:2]`: "ggplot"
── Failure ('test-powerPlot.R:6:3'): multiplication works ──────────────────────
@@ -15646,56 +10343,15 @@ ERROR: lazy loading failed for package ‘MultiTraits’
```
-# mvdalab
-
-
-
-* Version: 1.7
-* GitHub: NA
-* Source code: https://github.com/cran/mvdalab
-* Date/Publication: 2022-10-05 23:00:14 UTC
-* Number of recursive dependencies: 67
-
-Run `revdepcheck::cloud_details(, "mvdalab")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘mvdalab-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot.plusminus
- > ### Title: 2D Graph of the PCA scores associated with a plusminusFit
- > ### Aliases: plot.plusminus
- >
- > ### ** Examples
- >
- > ### PLUS-Minus CLASSIFIER WITH validation = 'none', i.e. no CV ###
- ...
- 15. │ └─ggplot2 (local) FUN(X[[i]], ...)
- 16. │ └─scale$map_df(df = df)
- 17. │ └─ggplot2 (local) map_df(..., self = self)
- 18. │ └─base::lapply(aesthetics, function(j) self$map(df[[j]]))
- 19. │ └─ggplot2 (local) FUN(X[[i]], ...)
- 20. │ └─self$map(df[[j]])
- 21. │ └─ggplot2 (local) map(..., self = self)
- 22. │ └─vctrs::`vec_slice<-`(`*tmp*`, is.na(x), value = na_value)
- 23. └─rlang::cnd_signal(x)
- Execution halted
- ```
-
# mverse
-* Version: 0.2.0
+* Version: 0.2.2
* GitHub: https://github.com/mverseanalysis/mverse
* Source code: https://github.com/cran/mverse
-* Date/Publication: 2025-04-24 08:10:02 UTC
-* Number of recursive dependencies: 135
+* Date/Publication: 2025-06-21 10:40:06 UTC
+* Number of recursive dependencies: 134
Run `revdepcheck::cloud_details(, "mverse")` for more info
@@ -15768,54 +10424,6 @@ Run `revdepcheck::cloud_details(, "mxnorm")` for more info
All declared Imports should be used.
```
-# neatmaps
-
-
-
-* Version: 2.1.0
-* GitHub: https://github.com/PhilBoileau/neatmaps
-* Source code: https://github.com/cran/neatmaps
-* Date/Publication: 2019-05-12 19:10:03 UTC
-* Number of recursive dependencies: 97
-
-Run `revdepcheck::cloud_details(, "neatmaps")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘neatmaps-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: consClustResTable
- > ### Title: Consensus Cluster Results in a Table
- > ### Aliases: consClustResTable
- >
- > ### ** Examples
- >
- > # create the data frame using the network, node and edge attributes
- ...
- > # run the neatmap code on df
- > neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100,
- + xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1)
- Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
- ℹ Please use `linewidth` instead.
- ℹ The deprecated feature was likely used in the dendextend package.
- Please report the issue at .
- Error in pm[[2]] : subscript out of bounds
- Calls: neatmap ... %>% -> layout -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.3Mb
- ```
-
# NHSRplotthedots
@@ -15859,199 +10467,11 @@ Run `revdepcheck::cloud_details(, "NHSRplotthedots")` for more info
## In both
-* checking dependencies in R code ... NOTE
- ```
- Namespaces in Imports field not imported from:
- ‘NHSRdatasets’ ‘grid’ ‘utils’
- All declared Imports should be used.
- ```
-
-# nichetools
-
-
-
-* Version: 0.3.2
-* GitHub: https://github.com/benjaminhlina/nichetools
-* Source code: https://github.com/cran/nichetools
-* Date/Publication: 2024-09-30 21:20:02 UTC
-* Number of recursive dependencies: 117
-
-Run `revdepcheck::cloud_details(, "nichetools")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘using-nichetools-with-the-package-SIBER.Rmd’ using rmarkdown
-
- Quitting from using-nichetools-with-the-package-SIBER.Rmd:96-118 [unnamed-chunk-6]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error:
- ! `object` must be an , not a S3
- ---
- Backtrace:
- ...
- 61. └─ggplot2 (local) f(init, x[[i]])
- 62. └─S7::props(e2)
- 63. └─S7::check_is_S7(object)
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'using-nichetools-with-the-package-SIBER.Rmd' failed with diagnostics:
- `object` must be an , not a S3
- --- failed re-building ‘using-nichetools-with-the-package-SIBER.Rmd’
-
- --- re-building ‘using-nichetools-with-the-package-nicheROVER.Rmd’ using rmarkdown
- ```
-
-# NiLeDAM
-
-
-
-* Version: 0.3
-* GitHub: NA
-* Source code: https://github.com/cran/NiLeDAM
-* Date/Publication: 2023-09-18 06:00:02 UTC
-* Number of recursive dependencies: 83
-
-Run `revdepcheck::cloud_details(, "NiLeDAM")` 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(NiLeDAM)
-
- ***********************************************************
-
- Welcome to the NiLeDAM package
- ...
- `expected[2:2]`: "ggplot"
- ── Failure ('test-popline.R:22:3'): test result on 'ageTests' plotted correctly ──
- typeof(p) (`actual`) not equal to "list" (`expected`).
-
- `actual`: "object"
- `expected`: "list"
-
- [ FAIL 8 | WARN 10 | SKIP 0 | PASS 49 ]
- Error: Test failures
- Execution halted
- ```
-
-# NIMAA
-
-
-
-* Version: 0.2.1
-* GitHub: https://github.com/jafarilab/NIMAA
-* Source code: https://github.com/cran/NIMAA
-* Date/Publication: 2022-04-11 14:12:45 UTC
-* Number of recursive dependencies: 179
-
-Run `revdepcheck::cloud_details(, "NIMAA")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘NIMAA-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: extractSubMatrix
- > ### Title: Extract the non-missing submatrices from a given matrix.
- > ### Aliases: extractSubMatrix
- >
- > ### ** Examples
- >
- > # load part of the beatAML data
- ...
- ℹ See also `vignette("ggplot2-in-packages")` for more information.
- ℹ The deprecated feature was likely used in the NIMAA package.
- Please report the issue at .
- Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
- ℹ Please use `linewidth` instead.
- ℹ The deprecated feature was likely used in the NIMAA package.
- Please report the issue at .
- Error in pm[[2]] : subscript out of bounds
- Calls: extractSubMatrix ... plotSubmatrix -> print -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(NIMAA)
- >
- > test_check("NIMAA")
- binmatnest.temperature
- 13.21346
- Size of Square: 66 rows x 66 columns
- ...
- 1. └─NIMAA::extractSubMatrix(...) at test-extract-nonmissing-submatrix.R:5:3
- 2. └─NIMAA:::plotSubmatrix(...)
- 3. ├─base::print(plotly::ggplotly(p))
- 4. ├─plotly::ggplotly(p)
- 5. └─plotly:::ggplotly.ggplot(p)
- 6. └─plotly::gg2list(...)
-
- [ FAIL 1 | WARN 8 | SKIP 0 | PASS 7 ]
- Error: Test failures
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘NIMAA-vignette.Rmd’ using rmarkdown
-
- Quitting from NIMAA-vignette.Rmd:48-57 [plotIncMatrix function]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'NIMAA-vignette.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘NIMAA-vignette.Rmd’
-
- SUMMARY: processing the following file failed:
- ‘NIMAA-vignette.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 6.5Mb
- sub-directories of 1Mb or more:
- data 2.0Mb
- doc 4.0Mb
- ```
-
-* checking data for non-ASCII characters ... NOTE
+* checking dependencies in R code ... NOTE
```
- Note: found 24 marked UTF-8 strings
+ Namespaces in Imports field not imported from:
+ ‘NHSRdatasets’ ‘grid’ ‘utils’
+ All declared Imports should be used.
```
# nlmixr2plot
@@ -16095,53 +10515,6 @@ Run `revdepcheck::cloud_details(, "nlmixr2plot")` for more info
Execution halted
```
-# nonmem2R
-
-
-
-* Version: 0.2.5
-* GitHub: NA
-* Source code: https://github.com/cran/nonmem2R
-* Date/Publication: 2024-03-11 17:30:02 UTC
-* Number of recursive dependencies: 61
-
-Run `revdepcheck::cloud_details(, "nonmem2R")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘nonmem2R-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: basic.GOF4
- > ### Title: Basic 4- and 6-panel GOF
- > ### Aliases: basic.GOF4 basic.GOF6
- >
- > ### ** Examples
- >
- > # Get path to the example files included in nonmem2R package
- ...
- 22. │ └─l$compute_position(d, layout)
- 23. │ └─ggplot2 (local) compute_position(..., self = self)
- 24. │ └─self$position$setup_data(data, params)
- 25. │ └─ggplot2 (local) setup_data(..., self = self)
- 26. └─base::.handleSimpleError(...)
- 27. └─rlang (local) h(simpleError(msg, call))
- 28. └─handlers[[1L]](cnd)
- 29. └─cli::cli_abort(...)
- 30. └─rlang::abort(...)
- Execution halted
- ```
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘GOFvignette.Rmd’ using rmarkdown
- ```
-
# normfluodbf
@@ -16171,14 +10544,14 @@ Run `revdepcheck::cloud_details(, "normfluodbf")` for more info
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
...
- ▆
- 1. ├─... %>% ... at test_plot_dev.R:13:3
- 2. └─normfluodbf:::plot_dev_with_custom_legends(...)
- 3. ├─plotly::ggplotly(p)
- 4. └─plotly:::ggplotly.ggplot(p)
- 5. └─plotly::gg2list(...)
+ ══ Failed tests ════════════════════════════════════════════════════════════════
+ ── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
+ "gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
- [ FAIL 4 | WARN 613 | SKIP 0 | PASS 15 ]
+ `actual`: "gg"
+ `expected`: "ggplot2::ggplot"
+
+ [ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
```
@@ -16219,60 +10592,6 @@ Run `revdepcheck::cloud_details(, "nzelect")` for more info
Note: found 6409 marked UTF-8 strings
```
-# occCite
-
-
-
-* Version: 0.5.9
-* GitHub: https://github.com/ropensci/occCite
-* Source code: https://github.com/cran/occCite
-* Date/Publication: 2024-10-28 13:30:06 UTC
-* Number of recursive dependencies: 131
-
-Run `revdepcheck::cloud_details(, "occCite")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(occCite)
- >
- > test_check("occCite")
-
- OccCite query occurred on: 20 June, 2024
-
- ...
- ── Failure ('test-sumFig.R:40:3'): sumFig works when plotting only source by species ──
- class(test[[1]][[1]]) not equal to "ggplot_built".
- Lengths differ: 4 is not 1
- ── Failure ('test-sumFig.R:48:3'): sumFig works when plotting only aggregator by species ──
- class(test[[1]][[1]]) not equal to "ggplot_built".
- Lengths differ: 4 is not 1
-
- [ FAIL 9 | WARN 1 | SKIP 20 | PASS 114 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking dependencies in R code ... NOTE
- ```
- Namespace in Imports field not imported from: ‘ape’
- All declared Imports should be used.
- ```
-
-* checking data for non-ASCII characters ... NOTE
- ```
- Note: found 7 marked UTF-8 strings
- ```
-
# ofpetrial
@@ -16407,15 +10726,15 @@ Run `revdepcheck::cloud_details(, "OmicNavigator")` for more info
testAdd.R..................... 0 tests
testAdd.R..................... 0 tests
...
- testPlot.R.................... 140 tests [0;31m1 fails[0m
- testPlot.R.................... 140 tests [0;31m1 fails[0m
- testPlot.R.................... 141 tests [0;31m1 fails[0m
- testPlot.R.................... 141 tests [0;31m1 fails[0m
- testPlot.R.................... 141 tests [0;31m1 fails[0m
- testPlot.R.................... 142 tests [0;31m1 fails[0m
- testPlot.R.................... 142 tests [0;31m1 fails[0m
- testPlot.R.................... 143 tests [0;31m1 fails[0m Error in pm[[2]] : subscript out of bounds
- Calls: suppressMessages ... plotStudy -> f -> -> ggplotly.ggplot -> gg2list
+ Please report the issue to the authors.
+ 2: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
+ ℹ Please use `linewidth` instead.
+ ℹ The deprecated feature was likely used in the UpSetR package.
+ Please report the issue to the authors.
+ 3: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
+ ℹ Please use the `linewidth` argument instead.
+ ℹ The deprecated feature was likely used in the UpSetR package.
+ Please report the issue to the authors.
Execution halted
```
@@ -16427,11 +10746,11 @@ Run `revdepcheck::cloud_details(, "OmicNavigator")` for more info
--- re-building ‘OmicNavigatorAPI.Rnw’ using Sweave
OmicNavigator R package version: 1.15.0
The app is not installed. Install it with installApp()
- Installing study "ABC" in /tmp/RtmppgkVeU/file1ce750eab033
+ Installing study "ABC" in /tmp/Rtmp2uYYGs/file1c972c78c294
Exporting study "ABC" as an R package
Note: No maintainer email was specified. Using the placeholder: Unknown
Calculating pairwise overlaps. This may take a while...
- Exported study to /tmp/RtmppgkVeU/ONstudyABC
+ Exported study to /tmp/Rtmp2uYYGs/ONstudyABC
Success!
...
l.14 ^^M
@@ -16575,43 +10894,6 @@ Run `revdepcheck::cloud_details(, "ordr")` for more info
Note: found 4 marked UTF-8 strings
```
-# pacu
-
-
-
-* Version: 0.1.63
-* GitHub: https://github.com/cldossantos/pacu
-* Source code: https://github.com/cran/pacu
-* Date/Publication: 2025-05-29 21:50:02 UTC
-* Number of recursive dependencies: 168
-
-Run `revdepcheck::cloud_details(, "pacu")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘pacu.Rmd’ using rmarkdown
- --- finished re-building ‘pacu.Rmd’
-
- --- re-building ‘pacu_faq.Rmd’ using rmarkdown
- --- finished re-building ‘pacu_faq.Rmd’
-
- --- re-building ‘pacu_sat.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 5.7Mb
- sub-directories of 1Mb or more:
- extdata 4.8Mb
- ```
-
# pafr
@@ -16713,244 +10995,49 @@ Run `revdepcheck::cloud_details(, "palettes")` for more info
* checking re-building of vignette outputs ... ERROR
```
- Error(s) in re-building vignettes:
- --- re-building ‘biscale.Rmd’ using rmarkdown
- ```
-
-# paramix
-
-
-
-* Version: 0.0.2
-* GitHub: NA
-* Source code: https://github.com/cran/paramix
-* Date/Publication: 2025-06-10 14:50:02 UTC
-* Number of recursive dependencies: 76
-
-Run `revdepcheck::cloud_details(, "paramix")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘intro.Rmd’ using rmarkdown
- ```
-
-# patchwork
-
-
-
-* Version: 1.3.0
-* GitHub: https://github.com/thomasp85/patchwork
-* Source code: https://github.com/cran/patchwork
-* Date/Publication: 2024-09-16 09:30:02 UTC
-* Number of recursive dependencies: 92
-
-Run `revdepcheck::cloud_details(, "patchwork")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘patchwork-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_arithmetic
- > ### Title: Plot arithmetic
- > ### Aliases: plot_arithmetic -.ggplot /.ggplot |.ggplot *.gg &.gg
- >
- > ### ** Examples
- >
- > library(ggplot2)
- ...
- > # Stacking and packing
- > (p1 | p2 | p3) /
- + p4
- >
- > # Add elements to the same nesting level
- > (p1 + (p2 + p3) + p4 + plot_layout(ncol = 1)) * theme_bw()
- Error: Can't find method for generic `*(e1, e2)`:
- - e1:
- - e2:
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(patchwork)
- >
- > test_check("patchwork")
- [ FAIL 1 | WARN 1 | SKIP 11 | PASS 0 ]
-
- ══ Skipped tests (11) ══════════════════════════════════════════════════════════
- ...
- • layout/insets-can-be-changed.svg
- • layout/other-alignments-work.svg
- • layout/patchworks-can-be-inset.svg
- • layout/setting-heights-as-units.svg
- • layout/setting-heights.svg
- • layout/setting-nrow.svg
- • layout/setting-widths-as-units.svg
- • layout/setting-widths.svg
- Error: Test failures
- Execution halted
- ```
-
-* checking S3 generic/method consistency ... WARNING
- ```
- ggplot_gtable:
- function(plot)
- ggplot_gtable.fixed_dim_build:
- function(data)
-
- ggplot_add:
- function(object, plot, ...)
- ggplot_add.formula:
- function(object, plot, object_name)
-
- ...
- function(object, plot, ...)
- ggplot_add.grob:
- function(object, plot, object_name)
-
- ggplot_build:
- function(plot, ...)
- ggplot_build.fixed_dim_ggplot:
- function(plot)
- See section ‘Generic functions and methods’ in the ‘Writing R
- Extensions’ manual.
- ```
-
-# pathfindR
-
-
-
-* Version: 2.4.2
-* GitHub: https://github.com/egeulgen/pathfindR
-* Source code: https://github.com/cran/pathfindR
-* Date/Publication: 2025-02-17 09:30:02 UTC
-* Number of recursive dependencies: 142
-
-Run `revdepcheck::cloud_details(, "pathfindR")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat-active_snw.R’
- Running ‘testthat-clustering.R’
- Running ‘testthat-comparison.R’
- Running ‘testthat-core.R’
- Running ‘testthat-data_generation.R’
- Running ‘testthat-enrichment.R’
- Running ‘testthat-scoring.R’
- Running the tests in ‘tests/testthat-scoring.R’ failed.
- Complete output:
- > library(testthat)
- ...
- ── Failure ('test-scoring.R:113:9'): `plot_scores()` -- creates term score heatmap ggplot object with correct labels ──
- g$labels$x not identical to "Sample".
- target is NULL, current is character
- ── Failure ('test-scoring.R:114:9'): `plot_scores()` -- creates term score heatmap ggplot object with correct labels ──
- g$labels$y not identical to "Term".
- target is NULL, current is character
-
- [ FAIL 8 | WARN 0 | SKIP 0 | PASS 37 ]
- Error: Test failures
- Execution halted
- ```
-
-# pathviewr
-
-
-
-* Version: 1.1.7
-* GitHub: https://github.com/ropensci/pathviewr
-* Source code: https://github.com/cran/pathviewr
-* Date/Publication: 2023-03-08 08:10:05 UTC
-* Number of recursive dependencies: 188
-
-Run `revdepcheck::cloud_details(, "pathviewr")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(pathviewr)
- > #library(vdiffr)
- >
- > test_check("pathviewr")
- [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ]
-
- ...
- ── Error ('test-plot_by_subject.R:168:3'): elev views wrangled correctly via tidyverse ──
- Error in `expect_match(elev_all_plots[[3]][[4]][["labels"]][["x"]], "position_height")`: is.character(act$val) is not TRUE
- Backtrace:
- ▆
- 1. └─testthat::expect_match(...) at test-plot_by_subject.R:168:3
- 2. └─base::stopifnot(is.character(act$val))
-
- [ FAIL 2 | WARN 1 | SKIP 0 | PASS 286 ]
- Error: Test failures
- Execution halted
- ```
+ Error(s) in re-building vignettes:
+ --- re-building ‘biscale.Rmd’ using rmarkdown
+ ```
-# PatientLevelPrediction
+# patchwork
-* Version: 6.4.1
-* GitHub: https://github.com/OHDSI/PatientLevelPrediction
-* Source code: https://github.com/cran/PatientLevelPrediction
-* Date/Publication: 2025-04-20 09:40:02 UTC
-* Number of recursive dependencies: 215
+* Version: 1.3.1
+* GitHub: https://github.com/thomasp85/patchwork
+* Source code: https://github.com/cran/patchwork
+* Date/Publication: 2025-06-21 13:20:05 UTC
+* Number of recursive dependencies: 92
-Run `revdepcheck::cloud_details(, "PatientLevelPrediction")` for more info
+Run `revdepcheck::cloud_details(, "patchwork")` for more info
## Newly broken
-* checking examples ... ERROR
+* checking S3 generic/method consistency ... WARNING
```
- Running examples in ‘PatientLevelPrediction-Ex.R’ failed
- The error most likely occurred in:
+ ggplot_add:
+ function(object, plot, ...)
+ ggplot_add.formula:
+ function(object, plot, object_name)
+
+ ggplot_add:
+ function(object, plot, ...)
+ ggplot_add.nativeRaster:
+ function(object, plot, object_name)
- > ### Name: outcomeSurvivalPlot
- > ### Title: Plot the outcome incidence over time
- > ### Aliases: outcomeSurvivalPlot
- >
- > ### ** Examples
- >
- > ## Don't show:
...
- Warning: Ignoring unknown labels:
- • fill : "Strata"
- • linetype : "1"
- Warning: Ignoring unknown labels:
- • fill : "Strata"
- • linetype : "1"
- Warning: Ignoring unknown labels:
- • colour : "Strata"
- Error: `object` must be an , not a S3
- Execution halted
+ function(object, plot, ...)
+ ggplot_add.grob:
+ function(object, plot, object_name)
+
+ ggplot_build:
+ function(plot, ...)
+ ggplot_build.fixed_dim_ggplot:
+ function(plot)
+ See section ‘Generic functions and methods’ in the ‘Writing R
+ Extensions’ manual.
```
# patientProfilesVis
@@ -17069,144 +11156,6 @@ Run `revdepcheck::cloud_details(, "pcr")` for more info
Execution halted
```
-# pdxTrees
-
-
-
-* Version: 0.4.0
-* GitHub: https://github.com/mcconvil/pdxTrees
-* Source code: https://github.com/cran/pdxTrees
-* Date/Publication: 2020-08-17 14:00:02 UTC
-* Number of recursive dependencies: 102
-
-Run `revdepcheck::cloud_details(, "pdxTrees")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘pdxTrees-vignette.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking LazyData ... NOTE
- ```
- 'LazyData' is specified without a 'data' directory
- ```
-
-# pedbp
-
-
-
-* Version: 2.0.2
-* GitHub: https://github.com/dewittpe/pedbp
-* Source code: https://github.com/cran/pedbp
-* Date/Publication: 2025-01-07 20:40:01 UTC
-* Number of recursive dependencies: 116
-
-Run `revdepcheck::cloud_details(, "pedbp")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘test-bmi_for_age.R’
- Running ‘test-bp-by-source.R’
- Running ‘test-bp_cdf.R’
- Running the tests in ‘tests/test-bp_cdf.R’ failed.
- Complete output:
- > library(pedbp)
- >
- > ################################################################################
- > x <- bp_cdf(age = 96, male = 1, sbp = 103, dbp = 55)
- > stopifnot(identical(class(x), c("gg", "ggplot")))
- Error: identical(class(x), c("gg", "ggplot")) is not TRUE
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.1Mb
- sub-directories of 1Mb or more:
- libs 5.3Mb
- ```
-
-# personalized
-
-
-
-* Version: 0.2.7
-* GitHub: https://github.com/jaredhuling/personalized
-* Source code: https://github.com/cran/personalized
-* Date/Publication: 2022-06-27 20:20:03 UTC
-* Number of recursive dependencies: 90
-
-Run `revdepcheck::cloud_details(, "personalized")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > Sys.setenv("R_TESTS" = "")
- > library(testthat)
- > library(personalized)
- Loading required package: glmnet
- Loading required package: Matrix
- Loaded glmnet 4.1-9
- Loading required package: mgcv
- ...
- 4. └─personalized:::plot.subgroup_validated(subgrp.val, type = "stability")
- 5. ├─plotly::subplot(...)
- 6. │ └─plotly:::dots2plots(...)
- 7. ├─plotly::ggplotly(p.primary, tooltip = paste0("tooltip", 1:4))
- 8. └─plotly:::ggplotly.ggplot(...)
- 9. └─plotly::gg2list(...)
-
- [ FAIL 1 | WARN 2 | SKIP 0 | PASS 215 ]
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking Rd files ... NOTE
- ```
- checkRd: (-1) fit.subgroup.Rd:56: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:57: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:58: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:59: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:60: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:61: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:62: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:63: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:64: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:65: Lost braces in \itemize; meant \describe ?
- ...
- checkRd: (-1) fit.subgroup.Rd:179-181: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:182: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:183: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) fit.subgroup.Rd:184: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) validate.subgroup.Rd:77-81: Lost braces in \enumerate; meant \describe ?
- checkRd: (-1) validate.subgroup.Rd:82-86: Lost braces in \enumerate; meant \describe ?
- checkRd: (-1) validate.subgroup.Rd:89-92: Lost braces in \enumerate; meant \describe ?
- checkRd: (-1) weighted.ksvm.Rd:21: Lost braces; missing escapes or markup?
- 21 | \item{y}{The response vector (either a character vector, factor vector, or numeric vector with values in {-1, 1})}
- | ^
- ```
-
# phylepic
@@ -17215,7 +11164,7 @@ Run `revdepcheck::cloud_details(, "personalized")` for more info
* GitHub: https://github.com/cidm-ph/phylepic
* Source code: https://github.com/cran/phylepic
* Date/Publication: 2024-05-31 19:10:02 UTC
-* Number of recursive dependencies: 85
+* Number of recursive dependencies: 84
Run `revdepcheck::cloud_details(, "phylepic")` for more info
@@ -17225,11 +11174,6 @@ Run `revdepcheck::cloud_details(, "phylepic")` for more info
* checking S3 generic/method consistency ... WARNING
```
- ggplot_gtable:
- function(plot)
- ggplot_gtable.phylepic_ggplot_build:
- function(data)
-
ggplot_build:
function(plot, ...)
ggplot_build.phylepic_ggplot:
@@ -17335,47 +11279,6 @@ Run `revdepcheck::cloud_details(, "plantTracker")` for more info
number of items to replace is not a multiple of replacement length
```
-# Plasmidprofiler
-
-
-
-* Version: 0.1.6
-* GitHub: NA
-* Source code: https://github.com/cran/Plasmidprofiler
-* Date/Publication: 2017-01-06 01:10:47
-* Number of recursive dependencies: 80
-
-Run `revdepcheck::cloud_details(, "Plasmidprofiler")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘Plasmidprofiler-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: main
- > ### Title: Main: Run everything
- > ### Aliases: main
- >
- > ### ** Examples
- >
- > main(blastdata,
- ...
- Saving 12 x 7 in image
- Warning: Vectorized input to `element_text()` is not officially supported.
- ℹ Results may be unexpected or may change in future versions of ggplot2.
- Warning in geom_tile(aes(x = Plasmid, y = Sample, label = AMR_gene, fill = Inc_group, :
- Ignoring unknown aesthetics: label and text
- Warning: Use of `report$Sureness` is discouraged.
- ℹ Use `Sureness` instead.
- Error in pm[[2]] : subscript out of bounds
- Calls: main ... -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# plotdap
@@ -17467,7 +11370,7 @@ Run `revdepcheck::cloud_details(, "plotDK")` for more info
> library(plotDK)
>
> test_check("plotDK")
- [ FAIL 4 | WARN 0 | SKIP 0 | PASS 46 ]
+ [ FAIL 3 | WARN 0 | SKIP 0 | PASS 48 ]
══ Failed tests ════════════════════════════════════════════════════════════════
...
@@ -17478,7 +11381,7 @@ Run `revdepcheck::cloud_details(, "plotDK")` for more info
labels$fill not equal to "fill".
target is NULL, current is character
- [ FAIL 4 | WARN 0 | SKIP 0 | PASS 46 ]
+ [ FAIL 3 | WARN 0 | SKIP 0 | PASS 48 ]
Error: Test failures
Execution halted
```
@@ -17537,82 +11440,6 @@ Run `revdepcheck::cloud_details(, "PlotFTIR")` for more info
Execution halted
```
-# plotly
-
-
-
-* Version: 4.10.4
-* GitHub: https://github.com/plotly/plotly.R
-* Source code: https://github.com/cran/plotly
-* Date/Publication: 2024-01-13 22:40:02 UTC
-* Number of recursive dependencies: 134
-
-Run `revdepcheck::cloud_details(, "plotly")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘plotly-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: style
- > ### Title: Modify trace(s)
- > ### Aliases: style
- >
- > ### ** Examples
- >
- > ## Don't show:
- ...
- + # this clobbers the previously supplied marker.line.color
- + style(p, marker.line = list(width = 2.5), marker.size = 10)
- + ## Don't show:
- + }) # examplesIf
- > (p <- ggplotly(qplot(data = mtcars, wt, mpg, geom = c("point", "smooth"))))
- Warning: `qplot()` was deprecated in ggplot2 3.4.0.
- `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
- Error in pm[[2]] : subscript out of bounds
- Calls: ... eval -> eval -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library("testthat")
- > library("plotly")
- Loading required package: ggplot2
-
- Attaching package: 'plotly'
-
- The following object is masked from 'package:ggplot2':
- ...
- • plotly-subplot/subplot-bump-axis-annotation.svg
- • plotly-subplot/subplot-bump-axis-image.svg
- • plotly-subplot/subplot-bump-axis-shape-shared.svg
- • plotly-subplot/subplot-bump-axis-shape.svg
- • plotly-subplot/subplot-reposition-annotation.svg
- • plotly-subplot/subplot-reposition-image.svg
- • plotly-subplot/subplot-reposition-shape-fixed.svg
- • plotly-subplot/subplot-reposition-shape.svg
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.1Mb
- sub-directories of 1Mb or more:
- R 1.0Mb
- htmlwidgets 4.0Mb
- ```
-
# plotor
@@ -17761,10 +11588,10 @@ Run `revdepcheck::cloud_details(, "plotROC")` for more info
-* Version: 0.7.0
+* Version: 0.7.1
* GitHub: https://github.com/pwwang/plotthis
* Source code: https://github.com/cran/plotthis
-* Date/Publication: 2025-05-31 05:00:02 UTC
+* Date/Publication: 2025-06-20 18:40:02 UTC
* Number of recursive dependencies: 212
Run `revdepcheck::cloud_details(, "plotthis")` for more info
@@ -17808,58 +11635,6 @@ Run `revdepcheck::cloud_details(, "plotthis")` for more info
help 3.3Mb
```
-# pmartR
-
-
-
-* Version: 2.5.0
-* GitHub: https://github.com/pmartR/pmartR
-* Source code: https://github.com/cran/pmartR
-* Date/Publication: 2025-04-23 18:00:02 UTC
-* Number of recursive dependencies: 143
-
-Run `revdepcheck::cloud_details(, "pmartR")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(pmartR)
- >
- > test_check("pmartR")
- [ FAIL 1 | WARN 11 | SKIP 11 | PASS 2380 ]
-
- ══ Skipped tests (11) ══════════════════════════════════════════════════════════
- ...
- • plots/plot-spansres-n-biomolecule-bar.svg
- • plots/plot-spansres.svg
- • plots/plot-statres-anova-volcano.svg
- • plots/plot-statres-anova.svg
- • plots/plot-statres-combined-volcano.svg
- • plots/plot-statres-combined.svg
- • plots/plot-statres-gtest.svg
- • plots/plot-totalcountfilt.svg
- Error: Test failures
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 10.7Mb
- sub-directories of 1Mb or more:
- R 1.5Mb
- help 1.5Mb
- libs 6.6Mb
- ```
-
# pmxTools
@@ -17968,69 +11743,8 @@ Run `revdepcheck::cloud_details(, "pollster")` for more info
object is invalid:
- every label must be named.
--- failed re-building ‘crosstab3way.Rmd’
-
- --- re-building ‘crosstabs.Rmd’ using rmarkdown
- ```
-
-# poppr
-
-
-
-* Version: 2.9.6
-* GitHub: https://github.com/grunwaldlab/poppr
-* Source code: https://github.com/cran/poppr
-* Date/Publication: 2024-03-15 17:40:02 UTC
-* Number of recursive dependencies: 94
-
-Run `revdepcheck::cloud_details(, "poppr")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘poppr-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: genotype_curve
- > ### Title: Produce a genotype accumulation curve
- > ### Aliases: genotype_curve
- >
- > ### ** Examples
- >
- > data(nancycats)
- > nan_geno <- genotype_curve(nancycats)
- Error: object is invalid:
- - every label must be named.
- Execution halted
- ```
-
-## In both
-
-* checking re-building of vignette outputs ... WARNING
- ```
- Error(s) in re-building vignettes:
- ...
- --- re-building ‘algo.Rnw’ using knitr
- Error: processing vignette 'algo.Rnw' failed with diagnostics:
- Running 'texi2dvi' on 'algo.tex' failed.
- LaTeX errors:
- ! LaTeX Error: File `colortbl.sty' not found.
-
- Type X to quit or to proceed,
- or enter new name. (Default extension: sty)
- ...
- l.4 \makeatletter
- ^^M
- ! ==> Fatal error occurred, no output PDF file produced!
- --- failed re-building ‘algo.Rnw’
-
- SUMMARY: processing the following file failed:
- ‘algo.Rnw’
-
- Error: Vignette re-building failed.
- Execution halted
+
+ --- re-building ‘crosstabs.Rmd’ using rmarkdown
```
# PoweREST
@@ -18074,95 +11788,6 @@ Run `revdepcheck::cloud_details(, "PoweREST")` for more info
Execution halted
```
-# PPQplan
-
-
-
-* Version: 1.1.0
-* GitHub: https://github.com/allenzhuaz/PPQplan
-* Source code: https://github.com/cran/PPQplan
-* Date/Publication: 2020-10-08 04:30:06 UTC
-* Number of recursive dependencies: 116
-
-Run `revdepcheck::cloud_details(, "PPQplan")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘PPQnote.Rmd’ using rmarkdown
- --- finished re-building ‘PPQnote.Rmd’
-
- --- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 12.1Mb
- sub-directories of 1Mb or more:
- doc 12.0Mb
- ```
-
-* checking LazyData ... NOTE
- ```
- 'LazyData' is specified without a 'data' directory
- ```
-
-# ppseq
-
-
-
-* Version: 0.2.5
-* GitHub: https://github.com/zabore/ppseq
-* Source code: https://github.com/cran/ppseq
-* Date/Publication: 2024-09-04 22:20:02 UTC
-* Number of recursive dependencies: 101
-
-Run `revdepcheck::cloud_details(, "ppseq")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘one_sample_expansion.Rmd’ using rmarkdown
-
- Quitting from one_sample_expansion.Rmd:182-188 [unnamed-chunk-13]
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error in `pm[[2]]`:
- ! subscript out of bounds
- ---
- Backtrace:
- ...
-
- Error: processing vignette 'two_sample_randomized.Rmd' failed with diagnostics:
- subscript out of bounds
- --- failed re-building ‘two_sample_randomized.Rmd’
-
- SUMMARY: processing the following files failed:
- ‘one_sample_expansion.Rmd’ ‘two_sample_randomized.Rmd’
-
- Error: Vignette re-building failed.
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 11.0Mb
- sub-directories of 1Mb or more:
- doc 10.5Mb
- ```
-
# precintcon
@@ -18389,47 +12014,6 @@ Run `revdepcheck::cloud_details(, "probably")` for more info
Execution halted
```
-# processmapR
-
-
-
-* Version: 0.5.6
-* GitHub: https://github.com/bupaverse/processmapr
-* Source code: https://github.com/cran/processmapR
-* Date/Publication: 2024-12-03 12:50:02 UTC
-* Number of recursive dependencies: 114
-
-Run `revdepcheck::cloud_details(, "processmapR")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(processmapR)
-
- Attaching package: 'processmapR'
-
- The following object is masked from 'package:stats':
-
- ...
- 10. └─processmapR:::return_plotly(p, plotly)
- 11. ├─plotly::ggplotly(p)
- 12. └─plotly:::ggplotly.ggplot(p)
- 13. └─plotly::gg2list(...)
- ── Failure ('test_trace_explorer.R:240:3'): test trace_explorer on eventlog with param `plotly` ──
- `chart` inherits from 'ggplot2::ggplot'/'ggplot'/'ggplot2::gg'/'S7_object'/'gg' not 'plotly'.
-
- [ FAIL 6 | WARN 0 | SKIP 11 | PASS 105 ]
- Error: Test failures
- Execution halted
- ```
-
# psborrow
@@ -18774,47 +12358,6 @@ Run `revdepcheck::cloud_details(, "qgcompint")` for more info
Execution halted
```
-# qicharts2
-
-
-
-* Version: 0.8.0
-* GitHub: https://github.com/anhoej/qicharts2
-* Source code: https://github.com/cran/qicharts2
-* Date/Publication: 2025-05-15 08:00:02 UTC
-* Number of recursive dependencies: 67
-
-Run `revdepcheck::cloud_details(, "qicharts2")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘qicharts2-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: bchart
- > ### Title: Bernoulli CUSUM chart for binary data (EXPERIMENTAL)
- > ### Aliases: bchart
- >
- > ### ** Examples
- >
- > # Generate 1000 random successes and failures with success rate = 0.02
- ...
- ℹ Please use tidy evaluation idioms with `aes()`
- ℹ The deprecated feature was likely used in the qicharts2 package.
- Please report the issue to the authors.
- Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
- ℹ Please use `linewidth` instead.
- ℹ The deprecated feature was likely used in the qicharts2 package.
- Please report the issue to the authors.
- Error: object is invalid:
- - every label must be named.
- Execution halted
- ```
-
# quantities
@@ -18952,47 +12495,6 @@ Run `revdepcheck::cloud_details(, "quickReg")` for more info
Package unavailable to check Rd xrefs: ‘PredictABEL’
```
-# R4GoodPersonalFinances
-
-
-
-* Version: 1.0.0
-* GitHub: https://github.com/R4GoodAcademy/R4GoodPersonalFinances
-* Source code: https://github.com/cran/R4GoodPersonalFinances
-* Date/Publication: 2025-06-04 11:00:09 UTC
-* Number of recursive dependencies: 107
-
-Run `revdepcheck::cloud_details(, "R4GoodPersonalFinances")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘R4GoodPersonalFinances-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot_retirement_ruin
- > ### Title: Plotting retirement ruin
- > ### Aliases: plot_retirement_ruin
- >
- > ### ** Examples
- >
- > plot_retirement_ruin(
- ...
- + portfolio_return_mean = 0.034,
- + portfolio_return_sd = 0.15,
- + age = 65,
- + gompertz_mode = 88,
- + gompertz_dispersion = 10,
- + portfolio_value = 1000000,
- + monthly_spendings = 3000
- + )
- Error: `object` must be an , not a S3
- Execution halted
- ```
-
# Radviz
@@ -19168,72 +12670,6 @@ Run `revdepcheck::cloud_details(, "randomForestExplainer")` for more info
'LazyData' is specified without a 'data' directory
```
-# rassta
-
-
-
-* Version: 1.0.6
-* GitHub: https://github.com/bafuentes/rassta
-* Source code: https://github.com/cran/rassta
-* Date/Publication: 2024-08-19 06:20:13 UTC
-* Number of recursive dependencies: 105
-
-Run `revdepcheck::cloud_details(, "rassta")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘rassta-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: select_functions
- > ### Title: Select Constrained Univariate Distribution Functions
- > ### Aliases: select_functions
- >
- > ### ** Examples
- >
- > require(terra)
- ...
- > tvars <- terra::rast(tf)
- > # Single-layer SpatRaster of topographic classification units
- > ## 5 classification units
- > tcf <- list.files(path = p, pattern = "topography.tif", full.names = TRUE)
- > tcu <- terra::rast(tcf)
- > # Automatic selection of distribution functions
- > tdif <- select_functions(cu.rast = tcu, var.rast = tvars, fun = mean)
- Error in pm[[2]] : subscript out of bounds
- Calls: select_functions -> -> ggplotly.ggplot -> gg2list
- 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("rassta")
- + }
-
- Attaching package: 'rassta'
-
- ...
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests
- test_select_functions.R....... 0 tests Error in pm[[2]] : subscript out of bounds
- Calls: ... select_functions -> -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
# rasterdiv
@@ -19417,7 +12853,7 @@ Run `revdepcheck::cloud_details(, "rbioacc")` for more info
`actual`: FALSE
`expected`: TRUE
- [ FAIL 20 | WARN 103 | SKIP 9 | PASS 60 ]
+ [ FAIL 20 | WARN 99 | SKIP 9 | PASS 60 ]
Error: Test failures
Execution halted
```
@@ -19481,10 +12917,10 @@ Run `revdepcheck::cloud_details(, "rbiom")` for more info
-* Version: 0.5.4
+* Version: 0.5.5
* GitHub: https://github.com/wenjie2wang/reda
* Source code: https://github.com/cran/reda
-* Date/Publication: 2022-07-08 21:50:02 UTC
+* Date/Publication: 2025-06-14 04:50:02 UTC
* Number of recursive dependencies: 50
Run `revdepcheck::cloud_details(, "reda")` for more info
@@ -19513,31 +12949,19 @@ Run `revdepcheck::cloud_details(, "reda")` for more info
call| expect_equivalent(class(plot(mcf_splineFit)), c("gg", "ggplot"))
diff| Lengths (2, 5) differ (string compare on first 2)
diff| 1 string mismatch
- Error: 8 out of 191 tests failed
+ Error: 5 out of 191 tests failed
In addition: There were 16 warnings (use warnings() to see them)
Execution halted
```
## In both
-* checking C++ specification ... NOTE
- ```
- Specified C++11: please drop specification unless essential
- ```
-
* checking installed package size ... NOTE
```
- installed size is 8.0Mb
+ installed size is 8.3Mb
sub-directories of 1Mb or more:
- doc 3.3Mb
- libs 4.0Mb
- ```
-
-* checking Rd files ... NOTE
- ```
- checkRd: (-1) simEvent.Rd:112: Lost braces; missing escapes or markup?
- 112 | and another argument named {zCoef} for covariate coefficient vector.
- | ^
+ doc 3.6Mb
+ libs 4.1Mb
```
# regtomean
@@ -19622,7 +13046,7 @@ Run `revdepcheck::cloud_details(, "rempsyc")` for more info
Journal of Open Source Software, 8(87), 5466. https://doi.org/10.21105/joss.05466
>
> test_check("rempsyc")
- [ FAIL 2 | WARN 2 | SKIP 20 | PASS 44 ]
+ Ignoring unknown labels:
...
33. │ └─ggplot2 (local) draw_group(..., self = self)
34. └─base::.handleSimpleError(...)
@@ -19631,7 +13055,7 @@ Run `revdepcheck::cloud_details(, "rempsyc")` for more info
37. └─cli::cli_abort(...)
38. └─rlang::abort(...)
- [ FAIL 2 | WARN 2 | SKIP 20 | PASS 44 ]
+ [ FAIL 2 | WARN 0 | SKIP 20 | PASS 44 ]
Error: Test failures
Execution halted
```
@@ -19643,99 +13067,17 @@ Run `revdepcheck::cloud_details(, "rempsyc")` for more info
Quitting from assumptions.Rmd:134-140 [unnamed-chunk-11]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- NULL
- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-
- Error: processing vignette 'assumptions.Rmd' failed with diagnostics:
- Problem while converting geom to grob.
- ℹ Error occurred in the 1st layer.
- Caused by error in `check_linewidth()`:
- ! could not find function "check_linewidth"
- --- failed re-building ‘assumptions.Rmd’
-
- --- re-building ‘contrasts.Rmd’ using rmarkdown
- ```
-
-# RevGadgets
-
-
-
-* Version: 1.2.1
-* GitHub: https://github.com/revbayes/RevGadgets
-* Source code: https://github.com/cran/RevGadgets
-* Date/Publication: 2023-11-29 20:30:02 UTC
-* Number of recursive dependencies: 131
-
-Run `revdepcheck::cloud_details(, "RevGadgets")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(RevGadgets)
- >
- > test_check("RevGadgets")
-
- |
- | | 0%
- ...
- Backtrace:
- ▆
- 1. ├─RevGadgets::plotFBDTree(...) at test_plotFBDTree.R:12:3
- 2. │ └─RevGadgets:::plotTreeFull(...)
- 3. └─base::loadNamespace(x)
- 4. └─base (local) runHook(".onLoad", env, package.lib, package)
-
- [ FAIL 1 | WARN 11 | SKIP 0 | PASS 138 ]
- Error: Test failures
- Execution halted
- ```
-
-# rifreg
-
-
-
-* Version: 0.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/rifreg
-* Date/Publication: 2024-05-01 18:42:07 UTC
-* Number of recursive dependencies: 79
-
-Run `revdepcheck::cloud_details(, "rifreg")` for more info
-
-
-
-## Newly broken
-
-* checking tests ... ERROR
- ```
- Running ‘testthat.R’
- Running the tests in ‘tests/testthat.R’ failed.
- Complete output:
- > library(testthat)
- > library(rifreg)
- Loading required package: ggplot2
- >
- > test_check("rifreg")
- Bootstrapping Standard Errors...
-
- ...
- `expected[2:2]`: "ggplot"
- ── Failure ('test-plot.R:190:3'): Generic plot method generates a plot for RIF of interquantile ratio ──
- class(rifreg_plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
-
- `actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
- `expected[2:2]`: "ggplot"
-
- [ FAIL 10 | WARN 3525 | SKIP 0 | PASS 66 ]
- Error: Test failures
- Execution halted
+ NULL
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+ Error: processing vignette 'assumptions.Rmd' failed with diagnostics:
+ Problem while converting geom to grob.
+ ℹ Error occurred in the 1st layer.
+ Caused by error in `check_linewidth()`:
+ ! could not find function "check_linewidth"
+ --- failed re-building ‘assumptions.Rmd’
+
+ --- re-building ‘contrasts.Rmd’ using rmarkdown
```
# rmweather
@@ -19779,117 +13121,6 @@ Run `revdepcheck::cloud_details(, "rmweather")` for more info
Execution halted
```
-# RNAseqQC
-
-
-
-* Version: 0.2.1
-* GitHub: https://github.com/frederikziebell/RNAseqQC
-* Source code: https://github.com/cran/RNAseqQC
-* Date/Publication: 2024-07-15 14:40:02 UTC
-* Number of recursive dependencies: 159
-
-Run `revdepcheck::cloud_details(, "RNAseqQC")` for more info
-
-
-
-## Newly broken
-
-* checking re-building of vignette outputs ... ERROR
- ```
- Error(s) in re-building vignettes:
- --- re-building ‘data.Rmd’ using rmarkdown
- --- finished re-building ‘data.Rmd’
-
- --- re-building ‘introduction.Rmd’ using rmarkdown
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.0Mb
- sub-directories of 1Mb or more:
- data 4.5Mb
- doc 2.3Mb
- ```
-
-# roahd
-
-
-
-* Version: 1.4.3
-* GitHub: https://github.com/astamm/roahd
-* Source code: https://github.com/cran/roahd
-* Date/Publication: 2021-11-04 00:10:02 UTC
-* Number of recursive dependencies: 84
-
-Run `revdepcheck::cloud_details(, "roahd")` for more info
-
-
-
-## Newly broken
-
-* checking examples ... ERROR
- ```
- Running examples in ‘roahd-Ex.R’ failed
- The error most likely occurred in:
-
- > ### Name: plot.depthgram
- > ### Title: Specialized method to plot 'depthgram' objects
- > ### Aliases: plot.depthgram
- >
- > ### ** Examples
- >
- > N <- 50
- ...
- + N,
- + centerline = sin(2 * pi * grid),
- + Cov = Cov
- + )
- > names <- paste0("id_", 1:nrow(Data[[1]]))
- > DG <- depthgram(Data, marginal_outliers = TRUE, ids = names)
- > plot(DG)
- Error in pm[[2]] : subscript out of bounds
- Calls: plot ... plotly_build -> ggplotly -> ggplotly.ggplot -> gg2list
- Execution halted
- ```
-
-## In both
-
-* checking installed package size ... NOTE
- ```
- installed size is 7.4Mb
- sub-directories of 1Mb or more:
- data 5.0Mb
- doc 1.7Mb
- ```
-
-* checking Rd files ... NOTE
- ```
- checkRd: (-1) fData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) fData.Rd:23-24: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) fData.Rd:25: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) fData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) fData.Rd:27-28: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) mfData.Rd:22: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) mfData.Rd:23: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) mfData.Rd:24-25: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) mfData.Rd:26: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) mfData.Rd:27: Lost braces in \itemize; \value handles \item{}{} directly
- ...
- checkRd: (-1) outliergram.Rd:49-51: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:52-54: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:55-58: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:59-62: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:63-65: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:66-69: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:70-71: Lost braces in \itemize; meant \describe ?
- checkRd: (-1) outliergram.Rd:94: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) outliergram.Rd:95-96: Lost braces in \itemize; \value handles \item{}{} directly
- checkRd: (-1) outliergram.Rd:97: Lost braces in \itemize; \value handles \item{}{} directly
- ```
-
# robCompositions
@@ -19978,173 +13209,6 @@ Run `revdepcheck::cloud_details(, "robCompositions")` for more info
Note: found 1 marked UTF-8 string
```
-# romic
-
-