From dffef8415d78f445770427307525301d02687670 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Wed, 3 Jun 2020 22:26:53 -0400
Subject: [PATCH 01/22] bump version to 2.0.0

---
 DESCRIPTION | 2 +-
 NEWS.md     | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2e42a36e0..042226f34 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: GGally
-Version: 1.5.0.9000
+Version: 2.0.0
 License: GPL (>= 2.0)
 Title: Extension to 'ggplot2'
 Type: Package
diff --git a/NEWS.md b/NEWS.md
index e6cdbeb41..e863d536d 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,4 @@
-GGally (development version)
----------------------
+# GGally 2.0.0
 
 ### New Vignettes
 * `vignette("ggally_plots", package = "GGally")` - List of available high-level plots

From 5607c9c6be8f1ff8130a686192f39a0adb6695f6 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Wed, 3 Jun 2020 22:36:10 -0400
Subject: [PATCH 02/22] Do not print as much

---
 R/ggpairs_add.R | 19 +++++++++++--------
 man/gg-add.Rd   | 19 +++++++++++--------
 2 files changed, 22 insertions(+), 16 deletions(-)

diff --git a/R/ggpairs_add.R b/R/ggpairs_add.R
index cfdd9b3f3..9be6136da 100644
--- a/R/ggpairs_add.R
+++ b/R/ggpairs_add.R
@@ -29,17 +29,20 @@
 #' @method + gg
 #' @rdname gg-add
 #' @examples
+#' # small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
 #' data(tips, package = "reshape")
+#'
 #' pm <- ggpairs(tips[, 2:4], ggplot2::aes(color = sex))
 #' ## change to black and white theme
 #' pm + ggplot2::theme_bw()
 #' ## change to linedraw theme
-#' # pm + ggplot2::theme_linedraw()
+#' p_(pm + ggplot2::theme_linedraw())
 #' ## change to custom theme
-#' # pm + ggplot2::theme(panel.background = ggplot2::element_rect(fill = "lightblue"))
+#' p_(pm + ggplot2::theme(panel.background = ggplot2::element_rect(fill = "lightblue")))
 #' ## add a list of information
 #' extra <- list(ggplot2::theme_bw(), ggplot2::labs(caption = "My caption!"))
-#' pm + extra
+#' p_(pm + extra)
 "+.gg" <- function(e1, e2) {
 
   if (!is.ggmatrix(e1)) {
@@ -127,17 +130,17 @@ add_theme_to_ggmatrix <- function(e1, e2) {
 #' @seealso \code{\link{ggmatrix_location}}
 #' @examples
 #' ## modify scale
-#' pm + scale_fill_brewer(type = "qual")
+#' p_(pm + scale_fill_brewer(type = "qual"))
 #' ## only first row
-#' add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), rows = 1:2)
+#' p_(add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), rows = 1:2))
 #' ## only second col
-#' add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), cols = 2:3)
+#' p_(add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), cols = 2:3))
 #' ## only to upper triangle of plot matrix
-#' add_to_ggmatrix(
+#' p_(add_to_ggmatrix(
 #'   pm,
 #'   scale_fill_brewer(type = "qual"),
 #'   location = "upper"
-#' )
+#' ))
 add_to_ggmatrix <- function(
   e1,
   e2,
diff --git a/man/gg-add.Rd b/man/gg-add.Rd
index 6b0a7d6a6..3a4685990 100644
--- a/man/gg-add.Rd
+++ b/man/gg-add.Rd
@@ -54,29 +54,32 @@ with elements from e2.
   only some subplots.  This function may be replaced and/or removed in the future. \Sexpr[results=rd, stage=render]{lifecycle::badge("experimental")}
 }
 \examples{
+# small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 data(tips, package = "reshape")
+
 pm <- ggpairs(tips[, 2:4], ggplot2::aes(color = sex))
 ## change to black and white theme
 pm + ggplot2::theme_bw()
 ## change to linedraw theme
-# pm + ggplot2::theme_linedraw()
+p_(pm + ggplot2::theme_linedraw())
 ## change to custom theme
-# pm + ggplot2::theme(panel.background = ggplot2::element_rect(fill = "lightblue"))
+p_(pm + ggplot2::theme(panel.background = ggplot2::element_rect(fill = "lightblue")))
 ## add a list of information
 extra <- list(ggplot2::theme_bw(), ggplot2::labs(caption = "My caption!"))
-pm + extra
+p_(pm + extra)
 ## modify scale
-pm + scale_fill_brewer(type = "qual")
+p_(pm + scale_fill_brewer(type = "qual"))
 ## only first row
-add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), rows = 1:2)
+p_(add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), rows = 1:2))
 ## only second col
-add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), cols = 2:3)
+p_(add_to_ggmatrix(pm, scale_fill_brewer(type = "qual"), cols = 2:3))
 ## only to upper triangle of plot matrix
-add_to_ggmatrix(
+p_(add_to_ggmatrix(
   pm,
   scale_fill_brewer(type = "qual"),
   location = "upper"
-)
+))
 }
 \seealso{
 \code{\link[ggplot2]{+.gg}} and \code{\link[ggplot2]{theme}}

From 0d91af2eb515ef9c023f49ab7fd9a65b7d9538c4 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Wed, 3 Jun 2020 23:01:15 -0400
Subject: [PATCH 03/22] Add back lifecycle macros

---
 DESCRIPTION              | 1 +
 R/deprecated.R           | 4 ++--
 R/ggpairs_add.R          | 2 +-
 man/ggmatrix_location.Rd | 2 +-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 042226f34..7ded34e83 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -68,3 +68,4 @@ VignetteBuilder: knitr
 SystemRequirements: openssl
 Encoding: UTF-8
 Language: en-US
+RdMacros: lifecycle
diff --git a/R/deprecated.R b/R/deprecated.R
index 15b8c88a9..43e29b497 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -1,6 +1,6 @@
 #' Modify a \code{\link{ggmatrix}} object by adding an \pkg{ggplot2} object to all
 #'
-# \Sexpr[results=rd, stage=render]{lifecycle::badge("deprecated")}
+# \lifecycle{deprecated}
 #'
 #' @export
 #' @examples
@@ -18,7 +18,7 @@ v1_ggmatrix_theme <- function() {
 
 #' Correlation value plot
 #'
-# \Sexpr[results=rd, stage=render]{lifecycle::badge("deprecated")}
+# \lifecycle{deprecated}
 #'
 #' (Deprecated. See \code{\link{ggally_cor}}.)
 #'
diff --git a/R/ggpairs_add.R b/R/ggpairs_add.R
index 9be6136da..322ede97b 100644
--- a/R/ggpairs_add.R
+++ b/R/ggpairs_add.R
@@ -175,7 +175,7 @@ add_to_ggmatrix <- function(
 
 #' \code{\link{ggmatrix}} plot locations
 #'
-#' \Sexpr[results=rd, stage=render]{lifecycle::badge("experimental")}
+#' \lifecycle{experimental}
 #'
 #' Convert many types of location values to a consistent \code{data.frame} of \code{row} and \code{col} values.
 #'
diff --git a/man/ggmatrix_location.Rd b/man/ggmatrix_location.Rd
index 2012e42e1..af24d9c65 100644
--- a/man/ggmatrix_location.Rd
+++ b/man/ggmatrix_location.Rd
@@ -32,7 +32,7 @@ ggmatrix_location(pm, location = NULL, rows = NULL, cols = NULL)
 Data frame with columns \code{c("row", "col")} containing locations for the plot matrix
 }
 \description{
-\Sexpr[results=rd, stage=render]{lifecycle::badge("experimental")}
+\lifecycle{experimental}
 }
 \details{
 Convert many types of location values to a consistent \code{data.frame} of \code{row} and \code{col} values.

From 3cdb23d2d5788d3fb760129a78032d94698cd713 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Wed, 3 Jun 2020 23:59:34 -0400
Subject: [PATCH 04/22] Update pkgdown.yaml

---
 .github/workflows/pkgdown.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index f7f036f1b..3be80c21c 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -52,7 +52,7 @@ jobs:
           CAN_PRINT: "TRUE"
         run: |
           pkgdown::build_site()
-          stopifnot(length(warnings) == 0)
+          stopifnot(length(warnings()) == 0)
         shell: Rscript {0}
 
       - name: Build and Deploy Site

From 27e82a03ba1a4f2c35da016f9dafe8df80576602 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Wed, 3 Jun 2020 23:59:38 -0400
Subject: [PATCH 05/22] Create rhub.R

---
 scripts/rhub.R | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 scripts/rhub.R

diff --git a/scripts/rhub.R b/scripts/rhub.R
new file mode 100644
index 000000000..4d75dfd3b
--- /dev/null
+++ b/scripts/rhub.R
@@ -0,0 +1,5 @@
+rhub_output <- devtools::check_rhub(
+  env_vars = c("_R_CHECK_FORCE_SUGGESTS_" = "0"),
+  interactive = FALSE
+)
+rhub_output$web()

From 887672b2d1a3dd8e509b18956e14e462ed6c9b0f Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 4 Jun 2020 01:12:53 -0400
Subject: [PATCH 06/22] speed up cran examples

---
 R/gg-plots.R     |  1 -
 R/ggscatmat.R    | 12 ++++++++++--
 R/ggtable.R      | 13 ++++++++-----
 man/ggscatmat.Rd |  6 +++++-
 man/ggtable.Rd   | 13 ++++++++-----
 man/scatmat.Rd   |  6 +++++-
 6 files changed, 36 insertions(+), 15 deletions(-)

diff --git a/R/gg-plots.R b/R/gg-plots.R
index 2bd9b2bb7..d1827ec25 100644
--- a/R/gg-plots.R
+++ b/R/gg-plots.R
@@ -1812,4 +1812,3 @@ mean_sd <- function(x, weights = NULL) {
   sd <- round(sqrt(Hmisc::wtd.var(x, weights = weights, na.rm = TRUE)), digits = 1)
   paste0("Mean: ", m, " (", sd, ")")
 }
-
diff --git a/R/ggscatmat.R b/R/ggscatmat.R
index f708a48a5..ea9e6b608 100644
--- a/R/ggscatmat.R
+++ b/R/ggscatmat.R
@@ -211,9 +211,13 @@ uppertriangle <- function(data, columns=1:ncol(data), color=NULL, corMethod = "p
 #' @param alpha an option to set the transparency in scatterplots for large data. Defaults to \code{1}.
 #' @author Mengjia Ni, Di Cook
 #' @examples
+#' # small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(flea)
+#'
 #' scatmat(flea, columns=2:4)
-#' scatmat(flea, columns= 2:4, color="species")
+#' p_(scatmat(flea, columns= 2:4, color="species"))
 scatmat <- function(data, columns=1:ncol(data), color=NULL, alpha=1) {
   data <- upgrade_scatmat_data(data)
   data.choose <- data[columns]
@@ -293,9 +297,13 @@ scatmat <- function(data, columns=1:ncol(data), color=NULL, alpha=1) {
 #' @param corMethod method argument supplied to \code{\link[stats]{cor}}
 #' @author Mengjia Ni, Di Cook
 #' @examples
+#' # small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(flea)
+#'
 #' ggscatmat(flea, columns = 2:4)
-#' ggscatmat(flea, columns = 2:4, color = "species")
+#' p_(ggscatmat(flea, columns = 2:4, color = "species"))
 ggscatmat <- function(data, columns = 1:ncol(data), color = NULL, alpha = 1, corMethod = "pearson"){
   ## if 'color' is not a factor, mold it into one
   if (!is.null(color)) {
diff --git a/R/ggtable.R b/R/ggtable.R
index ecc75504d..3d8c9b003 100644
--- a/R/ggtable.R
+++ b/R/ggtable.R
@@ -14,28 +14,31 @@
 #' @author Joseph Larmarange
 #' @export
 #' @examples
+#' # small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
 #' ggtable(tips, "smoker", c("day", "time", "sex"))
 #'
 #' # displaying row proportions
-#' ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop")
+#' p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
 #'
 #' # filling cells with standardized residuals
-#' ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres")
+#' p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
 #'
 #' # if continuous variables are provided, just displaying some summary statistics
-#' ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip"))
+#' p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))
 #'
 #' # specifying weights
 #' d <- as.data.frame(Titanic)
-#' ggtable(
+#' p_(ggtable(
 #'   d,
 #'   "Survived",
 #'   c("Class", "Sex", "Age"),
 #'   mapping = aes(weight = Freq),
 #'   cells = "row.prop",
 #'   fill = "stdres"
-#' )
+#' ))
 ggtable <- function(
   data,
   columnsX = 1:ncol(data),
diff --git a/man/ggscatmat.Rd b/man/ggscatmat.Rd
index 7376f41d2..a5dfc7281 100644
--- a/man/ggscatmat.Rd
+++ b/man/ggscatmat.Rd
@@ -29,9 +29,13 @@ This function makes a scatterplot matrix for quantitative variables with density
 and correlation printed in the upper triangle.
 }
 \examples{
+# small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(flea)
+
 ggscatmat(flea, columns = 2:4)
-ggscatmat(flea, columns = 2:4, color = "species")
+p_(ggscatmat(flea, columns = 2:4, color = "species"))
 }
 \author{
 Mengjia Ni, Di Cook
diff --git a/man/ggtable.Rd b/man/ggtable.Rd
index 5ee4509d4..427612c2f 100644
--- a/man/ggtable.Rd
+++ b/man/ggtable.Rd
@@ -35,28 +35,31 @@ weights (see examples)}
 cross-tabulated tables of discrete variables.
 }
 \examples{
+# small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
 ggtable(tips, "smoker", c("day", "time", "sex"))
 
 # displaying row proportions
-ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop")
+p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
 
 # filling cells with standardized residuals
-ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres")
+p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
 
 # if continuous variables are provided, just displaying some summary statistics
-ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip"))
+p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))
 
 # specifying weights
 d <- as.data.frame(Titanic)
-ggtable(
+p_(ggtable(
   d,
   "Survived",
   c("Class", "Sex", "Age"),
   mapping = aes(weight = Freq),
   cells = "row.prop",
   fill = "stdres"
-)
+))
 }
 \author{
 Joseph Larmarange
diff --git a/man/scatmat.Rd b/man/scatmat.Rd
index 0d479328e..3c07815be 100644
--- a/man/scatmat.Rd
+++ b/man/scatmat.Rd
@@ -19,9 +19,13 @@ scatmat(data, columns = 1:ncol(data), color = NULL, alpha = 1)
 Function for making scatterplots in the lower triangle and diagonal density plots.
 }
 \examples{
+# small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(flea)
+
 scatmat(flea, columns=2:4)
-scatmat(flea, columns= 2:4, color="species")
+p_(scatmat(flea, columns= 2:4, color="species"))
 }
 \author{
 Mengjia Ni, Di Cook

From 8a6b8ffbf6f7187dc9503ac51c3f5f48b3f72a1c Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 4 Jun 2020 01:13:20 -0400
Subject: [PATCH 07/22] Run Revdep

---
 revdep/README.md      |  120 ++-
 revdep/problems.md    | 1647 ++++++++++++++++++++++++++++++++++++++++-
 revdep/revdep_cran.md |   14 +
 3 files changed, 1775 insertions(+), 6 deletions(-)
 create mode 100644 revdep/revdep_cran.md

diff --git a/revdep/README.md b/revdep/README.md
index 8039b7f87..6b70bd723 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -2,20 +2,130 @@
 
 |field    |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.6.3 (2020-02-29) |
-|os       |macOS Catalina 10.15.3       |
-|system   |x86_64, darwin15.6.0         |
+|version  |R version 4.0.0 (2020-04-24) |
+|os       |macOS Catalina 10.15.5       |
+|system   |x86_64, darwin17.0           |
 |ui       |X11                          |
 |language |(EN)                         |
 |collate  |en_US.UTF-8                  |
 |ctype    |en_US.UTF-8                  |
 |tz       |America/New_York             |
-|date     |2020-03-19                   |
+|date     |2020-06-04                   |
 
 # Dependencies
 
 |package |old   |new   |Δ  |
 |:-------|:-----|:-----|:--|
-|GGally  |1.4.0 |1.5.0 |*  |
+|GGally  |1.5.0 |2.0.0 |*  |
 
 # Revdeps
+
+## New problems (1)
+
+|package                                          |version |error |warning |note |
+|:------------------------------------------------|:-------|:-----|:-------|:----|
+|[robustSingleCell](problems.md#robustsinglecell) |0.1.1   |      |__+1__  |     |
+
+## All (98)
+
+|package                                          |version |error |warning |note |
+|:------------------------------------------------|:-------|:-----|:-------|:----|
+|[adventr](problems.md#adventr)                   |0.1.8   |      |        |2    |
+|[alevinQC](problems.md#alevinqc)                 |1.4.0   |      |        |1    |
+|[ALPS](problems.md#alps)                         |1.2.0   |      |        |1    |
+|BAS                                              |1.5.5   |      |        |     |
+|bayestestR                                       |0.6.0   |      |        |     |
+|[BGGM](problems.md#bggm)                         |2.0.0   |      |        |2    |
+|[bigPint](problems.md#bigpint)                   |1.4.0   |      |        |1    |
+|brinton                                          |0.1.7   |      |        |     |
+|CARBayes                                         |5.2     |      |        |     |
+|CARBayesST                                       |3.1     |      |        |     |
+|[CeTF](problems.md#cetf)                         |1.0.2   |      |        |1    |
+|[CINNA](problems.md#cinna)                       |1.1.53  |      |        |1    |
+|[CluMSID](problems.md#clumsid)                   |1.4.0   |      |        |2    |
+|clustrd                                          |1.3.7-2 |      |        |     |
+|[ctsem](problems.md#ctsem)                       |3.2.1   |      |        |3    |
+|DescribeDisplay                                  |0.2.7   |      |        |     |
+|discourseGT                                      |1.0.0   |      |        |     |
+|eechidna                                         |1.4.0   |      |        |     |
+|egoTERGM                                         |2.1.1   |      |        |     |
+|EMMIXmfa                                         |2.0.11  |      |        |     |
+|[fic](problems.md#fic)                           |1.0.0   |      |        |1    |
+|[finalfit](problems.md#finalfit)                 |1.0.1   |1     |        |     |
+|[fingerPro](problems.md#fingerpro)               |1.1     |      |        |1    |
+|fpp2                                             |2.3     |      |        |     |
+|freqparcoord                                     |1.0.1   |      |        |     |
+|[GENESIS](problems.md#genesis)                   |2.18.0  |      |        |3    |
+|[ggbio](problems.md#ggbio)                       |1.36.0  |      |1       |2    |
+|ggmcmc                                           |1.4.1   |      |        |     |
+|[GGPA](problems.md#ggpa)                         |1.0.0   |      |        |2    |
+|ggPMX                                            |1.1.1   |      |        |     |
+|[ggquickeda](problems.md#ggquickeda)             |0.1.6   |      |        |1    |
+|glancedata                                       |1.0.1   |      |        |     |
+|growthPheno                                      |1.0-22  |      |        |     |
+|gsynth                                           |1.0.9   |      |        |     |
+|HierDpart                                        |0.5.0   |      |        |     |
+|[httk](problems.md#httk)                         |2.0.1   |      |        |1    |
+|[ICtest](problems.md#ictest)                     |0.3-2   |      |        |1    |
+|imageData                                        |0.1-60  |      |        |     |
+|[isomiRs](problems.md#isomirs)                   |1.16.1  |2     |        |3    |
+|ITNr                                             |0.6.0   |      |        |     |
+|[jmv](problems.md#jmv)                           |1.2.5   |      |        |1    |
+|[jsmodule](problems.md#jsmodule)                 |1.0.7   |      |        |1    |
+|[LANDD](problems.md#landd)                       |1.1.0   |      |        |1    |
+|[MAINT.Data](problems.md#maintdata)              |2.3.1   |      |        |1    |
+|[MAST](problems.md#mast)                         |1.14.0  |      |        |2    |
+|[MCbiclust](problems.md#mcbiclust)               |1.12.0  |      |        |1    |
+|metan                                            |1.6.0   |      |        |     |
+|[mgcViz](problems.md#mgcviz)                     |0.1.6   |      |        |1    |
+|[MissingDataGUI](problems.md#missingdatagui)     |0.2-5   |      |4       |4    |
+|mitch                                            |1.0.4   |      |        |     |
+|miWQS                                            |0.2.0   |      |        |     |
+|mlergm                                           |0.5     |      |        |     |
+|mlr3viz                                          |0.1.1   |      |        |     |
+|[mlrMBO](problems.md#mlrmbo)                     |1.1.4   |      |        |1    |
+|[MOFA](problems.md#mofa)                         |1.4.0   |1     |        |5    |
+|MRPC                                             |2.2.0   |      |        |     |
+|[NetworkChange](problems.md#networkchange)       |0.6     |      |        |1    |
+|[nzelect](problems.md#nzelect)                   |0.4.0   |      |        |2    |
+|[ORFik](problems.md#orfik)                       |1.8.1   |      |        |2    |
+|OutliersO3                                       |0.6.3   |      |        |     |
+|[PAFway](problems.md#pafway)                     |0.1.3   |      |        |1    |
+|ParamHelpers                                     |1.14    |      |        |     |
+|Pi                                               |2.0.0   |      |        |     |
+|[plotly](problems.md#plotly)                     |4.9.2.1 |      |        |1    |
+|[PopGenReport](problems.md#popgenreport)         |3.0.4   |      |        |1    |
+|PPforest                                         |0.1.1   |      |        |     |
+|[pubh](problems.md#pubh)                         |1.1.14  |      |        |1    |
+|qualvar                                          |0.2.0   |      |        |     |
+|QuantNorm                                        |1.0.5   |      |        |     |
+|randomForestExplainer                            |0.10.0  |      |        |     |
+|RHMS                                             |1.6     |      |        |     |
+|[robCompositions](problems.md#robcompositions)   |2.2.1   |      |        |1    |
+|[robustbase](problems.md#robustbase)             |0.93-6  |      |        |1    |
+|[robustSingleCell](problems.md#robustsinglecell) |0.1.1   |      |__+1__  |     |
+|[rrr](problems.md#rrr)                           |1.0.0   |      |        |1    |
+|rwty                                             |1.0.2   |      |        |     |
+|[scPipe](problems.md#scpipe)                     |1.10.0  |      |        |4    |
+|[SeqSQC](problems.md#seqsqc)                     |1.10.0  |      |        |1    |
+|SHELF                                            |1.7.0   |      |        |     |
+|SimBIID                                          |0.2.0   |      |        |     |
+|simplexdesign                                    |0.1.0   |      |        |     |
+|[SmartEDA](problems.md#smarteda)                 |0.3.5   |      |        |1    |
+|[spinifex](problems.md#spinifex)                 |0.1.0   |      |        |1    |
+|[spup](problems.md#spup)                         |1.3-2   |      |        |1    |
+|staRdom                                          |1.1.11  |      |        |     |
+|[statVisual](problems.md#statvisual)             |1.2.1   |      |        |1    |
+|[tidybulk](problems.md#tidybulk)                 |1.0.0   |2     |        |3    |
+|TNBC.CMS                                         |1.4.0   |      |        |     |
+|tsfeatures                                       |1.0.1   |      |        |     |
+|[TVTB](problems.md#tvtb)                         |1.14.0  |      |        |1    |
+|[ubiquity](problems.md#ubiquity)                 |1.0.1   |      |        |1    |
+|[ufs](problems.md#ufs)                           |0.3.1   |      |        |2    |
+|userfriendlyscience                              |0.7.2   |      |        |     |
+|ushr                                             |0.2.3   |      |        |     |
+|[vidger](problems.md#vidger)                     |1.8.0   |      |        |1    |
+|vortexR                                          |1.1.7   |      |        |     |
+|WRS2                                             |1.0-0   |      |        |     |
+|WRSS                                             |3.0     |      |        |     |
+
diff --git a/revdep/problems.md b/revdep/problems.md
index 9a2073633..4af15d300 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1 +1,1646 @@
-*Wow, no problems at all. :)*
\ No newline at end of file
+# adventr
+
+<details>
+
+* Version: 0.1.8
+* Source code: https://github.com/cran/adventr
+* Date/Publication: 2020-05-05 16:50:06 UTC
+* Number of recursive dependencies: 162
+
+Run `revdep_details(,"adventr")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.7Mb
+      sub-directories of 1Mb or more:
+        tutorials   5.5Mb
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘BayesFactor’ ‘GGally’ ‘Hmisc’ ‘WRS2’ ‘boot’ ‘car’ ‘dplyr’ ‘effects’
+      ‘effsize’ ‘forcats’ ‘ggplot2’ ‘lm.beta’ ‘nlme’ ‘readr’ ‘robust’
+      ‘sandwich’ ‘sjstats’ ‘tidyr’
+      All declared Imports should be used.
+    ```
+
+# alevinQC
+
+<details>
+
+* Version: 1.4.0
+* Source code: https://github.com/cran/alevinQC
+* URL: https://github.com/csoneson/alevinQC
+* BugReports: https://github.com/csoneson/alevinQC/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 87
+
+Run `revdep_details(,"alevinQC")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is 12.7Mb
+      sub-directories of 1Mb or more:
+        extdata  11.6Mb
+    ```
+
+# ALPS
+
+<details>
+
+* Version: 1.2.0
+* Source code: https://github.com/cran/ALPS
+* URL: https://github.com/itsvenu/ALPS
+* BugReports: https://github.com/itsvenu/ALPS/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 194
+
+Run `revdep_details(,"ALPS")` for more info
+
+</details>
+
+## In both
+
+*   checking for hidden files and directories ... NOTE
+    ```
+    Found the following hidden files and directories:
+      .BBSoptions
+    These were most likely included in error. See section ‘Package
+    structure’ in the ‘Writing R Extensions’ manual.
+    ```
+
+# BGGM
+
+<details>
+
+* Version: 2.0.0
+* Source code: https://github.com/cran/BGGM
+* BugReports: https://github.com/donaldRwilliams/BGGM/issues
+* Date/Publication: 2020-05-31 21:10:09 UTC
+* Number of recursive dependencies: 185
+
+Run `revdep_details(,"BGGM")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.1Mb
+      sub-directories of 1Mb or more:
+        doc   2.6Mb
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘RcppProgress’
+      All declared Imports should be used.
+    ```
+
+# bigPint
+
+<details>
+
+* Version: 1.4.0
+* Source code: https://github.com/cran/bigPint
+* URL: https://github.com/lindsayrutter/bigPint
+* BugReports: https://github.com/lindsayrutter/bigPint/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 165
+
+Run `revdep_details(,"bigPint")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  8.1Mb
+      sub-directories of 1Mb or more:
+        data             2.1Mb
+        doc              2.7Mb
+        shiny-examples   3.0Mb
+    ```
+
+# CeTF
+
+<details>
+
+* Version: 1.0.2
+* Source code: https://github.com/cran/CeTF
+* Date/Publication: 2020-05-31
+* Number of recursive dependencies: 224
+
+Run `revdep_details(,"CeTF")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.2Mb
+      sub-directories of 1Mb or more:
+        data   1.6Mb
+        doc    3.0Mb
+    ```
+
+# CINNA
+
+<details>
+
+* Version: 1.1.53
+* Source code: https://github.com/cran/CINNA
+* Date/Publication: 2019-02-25 12:50:14 UTC
+* Number of recursive dependencies: 136
+
+Run `revdep_details(,"CINNA")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘circlize’
+      All declared Imports should be used.
+    ```
+
+# CluMSID
+
+<details>
+
+* Version: 1.4.0
+* Source code: https://github.com/cran/CluMSID
+* URL: https://github.com/tdepke/CluMSID
+* BugReports: https://github.com/tdepke/CluMSID/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 164
+
+Run `revdep_details(,"CluMSID")` for more info
+
+</details>
+
+## In both
+
+*   checking package dependencies ... NOTE
+    ```
+    Package suggested but not available for checking: ‘xcms’
+    ```
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  6.2Mb
+      sub-directories of 1Mb or more:
+        doc   5.6Mb
+    ```
+
+# ctsem
+
+<details>
+
+* Version: 3.2.1
+* Source code: https://github.com/cran/ctsem
+* URL: https://github.com/cdriveraus/ctsem
+* Date/Publication: 2020-04-26 01:00:07 UTC
+* Number of recursive dependencies: 128
+
+Run `revdep_details(,"ctsem")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  9.6Mb
+      sub-directories of 1Mb or more:
+        R      2.0Mb
+        libs   6.3Mb
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘numDeriv’ ‘pkgbuild’
+      All declared Imports should be used.
+    ```
+
+*   checking for GNU extensions in Makefiles ... NOTE
+    ```
+    GNU make is a SystemRequirements.
+    ```
+
+# fic
+
+<details>
+
+* Version: 1.0.0
+* Source code: https://github.com/cran/fic
+* URL: https://github.com/chjackson/fic
+* BugReports: https://github.com/chjackson/fic/issues
+* Date/Publication: 2019-04-13 08:32:39 UTC
+* Number of recursive dependencies: 88
+
+Run `revdep_details(,"fic")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘numDeriv’
+      All declared Imports should be used.
+    ```
+
+# finalfit
+
+<details>
+
+* Version: 1.0.1
+* Source code: https://github.com/cran/finalfit
+* URL: https://github.com/ewenharrison/finalfit
+* BugReports: https://github.com/ewenharrison/finalfit/issues
+* Date/Publication: 2020-04-21 11:50:02 UTC
+* Number of recursive dependencies: 134
+
+Run `revdep_details(,"finalfit")` for more info
+
+</details>
+
+## In both
+
+*   checking examples ... ERROR
+    ```
+    ...
+      mort_5yr mort_5yr.num   n
+    1    Alive            1 511
+    2     Died            2 404
+    3     <NA>           NA  14
+
+    $counts[[19]]
+      sex.factor2 age.factor2   n
+    1           M   <60 years 204
+    2           M   60+ years 241
+    3           F   <60 years 210
+    4           F   60+ years 274
+
+
+    >
+    > # Select a tibble and expand
+    > out$counts[[9]] %>%
+    +   print(n = Inf)
+    Error in print.default(m, ..., quote = quote, right = right, max = max) :
+      invalid 'na.print' specification
+    Calls: %>% ... print -> print.data.frame -> print -> print.default
+    Execution halted
+    ```
+
+# fingerPro
+
+<details>
+
+* Version: 1.1
+* Source code: https://github.com/cran/fingerPro
+* URL: https://github.com/eead-csic-eesa
+* Date/Publication: 2018-08-28 10:04:54 UTC
+* Number of recursive dependencies: 154
+
+Run `revdep_details(,"fingerPro")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘RcppProgress’
+      All declared Imports should be used.
+    ```
+
+# GENESIS
+
+<details>
+
+* Version: 2.18.0
+* Source code: https://github.com/cran/GENESIS
+* URL: https://github.com/UW-GAC/GENESIS
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 150
+
+Run `revdep_details(,"GENESIS")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  6.9Mb
+      sub-directories of 1Mb or more:
+        doc       3.2Mb
+        extdata   3.1Mb
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    ':::' calls which should be '::':
+      ‘SPAtest:::Saddle_Prob’ ‘SPAtest:::Saddle_Prob_fast’
+      See the note in ?`:::` about the use of this operator.
+    Unexported object imported by a ':::' call: ‘survey:::saddle’
+      See the note in ?`:::` about the use of this operator.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    .pcrelate: no visible binding for global variable ‘k’
+    calcISAFBeta: no visible binding for global variable ‘k’
+    pcrelateSampBlock: no visible binding for global variable ‘k’
+    Undefined global functions or variables:
+      k
+    ```
+
+# ggbio
+
+<details>
+
+* Version: 1.36.0
+* Source code: https://github.com/cran/ggbio
+* URL: http://tengfei.github.com/ggbio/
+* BugReports: https://github.com/tengfei/ggbio/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 157
+
+Run `revdep_details(,"ggbio")` for more info
+
+</details>
+
+## In both
+
+*   checking examples ... WARNING
+    ```
+    Found the following significant warnings:
+
+      Warning: 'GenenameFilter' is deprecated.
+    Deprecated functions may be defunct as soon as of the next release of
+    R.
+    See ?Deprecated.
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    ':::' call which should be '::': 'ggplot2:::set_last_plot'
+      See the note in ?`:::` about the use of this operator.
+    Unexported objects imported by ':::' calls:
+      'S4Vectors:::top_prenv' 'ggplot2:::add_ggplot' 'ggplot2:::cunion'
+      'ggplot2:::rename_aes' 'ggplot2:::rescale01'
+      See the note in ?`:::` about the use of this operator.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    ...
+    layout_karyogram,GRanges: no visible binding for global variable 'xend'
+    layout_karyogram,GRanges: no visible binding for global variable 'yend'
+    layout_karyogram,GRanges: no visible binding for global variable 'y2'
+    layout_karyogram,GRanges: no visible binding for global variable
+      'yend2'
+    layout_karyogram,GRanges: no visible binding for global variable 'name'
+    plotFragLength,character-GRanges: no visible binding for global
+      variable '.fragLength'
+    plotSpliceSum,character-EnsDb: possible error in GRangesFilter(which,
+      condition = "overlapping"): unused argument (condition =
+      "overlapping")
+    stat_mismatch,GRanges: no visible binding for global variable 'sts'
+    stat_mismatch,GRanges: no visible binding for global variable 'eds'
+    stat_mismatch,GRanges: no visible binding for global variable 'read'
+    Undefined global functions or variables:
+      .fragLength .layout_circle.stats .x breaks coefs data eds fe fl
+      gieStain ideoCyto indexProbesProcessed midpoint mt name read se
+      stepping sts value variable x xend y y.text y2 yend yend2
+    Consider adding
+      importFrom("utils", "data")
+    to your NAMESPACE file.
+    ```
+
+# GGPA
+
+<details>
+
+* Version: 1.0.0
+* Source code: https://github.com/cran/GGPA
+* URL: https://github.com/dongjunchung/GGPA/
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 73
+
+Run `revdep_details(,"GGPA")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Packages in Depends field not imported from:
+      ‘network’ ‘scales’ ‘sna’
+      These packages need to be imported from (in the NAMESPACE file)
+      for when this namespace is loaded but not attached.
+    ```
+
+*   checking compiled code ... NOTE
+    ```
+    File ‘GGPA/libs/GGPA.so’:
+      Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
+        Object: ‘3_Param.o’
+
+    Compiled code should not call entry points which might terminate R nor
+    write to stdout/stderr instead of to the console, nor use Fortran I/O
+    nor system RNGs.
+
+    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
+    ```
+
+# ggquickeda
+
+<details>
+
+* Version: 0.1.6
+* Source code: https://github.com/cran/ggquickeda
+* URL: https://github.com/smouksassi/ggquickeda
+* BugReports: https://github.com/smouksassi/ggquickeda/issues
+* Date/Publication: 2020-04-17 14:00:03 UTC
+* Number of recursive dependencies: 157
+
+Run `revdep_details(,"ggquickeda")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘DT’ ‘Formula’ ‘GGally’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’
+      ‘ggpubr’ ‘ggrepel’ ‘ggstance’ ‘grDevices’ ‘grid’ ‘gridExtra’
+      ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjqui’
+      ‘shinyjs’ ‘survival’ ‘survminer’ ‘table1’ ‘tidyr’
+      All declared Imports should be used.
+    ```
+
+# httk
+
+<details>
+
+* Version: 2.0.1
+* Source code: https://github.com/cran/httk
+* URL: https://www.epa.gov/chemical-research/rapid-chemical-exposure-and-dose-research
+* BugReports: https://github.com/USEPA/CompTox-ExpoCast-httk
+* Date/Publication: 2020-03-02 06:00:12 UTC
+* Number of recursive dependencies: 111
+
+Run `revdep_details(,"httk")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is 12.7Mb
+      sub-directories of 1Mb or more:
+        data   9.1Mb
+        doc    2.1Mb
+    ```
+
+# ICtest
+
+<details>
+
+* Version: 0.3-2
+* Source code: https://github.com/cran/ICtest
+* Date/Publication: 2019-08-23 11:50:02 UTC
+* Number of recursive dependencies: 80
+
+Run `revdep_details(,"ICtest")` for more info
+
+</details>
+
+## In both
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Package unavailable to check Rd xrefs: ‘fICA’
+    ```
+
+# isomiRs
+
+<details>
+
+* Version: 1.16.1
+* Source code: https://github.com/cran/isomiRs
+* BugReports: https://github.com/lpantano/isomiRs/issues
+* Date/Publication: 2020-05-26
+* Number of recursive dependencies: 149
+
+Run `revdep_details(,"isomiRs")` for more info
+
+</details>
+
+## In both
+
+*   checking examples ... ERROR
+    ```
+    ...
+    Joining, by = "merge"
+    Error: Problem with `summarise()` input `n_genes`.
+    ✖ could not find function "n"
+    ℹ Input `n_genes` is `n()`.
+    ℹ The error occured in group 1: merge = "one_groupcontrol", cluster = 1, xaxis = "control", colored = "one_group".
+    Backtrace:
+         █
+      1. └─isomiRs::isoNetwork(...)
+      2.   └─isomiRs:::.viz_mirna_gene_enrichment(...)
+      3.     └─isomiRs:::.cluster_exp(...)
+      4.       └─DEGreport::degPatterns(ma, meta, time = "xaxis", minc = 0, plot = FALSE)
+      5.         └─`%>%`(...)
+      6.           ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
+      7.           └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
+      8.             └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
+      9.               └─DEGreport:::`_fseq`(`_lhs`)
+     10.                 └─magrittr::freduce(value, `_function_list`)
+     11.                   └─function_list[[i]](value)
+     12.                     ├─dplyr::summarise(., abundance = median(value), n_genes = n())
+     13.
+    Execution halted
+    ```
+
+*   checking tests ...
+    ```
+     ERROR
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+      ℹ The error occured in group 1: merge = "one_groupcontrol_1", cluster = 1, xaxis = "control_1", colored = "one_group".
+      Backtrace:
+        1. testthat::expect_equal(unique(.cluster_exp(gene)), c(1, 2))
+        5. isomiRs:::.cluster_exp(gene)
+        6. DEGreport::degPatterns(ma, meta, time = "xaxis", minc = 0, plot = FALSE)
+        4. dplyr::group_by(...)
+       11. dplyr::summarise(., abundance = median(value), n_genes = n())
+       16. dplyr:::summarise_cols(.data, ...)
+
+      ══ testthat results  ═══════════════════════════════════════════════════════════
+      [ OK: 27 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
+      1. Error: matrix (@test_calculus.R#23)
+
+      Error: testthat unit tests failed
+      Execution halted
+    ```
+
+*   checking package dependencies ... NOTE
+    ```
+    Package suggested but not available for checking: ‘targetscan.Hs.eg.db’
+    ```
+
+*   checking for hidden files and directories ... NOTE
+    ```
+    Found the following hidden files and directories:
+      .travis.yml
+    These were most likely included in error. See section ‘Package
+    structure’ in the ‘Writing R Extensions’ manual.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    ...
+      ‘targetscan.Hs.egMIRNA’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Hs.egMIRBASE2FAMILY’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Hs.egTARGETS’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Hs.egTARGETSFULL’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Mm.egMIRNA’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Mm.egMIRBASE2FAMILY’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Mm.egTARGETS’
+    mirna2targetscan: no visible binding for global variable
+      ‘targetscan.Mm.egTARGETSFULL’
+    Undefined global functions or variables:
+      as.tibble changes hits iso_sample pct targetscan.Hs.egMIRBASE2FAMILY
+      targetscan.Hs.egMIRNA targetscan.Hs.egTARGETS
+      targetscan.Hs.egTARGETSFULL targetscan.Mm.egMIRBASE2FAMILY
+      targetscan.Mm.egMIRNA targetscan.Mm.egTARGETS
+      targetscan.Mm.egTARGETSFULL total
+    ```
+
+# jmv
+
+<details>
+
+* Version: 1.2.5
+* Source code: https://github.com/cran/jmv
+* Date/Publication: 2020-02-17 16:40:14 UTC
+* Number of recursive dependencies: 193
+
+Run `revdep_details(,"jmv")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
+      ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
+      ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
+      All declared Imports should be used.
+    ```
+
+# jsmodule
+
+<details>
+
+* Version: 1.0.7
+* Source code: https://github.com/cran/jsmodule
+* URL: https://github.com/jinseob2kim/jsmodule
+* BugReports: https://github.com/jinseob2kim/jsmodule/issues
+* Date/Publication: 2020-04-29 17:20:09 UTC
+* Number of recursive dependencies: 188
+
+Run `revdep_details(,"jsmodule")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘Cairo’ ‘survC1’
+      All declared Imports should be used.
+    ```
+
+# LANDD
+
+<details>
+
+* Version: 1.1.0
+* Source code: https://github.com/cran/LANDD
+* Date/Publication: 2016-10-01 01:14:24
+* Number of recursive dependencies: 103
+
+Run `revdep_details(,"LANDD")` for more info
+
+</details>
+
+## In both
+
+*   checking R code for possible problems ... NOTE
+    ```
+    getGO: no visible global function definition for ‘new’
+    getGO: no visible global function definition for ‘getGeneric’
+    graph.kd: no visible global function definition for ‘as’
+    Undefined global functions or variables:
+      as getGeneric new
+    Consider adding
+      importFrom("methods", "as", "getGeneric", "new")
+    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
+    contains 'methods').
+    ```
+
+# MAINT.Data
+
+<details>
+
+* Version: 2.3.1
+* Source code: https://github.com/cran/MAINT.Data
+* Date/Publication: 2020-01-07 11:10:03 UTC
+* Number of recursive dependencies: 66
+
+Run `revdep_details(,"MAINT.Data")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  6.1Mb
+      sub-directories of 1Mb or more:
+        R      2.0Mb
+        libs   3.7Mb
+    ```
+
+# MAST
+
+<details>
+
+* Version: 1.14.0
+* Source code: https://github.com/cran/MAST
+* URL: https://github.com/RGLab/MAST/
+* BugReports: https://github.com/RGLab/MAST/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 194
+
+Run `revdep_details(,"MAST")` for more info
+
+</details>
+
+## In both
+
+*   checking for hidden files and directories ... NOTE
+    ```
+    Found the following hidden files and directories:
+      .travis.yml
+    These were most likely included in error. See section ‘Package
+    structure’ in the ‘Writing R Extensions’ manual.
+    ```
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is 10.5Mb
+      sub-directories of 1Mb or more:
+        data   4.1Mb
+        doc    5.2Mb
+    ```
+
+# MCbiclust
+
+<details>
+
+* Version: 1.12.0
+* Source code: https://github.com/cran/MCbiclust
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 177
+
+Run `revdep_details(,"MCbiclust")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  9.6Mb
+      sub-directories of 1Mb or more:
+        data   3.1Mb
+        doc    5.5Mb
+    ```
+
+# mgcViz
+
+<details>
+
+* Version: 0.1.6
+* Source code: https://github.com/cran/mgcViz
+* URL: https://github.com/mfasiolo/mgcViz
+* BugReports: https://github.com/mfasiolo/mgcViz/issues
+* Date/Publication: 2020-03-04 15:10:02 UTC
+* Number of recursive dependencies: 95
+
+Run `revdep_details(,"mgcViz")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.1Mb
+      sub-directories of 1Mb or more:
+        doc   4.4Mb
+    ```
+
+# MissingDataGUI
+
+<details>
+
+* Version: 0.2-5
+* Source code: https://github.com/cran/MissingDataGUI
+* Date/Publication: 2016-04-25 08:58:53
+* Number of recursive dependencies: 102
+
+Run `revdep_details(,"MissingDataGUI")` for more info
+
+</details>
+
+## In both
+
+*   checking S3 generic/method consistency ... WARNING
+    ```
+
+    (R:15348): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    See section ‘Generic functions and methods’ in the ‘Writing R
+    Extensions’ manual.
+    ```
+
+*   checking replacement functions ... WARNING
+    ```
+
+    (R:15410): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    The argument of a replacement function which corresponds to the right
+    hand side must be named ‘value’.
+    ```
+
+*   checking for missing documentation entries ... WARNING
+    ```
+
+    (R:15967): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    All user-level objects in a package should have documentation entries.
+    See chapter ‘Writing R documentation files’ in the ‘Writing R
+    Extensions’ manual.
+    ```
+
+*   checking for code/documentation mismatches ... WARNING
+    ```
+
+    (R:16060): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+
+    (R:16138): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+
+    (R:16267): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+
+    (R:15208): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    ```
+
+*   checking foreign function calls ... NOTE
+    ```
+
+    (R:15441): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
+    Extensions’ manual.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+
+    (R:15653): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    ```
+
+*   checking Rd \usage sections ... NOTE
+    ```
+
+    (R:16367): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    The \usage entries for S3 methods should use the \method markup and not
+    their full name.
+    See chapter ‘Writing R documentation files’ in the ‘Writing R
+    Extensions’ manual.
+    ```
+
+# mlrMBO
+
+<details>
+
+* Version: 1.1.4
+* Source code: https://github.com/cran/mlrMBO
+* URL: https://github.com/mlr-org/mlrMBO
+* BugReports: https://github.com/mlr-org/mlrMBO/issues
+* Date/Publication: 2020-02-28 21:20:03 UTC
+* Number of recursive dependencies: 131
+
+Run `revdep_details(,"mlrMBO")` for more info
+
+</details>
+
+## In both
+
+*   checking package dependencies ... NOTE
+    ```
+    Package suggested but not available for checking: ‘DiceOptim’
+    ```
+
+# MOFA
+
+<details>
+
+* Version: 1.4.0
+* Source code: https://github.com/cran/MOFA
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 97
+
+Run `revdep_details(,"MOFA")` for more info
+
+</details>
+
+## In both
+
+*   checking examples ... ERROR
+    ```
+    Running examples in ‘MOFA-Ex.R’ failed
+    The error most likely occurred in:
+
+    > ### Name: DataOptions
+    > ### Title: DataOptions: set and retrieve data options
+    > ### Aliases: DataOptions DataOptions<- DataOptions,MOFAmodel-method
+    > ###   DataOptions<-,MOFAmodel,list-method
+    >
+    > ### ** Examples
+    >
+    > # load a trained MOFAmodel object
+    > filepath <- system.file("extdata", "scMT_model.hdf5", package = "MOFAdata")
+    > MOFAobject <- loadModel(filepath)
+    Error in h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
+      Error in h5checktypeOrOpenLoc(). Cannot open file. File '' does not exist.
+    Calls: loadModel -> h5read -> h5checktypeOrOpenLoc
+    Execution halted
+    ```
+
+*   checking package dependencies ... NOTE
+    ```
+    Package suggested but not available for checking: ‘MOFAdata’
+    ```
+
+*   checking for hidden files and directories ... NOTE
+    ```
+    Found the following hidden files and directories:
+      .BBSoptions
+    These were most likely included in error. See section ‘Package
+    structure’ in the ‘Writing R Extensions’ manual.
+    ```
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.3Mb
+      sub-directories of 1Mb or more:
+        doc   4.6Mb
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    plotEnrichmentDetailed: no visible binding for global variable
+      ‘pathway’
+    plotEnrichmentDetailed: no visible binding for global variable
+      ‘feature.statistic’
+    Undefined global functions or variables:
+      feature.statistic pathway
+    ```
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Package unavailable to check Rd xrefs: ‘PCGSE’
+    ```
+
+# NetworkChange
+
+<details>
+
+* Version: 0.6
+* Source code: https://github.com/cran/NetworkChange
+* Date/Publication: 2020-02-06 05:20:02 UTC
+* Number of recursive dependencies: 135
+
+Run `revdep_details(,"NetworkChange")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘sna’
+      All declared Imports should be used.
+    ```
+
+# nzelect
+
+<details>
+
+* Version: 0.4.0
+* Source code: https://github.com/cran/nzelect
+* Date/Publication: 2017-10-02 20:35:23 UTC
+* Number of recursive dependencies: 73
+
+Run `revdep_details(,"nzelect")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.3Mb
+      sub-directories of 1Mb or more:
+        data   5.0Mb
+    ```
+
+*   checking data for non-ASCII characters ... NOTE
+    ```
+      Note: found 6409 marked UTF-8 strings
+    ```
+
+# ORFik
+
+<details>
+
+* Version: 1.8.1
+* Source code: https://github.com/cran/ORFik
+* URL: https://github.com/Roleren/ORFik
+* BugReports: https://github.com/Roleren/ORFik/issues
+* Date/Publication: 2020-04-29
+* Number of recursive dependencies: 128
+
+Run `revdep_details(,"ORFik")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Unexported objects imported by ':::' calls:
+      ‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’
+      ‘IRanges:::regroupBySupergroup’
+      See the note in ?`:::` about the use of this operator.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    ...
+    windowCoveragePlot: no visible binding for global variable
+      ‘fraction_min’
+    windowCoveragePlot: no visible binding for global variable ‘position’
+    Undefined global functions or variables:
+      . CDS CDSGrouping Hx LEADERS ORFGrouping ORFScores RRS RSS
+      StartCodons StopCodons TOP View chr codonSums count countRFP
+      count_seq_pos_with_count dif difPer disengagementScores distORFCDS
+      entropyRFP exon_rank feature forward fpkmRFP fpkmRNA fraction
+      fraction.x fraction.y fractionLengths fraction_min fractions frame
+      frame_one_RP frame_two_RP gene_sum grnames inFrameCDS ioScore
+      isOverlappingCds kozak leaders mRNA median_score offsets_start ones
+      position rankInTx ranks ratio_cds_leader ratio_cds_mrna
+      ratio_mrna_aligned read.csv2 read.table rowSums2 scalingFactor seq1
+      seq2 seq3 seq4 seq5 size startCodonCoverage startRegionRelative te
+      trailers tx utr3_len utr5_len value variable widths windowMean
+      windowSD write.csv write.table zscore
+    Consider adding
+      importFrom("graphics", "frame")
+      importFrom("utils", "View", "read.csv2", "read.table", "write.csv",
+                 "write.table")
+    to your NAMESPACE file.
+    ```
+
+# PAFway
+
+<details>
+
+* Version: 0.1.3
+* Source code: https://github.com/cran/PAFway
+* Date/Publication: 2020-02-05 16:40:02 UTC
+* Number of recursive dependencies: 75
+
+Run `revdep_details(,"PAFway")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘network’ ‘scales’ ‘sna’
+      All declared Imports should be used.
+    ```
+
+# plotly
+
+<details>
+
+* Version: 4.9.2.1
+* Source code: https://github.com/cran/plotly
+* URL: https://plotly-r.com, https://github.com/ropensci/plotly#readme, https://plot.ly/r
+* BugReports: https://github.com/ropensci/plotly/issues
+* Date/Publication: 2020-04-04 19:50:02 UTC
+* Number of recursive dependencies: 150
+
+Run `revdep_details(,"plotly")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  6.6Mb
+      sub-directories of 1Mb or more:
+        htmlwidgets   3.7Mb
+    ```
+
+# PopGenReport
+
+<details>
+
+* Version: 3.0.4
+* Source code: https://github.com/cran/PopGenReport
+* URL: https://github.com/green-striped-gecko/PopGenReport
+* Date/Publication: 2019-02-04 12:13:23 UTC
+* Number of recursive dependencies: 119
+
+Run `revdep_details(,"PopGenReport")` for more info
+
+</details>
+
+## In both
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Package unavailable to check Rd xrefs: ‘ecodist’
+    ```
+
+# pubh
+
+<details>
+
+* Version: 1.1.14
+* Source code: https://github.com/cran/pubh
+* URL: https://github.com/josie-athens/pubh
+* BugReports: https://github.com/josie-athens/pubh/issues
+* Date/Publication: 2020-06-02 06:50:02 UTC
+* Number of recursive dependencies: 203
+
+Run `revdep_details(,"pubh")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘Hmisc’
+      All declared Imports should be used.
+    ```
+
+# robCompositions
+
+<details>
+
+* Version: 2.2.1
+* Source code: https://github.com/cran/robCompositions
+* Date/Publication: 2020-02-11 17:20:02 UTC
+* Number of recursive dependencies: 123
+
+Run `revdep_details(,"robCompositions")` for more info
+
+</details>
+
+## In both
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Packages unavailable to check Rd xrefs: ‘mvoutlier’, ‘StatDA’
+    ```
+
+# robustbase
+
+<details>
+
+* Version: 0.93-6
+* Source code: https://github.com/cran/robustbase
+* URL: http://robustbase.r-forge.r-project.org/
+* Date/Publication: 2020-03-23 17:40:02 UTC
+* Number of recursive dependencies: 72
+
+Run `revdep_details(,"robustbase")` for more info
+
+</details>
+
+## In both
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Package unavailable to check Rd xrefs: ‘robustX’
+    ```
+
+# robustSingleCell
+
+<details>
+
+* Version: 0.1.1
+* Source code: https://github.com/cran/robustSingleCell
+* URL: https://github.com/asmagen/robustSingleCell
+* BugReports: https://github.com/asmagen/robustSingleCell/issues
+* Date/Publication: 2019-04-23 22:00:02 UTC
+* Number of recursive dependencies: 149
+
+Run `revdep_details(,"robustSingleCell")` for more info
+
+</details>
+
+## Newly broken
+
+*   checking whether package ‘robustSingleCell’ can be installed ... WARNING
+    ```
+    Found the following significant warnings:
+      Warning: replacing previous import ‘GGally::mean_sd’ by ‘ggpubr::mean_sd’ when loading ‘robustSingleCell’
+      Warning: replacing previous import ‘GGally::median_iqr’ by ‘ggpubr::median_iqr’ when loading ‘robustSingleCell’
+    ```
+
+# rrr
+
+<details>
+
+* Version: 1.0.0
+* Source code: https://github.com/cran/rrr
+* URL: http://github.com/chrisaddy/rrr
+* Date/Publication: 2016-12-09 15:15:55
+* Number of recursive dependencies: 85
+
+Run `revdep_details(,"rrr")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘Rcpp’
+      All declared Imports should be used.
+    ```
+
+# scPipe
+
+<details>
+
+* Version: 1.10.0
+* Source code: https://github.com/cran/scPipe
+* URL: https://github.com/LuyiTian/scPipe
+* BugReports: https://github.com/LuyiTian/scPipe
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 137
+
+Run `revdep_details(,"scPipe")` for more info
+
+</details>
+
+## In both
+
+*   checking for hidden files and directories ... NOTE
+    ```
+    Found the following hidden files and directories:
+      .BBSoptions
+    These were most likely included in error. See section ‘Package
+    structure’ in the ‘Writing R Extensions’ manual.
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘scater’
+      All declared Imports should be used.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    anno_to_saf: no visible binding for global variable ‘GeneID’
+    convert_geneid: no visible global function definition for ‘useMart’
+    get_genes_by_GO: no visible global function definition for ‘useMart’
+    infer_gene_id_from_parent: no visible binding for global variable
+      ‘type’
+    plot_demultiplex: no visible binding for global variable ‘status’
+    plot_demultiplex: no visible binding for global variable ‘count’
+    plot_demultiplex: no visible binding for global variable ‘label_y’
+    plot_demultiplex: no visible binding for global variable ‘label_tx’
+    Undefined global functions or variables:
+      GeneID count label_tx label_y status type useMart
+    ```
+
+*   checking for GNU extensions in Makefiles ... NOTE
+    ```
+    GNU make is a SystemRequirements.
+    ```
+
+# SeqSQC
+
+<details>
+
+* Version: 1.10.0
+* Source code: https://github.com/cran/SeqSQC
+* URL: https://github.com/Liubuntu/SeqSQC
+* BugReports: https://github.com/Liubuntu/SeqSQC/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 125
+
+Run `revdep_details(,"SeqSQC")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.7Mb
+      sub-directories of 1Mb or more:
+        doc       1.9Mb
+        extdata   3.3Mb
+    ```
+
+# SmartEDA
+
+<details>
+
+* Version: 0.3.5
+* Source code: https://github.com/cran/SmartEDA
+* URL: https://daya6489.github.io/SmartEDA/
+* BugReports: https://github.com/daya6489/SmartEDA/issues
+* Date/Publication: 2020-04-25 06:20:02 UTC
+* Number of recursive dependencies: 112
+
+Run `revdep_details(,"SmartEDA")` for more info
+
+</details>
+
+## In both
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Packages unavailable to check Rd xrefs: ‘InformationValue’, ‘DataExplorer’
+    ```
+
+# spinifex
+
+<details>
+
+* Version: 0.1.0
+* Source code: https://github.com/cran/spinifex
+* URL: https://github.com/nspyrison/spinifex/
+* BugReports: https://github.com/nspyrison/spinifex/issues
+* Date/Publication: 2019-04-09 12:00:04 UTC
+* Number of recursive dependencies: 89
+
+Run `revdep_details(,"spinifex")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘GGally’ ‘tibble’ ‘webshot’
+      All declared Imports should be used.
+    ```
+
+# spup
+
+<details>
+
+* Version: 1.3-2
+* Source code: https://github.com/cran/spup
+* Date/Publication: 2020-04-30 22:20:06 UTC
+* Number of recursive dependencies: 78
+
+Run `revdep_details(,"spup")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘sp’
+      All declared Imports should be used.
+    ```
+
+# statVisual
+
+<details>
+
+* Version: 1.2.1
+* Source code: https://github.com/cran/statVisual
+* Date/Publication: 2020-02-20 19:30:02 UTC
+* Number of recursive dependencies: 161
+
+Run `revdep_details(,"statVisual")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘gbm’ ‘ggfortify’ ‘tibble’ ‘tidyverse’
+      All declared Imports should be used.
+    ```
+
+# tidybulk
+
+<details>
+
+* Version: 1.0.0
+* Source code: https://github.com/cran/tidybulk
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 245
+
+Run `revdep_details(,"tidybulk")` for more info
+
+</details>
+
+## In both
+
+*   checking examples ... ERROR
+    ```
+    ...
+    ℹ Input `n` is `n()`.
+    ℹ The error occured in group 1: vs = 0, am = 0.
+    Backtrace:
+         █
+      1. └─by_vs_am %>% summarise(n = n())
+      2.   ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
+      3.   └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
+      4.     └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
+      5.       └─`_fseq`(`_lhs`)
+      6.         └─magrittr::freduce(value, `_function_list`)
+      7.           ├─base::withVisible(function_list[[k]](value))
+      8.           └─function_list[[k]](value)
+      9.             ├─tidybulk::summarise(., n = n())
+     10.             └─tidybulk:::summarise.default(., n = n())
+     11.               ├─dplyr::summarise(.data, ...)
+     12.               └─dplyr:::summarise.grouped_df(.data, ...)
+     13.                 └─dplyr:::summarise_cols(.data, ...)
+    <parent: error/simpleError>
+    Backtrace:
+    █
+    Execution halted
+    ```
+
+*   checking tests ...
+    ```
+     ERROR
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 13 lines of output:
+        `Fraction of variance`    PC
+                         <dbl> <int>
+      1                0.990       1
+      2                0.00310     2
+      Getting the 100 most variable genes
+      Getting the 5 most variable genes
+      Getting the 5 most variable genes
+      ══ testthat results  ═══════════════════════════════════════════════════════════
+      [ OK: 139 | SKIPPED: 0 | WARNINGS: 18 | FAILED: 3 ]
+      1. Error: Only scaled counts - no object (@test-bulk_methods.R#65)
+      2. Error: tidybulk SummarizedExperiment normalisation manual (@test-bulk_methods_SummarizedExperiment.R#29)
+      3. Error: tidybulk SummarizedExperiment normalisation (@test-bulk_methods_SummarizedExperiment.R#50)
+
+      Error: testthat unit tests failed
+      Execution halted
+    ```
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  8.4Mb
+      sub-directories of 1Mb or more:
+        data   7.1Mb
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Missing object imported by a ':::' call: ‘dplyr:::flatten_bindable’
+    package 'methods' is used but not declared
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    ...
+    tidybulk,RangedSummarizedExperiment: no visible binding for global
+      variable ‘.’
+    tidybulk,RangedSummarizedExperiment: no visible binding for global
+      variable ‘feature’
+    tidybulk,SummarizedExperiment: no visible binding for global variable
+      ‘.’
+    tidybulk,SummarizedExperiment: no visible binding for global variable
+      ‘feature’
+    Undefined global functions or variables:
+      (Intercept) . .a .abundance_scaled GeneID Status X_cibersort Y assay
+      buildIdx cluster cluster kmeans cmdscale.out correlation counts
+      data_base egsea egsea.base ensembl_id entrez
+      error_if_parameters_not_match feature genes item1 lowly_abundant m
+      med med.rank multiplier my_n n_aggr name pathway rc read count
+      ref_genome rotated dimensions rotation sample 1 sample 2 sample a
+      sample b sample_idx samples sdev seurat_clusters temp tot tot_filt
+      transcript tt_columns value variable x
+    Consider adding
+      importFrom("base", "sample")
+      importFrom("stats", "kmeans")
+    to your NAMESPACE file.
+    ```
+
+# TVTB
+
+<details>
+
+* Version: 1.14.0
+* Source code: https://github.com/cran/TVTB
+* URL: https://github.com/kevinrue/TVTB
+* BugReports: https://github.com/kevinrue/TVTB/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 158
+
+Run `revdep_details(,"TVTB")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.6Mb
+      sub-directories of 1Mb or more:
+        R     2.0Mb
+        doc   2.7Mb
+    ```
+
+# ubiquity
+
+<details>
+
+* Version: 1.0.1
+* Source code: https://github.com/cran/ubiquity
+* URL: https://r.ubiquity.tools/
+* BugReports: https://github.com/john-harrold/ubiquity/issues
+* Date/Publication: 2020-01-21 07:50:02 UTC
+* Number of recursive dependencies: 104
+
+Run `revdep_details(,"ubiquity")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  9.3Mb
+      sub-directories of 1Mb or more:
+        doc     6.4Mb
+        ubinc   2.0Mb
+    ```
+
+# ufs
+
+<details>
+
+* Version: 0.3.1
+* Source code: https://github.com/cran/ufs
+* URL: https://r-packages.gitlab.io/ufs
+* BugReports: https://gitlab.com/r-packages/ufs/issues
+* Date/Publication: 2019-08-22 17:30:02 UTC
+* Number of recursive dependencies: 116
+
+Run `revdep_details(,"ufs")` for more info
+
+</details>
+
+## In both
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘viridis’
+      All declared Imports should be used.
+    ```
+
+*   checking Rd cross-references ... NOTE
+    ```
+    Packages unavailable to check Rd xrefs: ‘userfriendlyscience’, ‘behaviorchange’
+    ```
+
+# vidger
+
+<details>
+
+* Version: 1.8.0
+* Source code: https://github.com/cran/vidger
+* URL: https://github.com/btmonier/vidger, https://bioconductor.org/packages/release/bioc/html/vidger.html
+* BugReports: https://github.com/btmonier/vidger/issues
+* Date/Publication: 2020-04-27
+* Number of recursive dependencies: 113
+
+Run `revdep_details(,"vidger")` for more info
+
+</details>
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is 11.2Mb
+      sub-directories of 1Mb or more:
+        data   4.7Mb
+        doc    6.1Mb
+    ```
diff --git a/revdep/revdep_cran.md b/revdep/revdep_cran.md
new file mode 100644
index 000000000..cca947750
--- /dev/null
+++ b/revdep/revdep_cran.md
@@ -0,0 +1,14 @@
+## revdepcheck results
+
+We checked 98 reverse dependencies (77 from CRAN + 21 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 1 new problems
+ * We failed to check 0 packages
+
+Issues with CRAN packages are summarised below.
+
+### New problems
+(This reports the first line of each new failure)
+
+* robustSingleCell
+  checking whether package ‘robustSingleCell’ can be installed ... WARNING

From fb5adfa5b7d601de51a58c0086e147b7e5ae022e Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 4 Jun 2020 01:15:43 -0400
Subject: [PATCH 08/22] Update cran-comments.md

---
 cran-comments.md | 82 +++++++++++++++++++++++++++++++-----------------
 1 file changed, 53 insertions(+), 29 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index ab4895588..0724be103 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,9 +1,11 @@
 
 ## Comments
 
-### 2020-3-19
+### 2020-6-3
 
-I've fixed the tests and the package now works with the latest (and prior) ggplot2 versions.
+I have removed `packagedocs` as a dependency.  This fixes the errors on CRAN check.
+
+With the removal of `packagedocs` and switching to true vignettes, the package size has grown a bit due to the nature of having vignettes containing **many** `ggplot2` images.
 
 Please let me know if there is anything else I can do.
 
@@ -11,55 +13,77 @@ Best,
 Barret
 
 
-### 2020-3-6
+### 2020-5-20
 
-Dear maintainer,
+Package `lazyrmd` is orphaned.
 
-Please see the problems shown on
-<https://cran.r-project.org/web/checks/check_results_GGally.html>.
+Package `packagedocs` requires it, which is not allowed under the CRAN policy.
 
-Please correct before 2020-03-20 to safely retain your package on CRAN.
+Packages `GGally` and `geofacet` suggest `packagedocs` but do not use it
+conditionally.
 
-Best,
--k
+We need one of
+
+a) `lazyrmd` to be maintained (as we have asked before) or
+b) `packagedocs` to work without lazyrmd or
+c) `lazyrmd` and `packagedocs` to be archived and `geofacet`/`GGally` use a
+different vignette builder.
+
+Please resolve one way or the other before Jun 3.
 
+--
+Brian D. Ripley
 
-#### Test environments and R CMD check results
 
-* local macOS install 10.15.3
-  * R 3.6.3
-* travis-ci ubuntu
-  * oldrelease, R version 3.5.3 (2017-01-27)
-  * release, R version 3.6.2 (2017-01-27)
-  * devel, R Under development (unstable) (2020-03-13 r77948)
 
-* rhub
-  * Windows Server 2008 R2 SP1, R-devel, 32/64 bit
-  * Ubuntu Linux 16.04 LTS, R-release, GCC
-  * Fedora Linux, R-devel, clang, gfortran
+## Test environments and R CMD check results
+
+* local macOS install 10.15.5
+  * R 4.0
+* GitHub Actions - https://github.com/ggobi/ggally/pull/364/checks
+  * macOS, windows - R devel
+  * macOS, windows, ubuntu 16 - R 4.0
+  * macOS, windows, ubuntu 16 - R 3.6
 
 * win-builder
   * oldrelease
   * release
   * devel
 
+#### R CMD check results
 
+win-builder
+* 0 errors | 0 warnings | 0 notes
 
-#### R CMD check results
 
-rhub - Fedora R-devel
-* 0 errors | 0 warnings | 1 note
-* checking package dependencies ... NOTE
-  Package suggested but not available for checking: ‘scagnostics’
+Local & GitHub Actions
+* 0 errors | 0 warnings | 1 notes
 
-Everything else
-* 0 errors | 0 warnings | 0 notes
+N  checking installed package size ...
+     installed size is  7.8Mb
+     sub-directories of 1Mb or more:
+       doc   6.1Mb
 
 
 
 ## revdepcheck results
 
-We checked 89 reverse dependencies (72 from CRAN + 17 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
+Link: https://github.com/ggobi/ggally/commit/8a6b8ffbf6f7187dc9503ac51c3f5f48b3f72a1c
+
+We checked 98 reverse dependencies (77 from CRAN + 21 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 0 new problems
+ * We saw 1 new problems
  * We failed to check 0 packages
+
+#### New revdepcheck problems
+
+One package had an extra warning produced due to a import clash. A PR was made here: https://github.com/asmagen/robustSingleCell/pull/34
+This is not a breaking change, so I did not deem it necessary to wait two weeks before submitting to CRAN (delaying a CRAN deadline).
+
+* robustSingleCell
+  * checking whether package ‘robustSingleCell’ can be installed ... WARNING
+    ```
+    Found the following significant warnings:
+      Warning: replacing previous import ‘GGally::mean_sd’ by ‘ggpubr::mean_sd’ when loading ‘robustSingleCell’
+      Warning: replacing previous import ‘GGally::median_iqr’ by ‘ggpubr::median_iqr’ when loading ‘robustSingleCell’
+    ```

From 3b451bc0d898d61656bab73b3dd06d9cc16f77d6 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 4 Jun 2020 01:25:21 -0400
Subject: [PATCH 09/22] only spell check on CI. Safeguard testthat

---
 tests/spelling.R | 12 +++++++++---
 tests/testthat.R |  9 ++++++---
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/tests/spelling.R b/tests/spelling.R
index 6713838fc..2651c5a29 100644
--- a/tests/spelling.R
+++ b/tests/spelling.R
@@ -1,3 +1,9 @@
-if(requireNamespace('spelling', quietly = TRUE))
-  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
-                             skip_on_cran = TRUE)
+# `devtools::spell_check()`
+
+# only check spelling if on CI and spelling is available
+if (requireNamespace('spelling', quietly = TRUE)) {
+  if (isTRUE(as.logical(Sys.getenv("CI"))) {
+    spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
+  }
+}
diff --git a/tests/testthat.R b/tests/testthat.R
index 525fa2e7e..5a8a1f937 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,4 +1,7 @@
-library(testthat)
-library(GGally)
 
-test_check("GGally")
+if (requireNamespace('testthat', quietly = TRUE)) {
+  library(testthat)
+  library(GGally)
+
+  test_check("GGally")
+}

From 415e109e64cea0c031e7806c082b53303bbc06f4 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 4 Jun 2020 01:39:46 -0400
Subject: [PATCH 10/22] fix typo

---
 tests/spelling.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/spelling.R b/tests/spelling.R
index 2651c5a29..56642bb41 100644
--- a/tests/spelling.R
+++ b/tests/spelling.R
@@ -2,7 +2,7 @@
 
 # only check spelling if on CI and spelling is available
 if (requireNamespace('spelling', quietly = TRUE)) {
-  if (isTRUE(as.logical(Sys.getenv("CI"))) {
+  if (isTRUE(as.logical(Sys.getenv("CI")))) {
     spelling::spell_check_test(vignettes = TRUE, error = FALSE,
                               skip_on_cran = TRUE)
   }

From b0de56d4da01f09198025a6d7426c3ce1ec0ce22 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <barret@rstudio.com>
Date: Thu, 4 Jun 2020 22:49:35 -0400
Subject: [PATCH 11/22] Remove Vignettes from CRAN pkg (#367)

---
 .Rbuildignore                        |  2 +
 .github/workflows/R-CMD-check.yaml   |  3 +-
 .github/workflows/pkgdown.yaml       |  1 +
 .github/workflows/test-coverage.yaml |  1 +
 CRAN-RELEASE                         |  2 +
 DESCRIPTION                          |  1 -
 NAMESPACE                            |  1 +
 NEWS.md                              | 14 +++---
 R/ggpairs_internal_plots.R           |  2 +-
 R/vig_ggally.R                       | 50 +++++++++++++++++++++
 _pkgdown.yml                         | 66 +++++++++++++++++++++++-----
 man/vig_ggally.Rd                    | 24 ++++++++++
 tests/testthat/test-vig_ggally.R     | 12 +++++
 vignettes/ggally_plots.Rmd           |  4 +-
 vignettes/ggally_stats.Rmd           |  4 +-
 vignettes/ggbivariate.Rmd            |  2 +-
 vignettes/ggduo.Rmd                  |  2 +-
 vignettes/ggnostic.Rmd               |  4 +-
 vignettes/ggpairs.Rmd                |  2 +-
 19 files changed, 166 insertions(+), 31 deletions(-)
 create mode 100644 CRAN-RELEASE
 create mode 100644 R/vig_ggally.R
 create mode 100644 man/vig_ggally.Rd
 create mode 100644 tests/testthat/test-vig_ggally.R

diff --git a/.Rbuildignore b/.Rbuildignore
index 45a6db7ed..78b9c2c07 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -31,3 +31,5 @@ ggduo_paper.txt
 ^\.github$
 ^doc$
 ^Meta$
+^CRAN-RELEASE$
+^vignettes$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 460e11643..eca13d31e 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -5,6 +5,7 @@ on:
   pull_request:
     branches:
       - master
+      - rc-*
 
 name: R-CMD-check
 
@@ -96,7 +97,7 @@ jobs:
       - name: Check as CRAN
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "note", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 3be80c21c..de3620e74 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -6,6 +6,7 @@ on:
   pull_request:
     branches:
       - master
+      - rc-*
 
 
 name: pkgdown
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index fd5515c8d..03e9c34b4 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -5,6 +5,7 @@ on:
   pull_request:
     branches:
       - master
+      - rc-*
 
 name: test-coverage
 
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
new file mode 100644
index 000000000..8fe858a41
--- /dev/null
+++ b/CRAN-RELEASE
@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2020-06-04.
+Once it is accepted, delete this file and tag the release (commit 415e109e64).
diff --git a/DESCRIPTION b/DESCRIPTION
index 7ded34e83..1732b63be 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -64,7 +64,6 @@ Suggests:
     spelling
 Roxygen: list(markdown = FALSE)
 RoxygenNote: 7.1.0
-VignetteBuilder: knitr
 SystemRequirements: openssl
 Encoding: UTF-8
 Language: en-US
diff --git a/NAMESPACE b/NAMESPACE
index c3fc1f922..3045e4380 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -118,6 +118,7 @@ export(stat_prop)
 export(stat_weighted_mean)
 export(uppertriangle)
 export(v1_ggmatrix_theme)
+export(vig_ggally)
 export(wrap)
 export(wrap_fn_with_param_arg)
 export(wrap_fn_with_params)
diff --git a/NEWS.md b/NEWS.md
index e863d536d..b2ede00d4 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,22 +1,22 @@
 # GGally 2.0.0
 
 ### New Vignettes
-* `vignette("ggally_plots", package = "GGally")` - List of available high-level plots
-* `vignette("ggally_stats", package = "GGally")` - Additional statistics for ggplot2
-* `vignette("ggbivariate", package = "GGally")` - ggbivariate(): Plot an outcome with several potential explanatory variables
-* `vignette("ggtable", package = "GGally")` - ggtable(): Cross-tabulated tables
-* Call `browseVignettes(package = "GGally")` to view all vignettes for `GGally`
+* `vig_ggally("ggally_plots")` - ggally_*(): List of available high-level plots
+* `vig_ggally("ggally_stats")` - stat_*(): Additional statistics for ggplot2
+* `vig_ggally("ggbivariate")` - ggbivariate(): Plot an outcome with several potential explanatory variables
+* `vig_ggally("ggtable")` - ggtable(): Cross-tabulated tables
+* To view all vignettes for `GGally`, call `GGally::vig_ggally()`
 
 
 ### New functions
 
 `ggbivariate()` (@larmarange, #324)
 * Display an outcome using several potential explanatory variables
-* `vignette("ggbivariate")`
+* `vig_ggally("ggbivariate")`
 
 `ggtable()` (@larmarange, #351)
 * Cross-tabulated tables of discrete variables
-* `vignette("ggtable")`
+* `vig_ggally("ggtable")`
 
 `add_to_ggmatrix()` (#362)
 * Add ggplot2 objects to `ggmatrix` objects at selected locations
diff --git a/R/ggpairs_internal_plots.R b/R/ggpairs_internal_plots.R
index d7d2e4c85..7a7dfdd57 100644
--- a/R/ggpairs_internal_plots.R
+++ b/R/ggpairs_internal_plots.R
@@ -108,7 +108,7 @@ wrap_fn_with_param_arg <- function(
         stop(str_c(
           "Error retrieving `GGally` function.\n",
           "Please provide a string such as `'points'` for `ggally_points()`\n",
-          "For a list of all predefined functions, check out `vignette(\"ggally_plots\", package = \"GGally\")`\n",
+          "For a list of all predefined functions, check out `vig_ggally(\"ggally_plots\")`\n",
           "A custom function may be supplied directly: `wrap(my_fn, param = val)`\n",
           "Function provided: ", funcVal
         ))
diff --git a/R/vig_ggally.R b/R/vig_ggally.R
new file mode 100644
index 000000000..d05df9715
--- /dev/null
+++ b/R/vig_ggally.R
@@ -0,0 +1,50 @@
+#' View \pkg{GGally} vignettes
+#'
+#' This function will open the directly to the vignette requested. If no \code{name} is provided, the index of all \pkg{GGally} vignettes will be opened.
+#'
+#' This method allows for vignettes to be hosted remotely, reducing \pkg{GGally}'s package size, and installation time.
+#'
+#' @param name Vignette name to open. If no name is provided, the vignette index will be opened
+#' @export
+#' @examples
+#' # View `ggnostic` vignette
+#' vig_ggally("ggnostic")
+#'
+#' # View all vignettes by GGally
+#' vig_ggally()
+vig_ggally <- function(name) {
+
+  vig_url <-
+    if (missing(name) || is.null(name)) {
+      "https://ggobi.github.io/ggally/articles/"
+    } else {
+      tryCatch({
+        paste0(
+          "https://ggobi.github.io/ggally/articles/",
+          match.arg(name, vignettes_for_ggally),
+          ".html"
+        )
+      }, error = function(e) {
+        message("Unknown vignette: ", name, ". Opening Vignette index page")
+        "https://ggobi.github.io/ggally/articles/"
+      })
+    }
+
+  browseURL(vig_url)
+}
+
+vignettes_for_ggally <- c(
+  "ggally_plots",
+  "ggally_stats",
+  "ggbivariate",
+  "ggcoef",
+  "ggduo",
+  "ggmatrix",
+  "ggnetworkmap",
+  "ggnostic",
+  "ggpairs",
+  "ggscatmat",
+  "ggsurv",
+  "ggtable",
+  "glyph"
+)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 99c9d3203..e6bed066e 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -24,11 +24,43 @@ authors:
   Hadley Wickham:
     href: http://hadley.nz/
 
+articles:
+- title: Generic plot matrix
+  navbar: Generic plot matrix
+  # desc: description here
+  contents:
+  - ggpairs
+  - ggduo
+  - ggmatrix
+  - ggally_plots
+
+- title: Specialized plot matrix
+  navbar: Specialized plot matrix
+  # desc: description here
+  contents:
+  - ggbivariate
+  - ggnostic
+  - ggscatmat
+  - ggtable
+  - ggally_stats
+
+- title: Specialized ggplot2 plot
+  navbar: Specialized ggplot2 plot
+  # desc: description here
+  contents:
+  - ggcoef
+  - ggnetworkmap
+  - ggsurv
+  - glyph
+
 
 reference:
 - title: Plot Matrix
   desc: >
-    More details in `vignette("ggpairs")`, `vignette("ggmatrix")` and `vignette("ggscatmat")`
+    More details in
+    [`vig_ggally("ggpairs")`](https://ggobi.github.io/ggally/articles/ggpairs.html),
+    [`vig_ggally("ggmatrix")`](https://ggobi.github.io/ggally/articles/ggmatrix.html),
+    and [`vig_ggally("ggscatmat")`](https://ggobi.github.io/ggally/articles/ggscatmat.html)
   contents:
   - ggmatrix
   - ggpairs
@@ -39,8 +71,9 @@ reference:
 
 - title: High-Level Plots
   desc: >
-    See `vignette("ggally_plots")` for a list with examples
-    of all high-level plots.
+    See
+    [`vig_ggally("ggally_plots")`](https://ggobi.github.io/ggally/articles/ggally_plots.html)
+    for a list with examples of all high-level plots.
   contents:
   - ggally_autopoint
   - ggally_barDiag
@@ -72,7 +105,11 @@ reference:
 
 - title: Major Plotting Functions
   desc: >
-    More details in `vignette("ggbivariate")`, `vignette("ggcoef")`, `vignette("ggsurv")`, and `vignette("ggtable")`
+    More details in
+    [`vig_ggally("ggbivariate")`](https://ggobi.github.io/ggally/articles/ggbivariate.html),
+    [`vig_ggally("ggcoef")`](https://ggobi.github.io/ggally/articles/ggcoef.html),
+    [`vig_ggally("ggsurv")`](https://ggobi.github.io/ggally/articles/ggsurv.html),
+    and [`vig_ggally("ggtable")`](https://ggobi.github.io/ggally/articles/ggtable.html)
   contents:
   - ggbivariate
   - ggcoef
@@ -83,7 +120,8 @@ reference:
 
 - title: Modeling Diagnostics
   desc: >
-    More details in `vignette("ggnostic")`
+    More details in
+    [`vig_ggally("ggnostic")`](https://ggobi.github.io/ggally/articles/ggpairs.html)
   contents:
   - ggnostic
   - broomify
@@ -97,7 +135,8 @@ reference:
 
 - title: Glyph Plot
   desc: >
-    More details in `vignette("glyph")`
+    More details in
+    [`vig_ggally("glyph")`](https://ggobi.github.io/ggally/articles/glyph.html)
   contents:
   - glyphs
   - add_ref_boxes
@@ -107,7 +146,8 @@ reference:
 
 - title: Network Plots
   desc: >
-    More details in `vignette("ggnetworkmap")`
+    More details in
+    [`vig_ggally("ggnetworkmap")`](https://ggobi.github.io/ggally/articles/ggnetworkmap.html)
   contents:
   - ggnet
   - ggnet2
@@ -115,7 +155,8 @@ reference:
 
 - title: Additional Statistics for `ggplot2`
   desc: >
-    More details in `vignette("ggally_stats")`
+    More details in
+    [`vig_ggally("ggally_stats")`](https://ggobi.github.io/ggally/articles/ggally_stats.html)
   contents:
   - stat_cross
   - stat_prop
@@ -123,7 +164,7 @@ reference:
 
 - title: "ggmatrix() Helpers"
   contents:
-  - eval_data_col
+  - +.gg
   - ggmatrix_location
   - wrap_fn_with_param_arg
   - getPlot
@@ -131,15 +172,15 @@ reference:
   - fn_switch
   - grab_legend
   - gglegend
-  - ggmatrix_progress
+  - eval_data_col
   - mapping_swap_x_y
   - mapping_color_to_fill
   - remove_color_unless_equal
   - print.ggmatrix
   - ggmatrix_gtable
-  - print_if_interactive
+  - ggmatrix_progress
   - str.ggmatrix
-  - +.gg
+  - print_if_interactive
 
 - title: Utilities
   contents:
@@ -155,6 +196,7 @@ reference:
   - skewness
   - signif_stars
   - uppertriangle
+  - vig_ggally
 
 - title: Datasets
   contents:
diff --git a/man/vig_ggally.Rd b/man/vig_ggally.Rd
new file mode 100644
index 000000000..9cdffc327
--- /dev/null
+++ b/man/vig_ggally.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/vig_ggally.R
+\name{vig_ggally}
+\alias{vig_ggally}
+\title{View \pkg{GGally} vignettes}
+\usage{
+vig_ggally(name)
+}
+\arguments{
+\item{name}{Vignette name to open. If no name is provided, the vignette index will be opened}
+}
+\description{
+This function will open the directly to the vignette requested. If no \code{name} is provided, the index of all \pkg{GGally} vignettes will be opened.
+}
+\details{
+This method allows for vignettes to be hosted remotely, reducing \pkg{GGally}'s package size, and installation time.
+}
+\examples{
+# View `ggnostic` vignette
+vig_ggally("ggnostic")
+
+# View all vignettes by GGally
+vig_ggally()
+}
diff --git a/tests/testthat/test-vig_ggally.R b/tests/testthat/test-vig_ggally.R
new file mode 100644
index 000000000..72159b62d
--- /dev/null
+++ b/tests/testthat/test-vig_ggally.R
@@ -0,0 +1,12 @@
+test_that("all vignetts are accounted for", {
+  # only run on CI
+  testthat::skip_if_not(isTRUE(as.logical(Sys.getenv("CI"))))
+
+  # make sure vig dir exists
+  vig_dir <- file.path("..", "..", "vignettes")
+  testthat::skip_if_not(dir.exists(vig_dir))
+
+  vigs <- dir(vig_dir, pattern = "\\.Rmd$")
+  vigs <- sub(".Rmd", "", vigs, fixed = TRUE)
+  expect_equal(vignettes_for_ggally, vigs)
+})
diff --git a/vignettes/ggally_plots.Rmd b/vignettes/ggally_plots.Rmd
index f7872cc02..8f44d8739 100644
--- a/vignettes/ggally_plots.Rmd
+++ b/vignettes/ggally_plots.Rmd
@@ -1,12 +1,12 @@
 ---
-title: "List of available high-level plots"
+title: "ggally_*(): List of available high-level plots"
 output: 
   rmarkdown::html_vignette:
     toc: true
 author: GGally Team
 date: May 28, 2020
 vignette: >
-  %\VignetteIndexEntry{List of available high-level plots}
+  %\VignetteIndexEntry{ggally_*(): List of available high-level plots}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/vignettes/ggally_stats.Rmd b/vignettes/ggally_stats.Rmd
index 984a8c040..6fe9c7f74 100644
--- a/vignettes/ggally_stats.Rmd
+++ b/vignettes/ggally_stats.Rmd
@@ -1,10 +1,10 @@
 ---
-title: "Additional statistics for ggplot2"
+title: "stat_*(): Additional statistics for ggplot2"
 output: rmarkdown::html_vignette
 author: GGally team
 date: May 28, 2020
 vignette: >
-  %\VignetteIndexEntry{Additional statistics for ggplot2}
+  %\VignetteIndexEntry{stat_*(): Additional statistics for ggplot2}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/vignettes/ggbivariate.Rmd b/vignettes/ggbivariate.Rmd
index ae89e9c16..2532f7cea 100644
--- a/vignettes/ggbivariate.Rmd
+++ b/vignettes/ggbivariate.Rmd
@@ -107,4 +107,4 @@ ggbivariate(
 )
 ```
 
-For more customization options, you could directly use `ggduo()` (see also `vignette("ggduo")`).
+For more customization options, you could directly use `ggduo()` (see also `vig_ggally("ggduo")`).
diff --git a/vignettes/ggduo.Rmd b/vignettes/ggduo.Rmd
index 82183adab..94b5e4a7b 100644
--- a/vignettes/ggduo.Rmd
+++ b/vignettes/ggduo.Rmd
@@ -239,5 +239,5 @@ You can customize the type of plots to display with the `types` argument. `types
 * `discrete`: when both x and y variables are discrete
 * `na`: when all x data and all y data is `NA`
 
-The list of current valid `ggally_NAME` functions is visible in `vignette("ggally_plots")`.
+The list of current valid `ggally_NAME` functions is visible in `vig_ggally("ggally_plots")`.
 
diff --git a/vignettes/ggnostic.Rmd b/vignettes/ggnostic.Rmd
index 26cb7dc92..c9ec4b3df 100644
--- a/vignettes/ggnostic.Rmd
+++ b/vignettes/ggnostic.Rmd
@@ -1,10 +1,10 @@
 ---
-title: "ggnostic(): Model diagnostics plot matrix"
+title: "ggnostic(): Model diagnostics"
 output: rmarkdown::html_vignette
 author: Barret Schloerke
 date: Oct 1, 2016
 vignette: >
-  %\VignetteIndexEntry{ggnostic(): Model diagnostics plot matrix}
+  %\VignetteIndexEntry{ggnostic(): Model diagnostics}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
diff --git a/vignettes/ggpairs.Rmd b/vignettes/ggpairs.Rmd
index f995cfe8a..e3f01bc52 100644
--- a/vignettes/ggpairs.Rmd
+++ b/vignettes/ggpairs.Rmd
@@ -71,7 +71,7 @@ To make adjustments to each section, a list of information may be supplied.  The
 * `discrete`: a character string representing the tail end of a `ggally_NAME` function, or a custom function
 * `mapping`:  if mapping is provided, only the section's mapping will be overwritten
 
-The list of current valid `ggally_NAME` functions is visible in `vignette("ggally_plots")`.
+The list of current valid `ggally_NAME` functions is visible in `vig_ggally("ggally_plots")`.
 
 ```{r ggpairs_section}
 library(ggplot2)

From c5f13975650613178c7e550bf2d78188c964033f Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Thu, 4 Jun 2020 23:17:01 -0400
Subject: [PATCH 12/22] use skip on cran. Not test on CI. Skip subplots tests
 on cran.

---
 tests/testthat/test-vig_ggally.R  | 3 +--
 tests/testthat/test-zzz_ggpairs.R | 2 ++
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-vig_ggally.R b/tests/testthat/test-vig_ggally.R
index 72159b62d..ac4275f3c 100644
--- a/tests/testthat/test-vig_ggally.R
+++ b/tests/testthat/test-vig_ggally.R
@@ -1,6 +1,5 @@
 test_that("all vignetts are accounted for", {
-  # only run on CI
-  testthat::skip_if_not(isTRUE(as.logical(Sys.getenv("CI"))))
+  testthat::skip_on_cran()
 
   # make sure vig dir exists
   vig_dir <- file.path("..", "..", "vignettes")
diff --git a/tests/testthat/test-zzz_ggpairs.R b/tests/testthat/test-zzz_ggpairs.R
index 118840142..6648ce830 100644
--- a/tests/testthat/test-zzz_ggpairs.R
+++ b/tests/testthat/test-zzz_ggpairs.R
@@ -557,6 +557,8 @@ test_that("strip-top and strip-right", {
 
 test_that("subtypes", {
 
+  testthat::skip_on_cran()
+
 # list of the different plot types to check
 # continuous
 #    points

From 174e88cb9c30c4cc510230c3fce05016c27f2de1 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <barret@rstudio.com>
Date: Fri, 5 Jun 2020 01:20:42 -0400
Subject: [PATCH 13/22] All examples use `p_()` (#368)

---
 R/deprecated.R                    |  54 +++--
 R/gg-plots.R                      | 341 ++++++++++++++++++------------
 R/ggbivariate.R                   |  27 +--
 R/ggcoef.R                        |   5 +-
 R/ggcorr.R                        |  19 +-
 R/gglyph.R                        |  33 +--
 R/ggmatrix.R                      |   3 +-
 R/ggmatrix_legend.R               |  24 ++-
 R/ggnet.R                         |   7 +-
 R/ggnet2.R                        |  27 +--
 R/ggnostic.R                      |  35 ++-
 R/ggpairs.R                       |   6 +-
 R/ggpairs_add.R                   |   1 -
 R/ggpairs_getput.R                |  14 +-
 R/ggscatmat.R                     |   4 +-
 R/ggsurv.R                        |  22 +-
 R/ggtable.R                       |  38 ++--
 R/stat_cross.R                    | 123 ++++++-----
 R/stat_prop.R                     |  38 ++--
 R/stat_weighted_mean.R            |  57 ++---
 R/vig_ggally.R                    |   3 +-
 man/getPlot.Rd                    |   9 +-
 man/ggally_autopoint.Rd           |  21 +-
 man/ggally_barDiag.Rd             |   7 +-
 man/ggally_box.Rd                 |  23 +-
 man/ggally_colbar.Rd              |  23 +-
 man/ggally_cor.Rd                 |  47 ++--
 man/ggally_cor_v1_5.Rd            |  48 +++--
 man/ggally_count.Rd               |  21 +-
 man/ggally_cross.Rd               |  27 +--
 man/ggally_crosstable.Rd          |  21 +-
 man/ggally_density.Rd             |  25 ++-
 man/ggally_densityDiag.Rd         |   9 +-
 man/ggally_denstrip.Rd            |  17 +-
 man/ggally_diagAxis.Rd            |   9 +-
 man/ggally_dot.Rd                 |  25 ++-
 man/ggally_dot_and_box.Rd         |  25 ++-
 man/ggally_facetbar.Rd            |   9 +-
 man/ggally_facetdensity.Rd        |  15 +-
 man/ggally_facethist.Rd           |   9 +-
 man/ggally_nostic_cooksd.Rd       |   5 +-
 man/ggally_nostic_hat.Rd          |   5 +-
 man/ggally_nostic_resid.Rd        |   5 +-
 man/ggally_nostic_se_fit.Rd       |   5 +-
 man/ggally_nostic_sigma.Rd        |   5 +-
 man/ggally_nostic_std_resid.Rd    |   5 +-
 man/ggally_points.Rd              |  11 +-
 man/ggally_ratio.Rd               |  11 +-
 man/ggally_smooth.Rd              |  11 +-
 man/ggally_summarise_by.Rd        |  37 ++--
 man/ggally_table.Rd               |  28 ++-
 man/ggally_text.Rd                |   7 +-
 man/ggally_trends.Rd              |  26 +--
 man/ggbivariate.Rd                |  27 +--
 man/ggcoef.Rd                     |   5 +-
 man/ggcorr.Rd                     |  19 +-
 man/ggduo.Rd                      |   2 +-
 man/gglegend.Rd                   |  13 +-
 man/ggmatrix.Rd                   |   2 +-
 man/ggmatrix_location.Rd          |   1 -
 man/ggnet.Rd                      |   7 +-
 man/ggnet2.Rd                     |  27 +--
 man/ggpairs.Rd                    |   4 +-
 man/ggscatmat.Rd                  |   2 +-
 man/ggsurv.Rd                     |  22 +-
 man/ggtable.Rd                    |  38 ++--
 man/ggts.Rd                       |   5 +-
 man/glyphs.Rd                     |  33 +--
 man/grab_legend.Rd                |  11 +-
 man/putPlot.Rd                    |   5 +-
 man/scatmat.Rd                    |   2 +-
 man/stat_cross.Rd                 |  47 ++--
 man/stat_prop.Rd                  |  15 +-
 man/stat_weighted_mean.Rd         |  31 +--
 man/v1_ggmatrix_theme.Rd          |   6 +-
 man/vig_ggally.Rd                 |   3 +-
 tests/testthat/test-zzz_ggpairs.R |   1 +
 77 files changed, 1022 insertions(+), 738 deletions(-)

diff --git a/R/deprecated.R b/R/deprecated.R
index 43e29b497..d38e95042 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -4,10 +4,12 @@
 #'
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
 #'
-#' ggpairs(iris, 1:2) + v1_ggmatrix_theme()
+#' p_(ggpairs(iris, 1:2) + v1_ggmatrix_theme())
 #' # move the column names to the left and bottom
-#' ggpairs(iris, 1:2, switch = "both") + v1_ggmatrix_theme()
+#' p_(ggpairs(iris, 1:2, switch = "both") + v1_ggmatrix_theme())
 v1_ggmatrix_theme <- function() {
   theme(
     strip.background = element_rect(fill = "white"),
@@ -40,27 +42,33 @@ v1_ggmatrix_theme <- function() {
 #' @export
 #' @keywords hplot
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_cor_v1_5(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
-#'  # display with no grid
-#'  ggally_cor_v1_5(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
-#'    displayGrid = FALSE
-#'  )
-#'  # change text attributes
-#'  ggally_cor_v1_5(
-#'    tips,
-#'    mapping = ggplot2::aes(x = total_bill, y = tip),
-#'    size = 15,
-#'    colour = I("red")
-#'  )
-#'  # split by a variable
-#'  ggally_cor_v1_5(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
-#'    size = 5
-#'  )
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_cor_v1_5(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+#'
+#' # display with no grid
+#' p_(ggally_cor_v1_5(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
+#'   displayGrid = FALSE
+#' ))
+#'
+#' # change text attributes
+#' p_(ggally_cor_v1_5(
+#'   tips,
+#'   mapping = ggplot2::aes(x = total_bill, y = tip),
+#'   size = 15,
+#'   colour = I("red")
+#' ))
+#'
+#' # split by a variable
+#' p_(ggally_cor_v1_5(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
+#'   size = 5
+#' ))
 ggally_cor_v1_5 <- function(
   data,
   mapping,
diff --git a/R/gg-plots.R b/R/gg-plots.R
index d1827ec25..85a947175 100644
--- a/R/gg-plots.R
+++ b/R/gg-plots.R
@@ -116,10 +116,13 @@ remove_color_unless_equal <- function(mapping, to = c("x", "y")) {
 #' @export
 #' @keywords hplot
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(mtcars)
-#' ggally_points(mtcars, mapping = ggplot2::aes(x = disp, y = hp))
-#' ggally_points(mtcars, mapping = ggplot2::aes_string(x = "disp", y = "hp"))
-#' ggally_points(
+#' p_(ggally_points(mtcars, mapping = ggplot2::aes(x = disp, y = hp)))
+#' p_(ggally_points(mtcars, mapping = ggplot2::aes_string(x = "disp", y = "hp")))
+#' p_(ggally_points(
 #'   mtcars,
 #'   mapping = ggplot2::aes_string(
 #'     x     = "disp",
@@ -127,7 +130,7 @@ remove_color_unless_equal <- function(mapping, to = c("x", "y")) {
 #'     color = "as.factor(cyl)",
 #'     size  = "gear"
 #'   )
-#' )
+#' ))
 ggally_points <- function(data, mapping, ...){
 
   p <- ggplot(data = data, mapping = mapping) + geom_point(...)
@@ -151,10 +154,13 @@ ggally_points <- function(data, mapping, ...){
 #' @keywords hplot
 #' @rdname ggally_smooth
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_smooth(tips, mapping = ggplot2::aes(x = total_bill, y = tip))
-#'  ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
-#'  ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_smooth(tips, mapping = ggplot2::aes(x = total_bill, y = tip)))
+#' p_(ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+#' p_(ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex")))
 ggally_smooth <- function(data, mapping, ..., method = "lm", formula = y ~ x, se = TRUE, shrink = TRUE) {
 
   p <- ggplot(data = data, mapping)
@@ -201,17 +207,20 @@ ggally_smooth_lm <- function(data, mapping, ...) {
 #' @export
 #' @keywords hplot
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_density(tips, mapping = ggplot2::aes(x = total_bill, y = tip))
-#'  ggally_density(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
-#'  ggally_density(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
-#'  )
-#'  ggally_density(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
-#'  ) + ggplot2::scale_fill_gradient(breaks = c(0.05, 0.1, 0.15, 0.2))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_density(tips, mapping = ggplot2::aes(x = total_bill, y = tip)))
+#' p_(ggally_density(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+#' p_(ggally_density(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
+#' ))
+#' p_(ggally_density(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
+#' ) + ggplot2::scale_fill_gradient(breaks = c(0.05, 0.1, 0.15, 0.2)))
 ggally_density <- function(data, mapping, ...){
   rangeX <- range(eval_data_col(data, mapping$x), na.rm = TRUE)
   rangeY <- range(eval_data_col(data, mapping$y), na.rm = TRUE)
@@ -263,28 +272,31 @@ ggally_density <- function(data, mapping, ...){
 #' @export
 #' @keywords hplot
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_cor(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
-#'  # display with grid
-#'  ggally_cor(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
-#'    display_grid = TRUE
-#'  )
-#'  # change text attributes
-#'  ggally_cor(
-#'    tips,
-#'    mapping = ggplot2::aes(x = total_bill, y = tip),
-#'    size = 15,
-#'    colour = I("red"),
-#'    title = "Correlation"
-#'  )
-#'  # split by a variable
-#'  ggally_cor(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
-#'    size = 5
-#'  )
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_cor(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+#' # display with grid
+#' p_(ggally_cor(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
+#'   display_grid = TRUE
+#' ))
+#' # change text attributes
+#' p_(ggally_cor(
+#'   tips,
+#'   mapping = ggplot2::aes(x = total_bill, y = tip),
+#'   size = 15,
+#'   colour = I("red"),
+#'   title = "Correlation"
+#' ))
+#' # split by a variable
+#' p_(ggally_cor(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
+#'   size = 5
+#' ))
 ggally_cor <- function(
   data,
   mapping,
@@ -592,16 +604,19 @@ ggally_statistic <- function(
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_box(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
-#'  ggally_box(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex"))
-#'  ggally_box(
-#'    tips,
-#'    mapping        = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex"),
-#'    outlier.colour = "red",
-#'    outlier.shape  = 13,
-#'    outlier.size   = 8
-#'  )
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_box(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+#' p_(ggally_box(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex")))
+#' p_(ggally_box(
+#'   tips,
+#'   mapping        = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex"),
+#'   outlier.colour = "red",
+#'   outlier.shape  = 13,
+#'   outlier.size   = 8
+#' ))
 ggally_box <- function(data, mapping, ...){
   mapping <- mapping_color_to_fill(mapping)
 
@@ -627,17 +642,20 @@ ggally_box_no_facet <- function(data, mapping, ...) {
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_dot(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
-#'  ggally_dot(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex"))
-#'  ggally_dot(
-#'    tips,
-#'    mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
-#'  )
-#'  ggally_dot(
-#'    tips,
-#'    mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex", shape = "sex")
-#'  ) + ggplot2::scale_shape(solid=FALSE)
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_dot(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+#' p_(ggally_dot(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex")))
+#' p_(ggally_dot(
+#'   tips,
+#'   mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
+#' ))
+#' p_(ggally_dot(
+#'   tips,
+#'   mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex", shape = "sex")
+#' ) + ggplot2::scale_shape(solid=FALSE))
 ggally_dot <- function(data, mapping, ...){
   ggally_dot_and_box(data, mapping, ..., boxPlot = FALSE)
 }
@@ -660,17 +678,20 @@ ggally_dot_no_facet <- function(data, mapping, ...) {
 #' @keywords internal
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_dot_and_box(
-#'    tips,
-#'    mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
-#'    boxPlot = TRUE
-#'  )
-#'  ggally_dot_and_box(
-#'    tips,
-#'    mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
-#'    boxPlot = FALSE
-#'  )
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_dot_and_box(
+#'   tips,
+#'   mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
+#'   boxPlot = TRUE
+#' ))
+#' p_(ggally_dot_and_box(
+#'   tips,
+#'   mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
+#'   boxPlot = FALSE
+#' ))
 ggally_dot_and_box <- function(data, mapping, ..., boxPlot = TRUE){
 
   horizontal <- is_horizontal(data, mapping)
@@ -744,9 +765,12 @@ ggally_dot_and_box_no_facet <- function(data, mapping, ..., boxPlot = TRUE) {
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_facethist(tips, mapping = ggplot2::aes(x = tip, y = sex))
-#'  ggally_facethist(tips, mapping = ggplot2::aes_string(x = "tip", y = "sex"), binwidth = 0.1)
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_facethist(tips, mapping = ggplot2::aes(x = tip, y = sex)))
+#' p_(ggally_facethist(tips, mapping = ggplot2::aes_string(x = "tip", y = "sex"), binwidth = 0.1))
 ggally_facethist <- function(data, mapping, ...){
 
   mapping <- mapping_color_to_fill(mapping)
@@ -791,12 +815,15 @@ ggally_facethist <- function(data, mapping, ...){
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_facetdensity(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
-#'  ggally_facetdensity(
-#'    tips,
-#'    mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
-#'  )
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_facetdensity(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+#' p_(ggally_facetdensity(
+#'   tips,
+#'   mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
+#' ))
 ggally_facetdensity <- function(data, mapping, ...){
   ggally_facetdensitystrip(data, mapping, ..., den_strip = FALSE)
 }
@@ -812,13 +839,16 @@ ggally_facetdensity <- function(data, mapping, ...){
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_denstrip(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
-#'  ggally_denstrip(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex"))
-#'  ggally_denstrip(
-#'    tips,
-#'    mapping = ggplot2::aes_string(x = "sex", y = "tip", binwidth = "0.2")
-#'  ) + ggplot2::scale_fill_gradient(low = "grey80", high = "black")
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_denstrip(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+#' p_(ggally_denstrip(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex")))
+#' p_(ggally_denstrip(
+#'   tips,
+#'   mapping = ggplot2::aes_string(x = "sex", y = "tip", binwidth = "0.2")
+#' ) + ggplot2::scale_fill_gradient(low = "grey80", high = "black"))
 ggally_denstrip <- function(data, mapping, ...){
   mapping <- mapping_color_to_fill(mapping)
 
@@ -910,9 +940,12 @@ ggally_facetdensitystrip <- function(data, mapping, ..., den_strip = FALSE){
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill))
-#'  ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill, color = day))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill)))
+#' p_(ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill, color = day)))
 ggally_densityDiag <- function(data, mapping, ..., rescale = FALSE){
 
   mapping <- mapping_color_to_fill(mapping)
@@ -949,9 +982,12 @@ ggally_densityDiag <- function(data, mapping, ..., rescale = FALSE){
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_barDiag(tips, mapping = ggplot2::aes(x = day))
-#' ggally_barDiag(tips, mapping = ggplot2::aes(x = tip), binwidth = 0.25)
+#' p_(ggally_barDiag(tips, mapping = ggplot2::aes(x = day)))
+#' p_(ggally_barDiag(tips, mapping = ggplot2::aes(x = tip), binwidth = 0.25))
 ggally_barDiag <- function(data, mapping, ..., rescale = FALSE){
 
   mapping <- mapping_color_to_fill(mapping)
@@ -1006,8 +1042,11 @@ ggally_barDiag <- function(data, mapping, ..., rescale = FALSE){
 #' @keywords hplot
 #' @export
 #' @examples
-#' ggally_text("Example 1")
-#' ggally_text("Example\nTwo", mapping = ggplot2::aes(size = 15), color = I("red"))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' p_(ggally_text("Example 1"))
+#' p_(ggally_text("Example\nTwo", mapping = ggplot2::aes(size = 15), color = I("red")))
 ggally_text <- function(
   label,
   mapping = ggplot2::aes(color = "black"),
@@ -1154,9 +1193,12 @@ get_x_axis_labels <- function(p, xRange) {
 #' @author Jason Crowley and Barret Schloerke
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_diagAxis(tips, ggplot2::aes(x=tip))
-#'  ggally_diagAxis(tips, ggplot2::aes(x=sex))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_diagAxis(tips, ggplot2::aes(x=tip)))
+#' p_(ggally_diagAxis(tips, ggplot2::aes(x=sex)))
 ggally_diagAxis <- function(
   data,
   mapping,
@@ -1275,9 +1317,12 @@ ggally_diagAxis <- function(
 #' @keywords hplot
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  ggally_facetbar(tips, ggplot2::aes(x = sex, y = smoker, fill = time))
-#'  ggally_facetbar(tips, ggplot2::aes(x = smoker, y = sex, fill = time))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' p_(ggally_facetbar(tips, ggplot2::aes(x = sex, y = smoker, fill = time)))
+#' p_(ggally_facetbar(tips, ggplot2::aes(x = smoker, y = sex, fill = time)))
 ggally_facetbar <- function(data, mapping, ...){
 
   mapping <- mapping_color_to_fill(mapping)
@@ -1307,14 +1352,17 @@ ggally_facetbar <- function(data, mapping, ...){
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_ratio(tips, ggplot2::aes(sex, day))
-#' ggally_ratio(tips, ggplot2::aes(sex, day)) + ggplot2::coord_equal()
+#' p_(ggally_ratio(tips, ggplot2::aes(sex, day)))
+#' p_(ggally_ratio(tips, ggplot2::aes(sex, day)) + ggplot2::coord_equal())
 #' # only plot tiles greater or equal to 20 and scale to a max of 50
-#' ggally_ratio(
+#' p_(ggally_ratio(
 #'   tips, ggplot2::aes(sex, day),
 #'   floor = 20, ceiling = 50
-#' ) + ggplot2::theme(aspect.ratio = 4/2)
+#' ) + ggplot2::theme(aspect.ratio = 4/2))
 ggally_ratio <- function(
   data,
   mapping = do.call(ggplot2::aes_string, as.list(colnames(data)[1:2])),
@@ -1406,19 +1454,22 @@ ggally_ratio <- function(
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex))
-#' ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex, fill = day))
+#' p_(ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex)))
+#' p_(ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex, fill = day)))
 #'
-#' ggally_count(
+#' p_(ggally_count(
 #'   as.data.frame(Titanic),
 #'   mapping = ggplot2::aes(x = Class, y = Survived, weight = Freq)
-#' )
-#' ggally_count(
+#' ))
+#' p_(ggally_count(
 #'   as.data.frame(Titanic),
 #'   mapping = ggplot2::aes(x = Class, y = Survived, weight = Freq),
 #'   x.width = 0.5
-#' )
+#' ))
 ggally_count <- function(data, mapping, ...) {
   mapping <- mapping_color_to_fill(mapping)
   if (is.null(mapping$x)) stop("'x' aesthetic is required.")
@@ -1534,9 +1585,11 @@ StatGGallyCount <- ggproto("StatGGallyCount", Stat,
 #' @rdname ggally_count
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
 #'
-#' ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker))
-#' ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker, fill = sex))
+#' p_(ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker)))
+#' p_(ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker, fill = sex)))
 ggally_countDiag <- function(data, mapping, ...) {
   mapping$y <- mapping$x
   ggally_count(data = data, mapping = mapping, ...)
@@ -1655,22 +1708,23 @@ ggally_naDiag <- function(...) {
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_autopoint(tips, mapping = aes(x = tip, y = total_bill))
-#' ggally_autopoint(tips, mapping = aes(x = tip, y = sex))
-#' ggally_autopoint(tips, mapping = aes(x = smoker, y = sex))
-#' ggally_autopoint(tips, mapping = aes(x = smoker, y = sex, color = day))
-#' ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), size = 8)
-#' ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), alpha = .9)
-#'
-#' \dontrun{
-#' ggpairs(
+#' p_(ggally_autopoint(tips, mapping = aes(x = tip, y = total_bill)))
+#' p_(ggally_autopoint(tips, mapping = aes(x = tip, y = sex)))
+#' p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex)))
+#' p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex, color = day)))
+#' p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), size = 8))
+#' p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), alpha = .9))
+#'
+#' p_(ggpairs(
 #'   tips,
 #'   mapping = aes(colour = sex),
 #'   upper = list(discrete = "autopoint", combo = "autopoint", continuous = "autopoint"),
 #'   diag = list(discrete = "autopointDiag", continuous = "autopointDiag")
-#' )
-#' }
+#' ))
 ggally_autopoint <- function(data, mapping, ...) {
   require_namespaces("ggforce")
 
@@ -1705,27 +1759,32 @@ ggally_autopointDiag <- function(data, mapping, ...) {
 #' @keywords hplot
 #' @export
 #' @examples
-#' data(tips, package = "reshape")
-#' ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day))
-#' ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' if (require(Hmisc)) {
+#'   data(tips, package = "reshape")
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day)))
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill)))
 #'
-#' # colour is kept only if equal to the discrete variable
-#' ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = day))
-#' ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = sex))
-#' ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill, color = day))
+#'   # colour is kept only if equal to the discrete variable
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = day)))
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = sex)))
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill, color = day)))
 #'
-#' # custom text size
-#' ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), size = 6)
+#'   # custom text size
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), size = 6))
 #'
-#' # change statistic to display
-#' ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = mean_sd)
+#'   # change statistic to display
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = mean_sd))
 #'
-#' # custom stat function
-#' weighted_sum <- function(x, weights = NULL) {
-#'   if (is.null(weights)) weights <- 1
-#'   paste0("Total : ", round(sum(x * weights, na.rm = TRUE), digits = 1))
+#'   # custom stat function
+#'   weighted_sum <- function(x, weights = NULL) {
+#'     if (is.null(weights)) weights <- 1
+#'     paste0("Total : ", round(sum(x * weights, na.rm = TRUE), digits = 1))
+#'   }
+#'   p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = weighted_sum))
 #' }
-#' ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = weighted_sum)
 ggally_summarise_by <- function(
   data,
   mapping,
diff --git a/R/ggbivariate.R b/R/ggbivariate.R
index 4b5e9176a..5e40c0a9d 100644
--- a/R/ggbivariate.R
+++ b/R/ggbivariate.R
@@ -17,23 +17,25 @@
 #' @author Joseph Larmarange
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggbivariate(tips, "smoker", c("day", "time", "sex", "tip"))
+#' p_(ggbivariate(tips, "smoker", c("day", "time", "sex", "tip")))
 #'
-#' \dontrun{
 #' # Personalize plot title and legend title
-#' ggbivariate(
+#' p_(ggbivariate(
 #'   tips, "smoker", c("day", "time", "sex", "tip"),
 #'   title = "Custom title"
 #' ) +
-#'   labs(fill = "Smoker ?")
+#'   labs(fill = "Smoker ?"))
 #'
 #' # Customize fill colour scale
-#' ggbivariate(tips, "smoker", c("day", "time", "sex", "tip")) +
-#'   scale_fill_brewer(type = "qual")
+#' p_(ggbivariate(tips, "smoker", c("day", "time", "sex", "tip")) +
+#'   scale_fill_brewer(type = "qual"))
 #'
 #' # Customize labels
-#' ggbivariate(
+#' p_(ggbivariate(
 #'   tips, "smoker", c("day", "time", "sex", "tip"),
 #'   rowbar_args = list(
 #'     colour = "white",
@@ -41,19 +43,18 @@
 #'     fontface = "bold",
 #'     label_format = scales::label_percent(accurary = 1)
 #'   )
-#' )
+#' ))
 #'
 #' # Choose the sub-plot from which get legend
-#' ggbivariate(tips, "smoker")
-#' ggbivariate(tips, "smoker", legend = 3)
+#' p_(ggbivariate(tips, "smoker"))
+#' p_(ggbivariate(tips, "smoker", legend = 3))
 #'
 #' # Use mapping to indicate weights
 #' d <- as.data.frame(Titanic)
-#' ggbivariate(d, "Survived", mapping = aes(weight = Freq))
+#' p_(ggbivariate(d, "Survived", mapping = aes(weight = Freq)))
 #'
 #' # outcome can be numerical
-#' ggbivariate(tips, outcome = "tip", title = "tip")
-#' }
+#' p_(ggbivariate(tips, outcome = "tip", title = "tip"))
 ggbivariate <- function(
   data,
   outcome,
diff --git a/R/ggcoef.R b/R/ggcoef.R
index e6910ffd8..d60535517 100644
--- a/R/ggcoef.R
+++ b/R/ggcoef.R
@@ -23,9 +23,12 @@
 #' @param sort \code{"none"} (default) do not sort, \code{"ascending"} sort by increasing coefficient value, or \code{"descending"} sort by decreasing coefficient value
 #' @param ... additional arguments sent to \code{\link[ggplot2]{geom_point}}
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' library(broom)
 #' reg <- lm(Sepal.Length ~ Sepal.Width + Petal.Length + Petal.Width, data = iris)
-#' ggcoef(reg)
+#' p_(ggcoef(reg))
 #' \donttest{d <- as.data.frame(Titanic)
 #' reg2 <- glm(Survived ~ Sex + Age + Class, family = binomial, data = d, weights = d$Freq)
 #' ggcoef(reg2, exponentiate = TRUE)
diff --git a/R/ggcorr.R b/R/ggcorr.R
index 7cf1b811f..c2503e9d7 100644
--- a/R/ggcorr.R
+++ b/R/ggcorr.R
@@ -99,19 +99,22 @@ if (getRversion() >= "2.15.1") {
 #' @importFrom stats cor
 #' @importFrom grDevices colorRampPalette
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' # Basketball statistics provided by Nathan Yau at Flowing Data.
 #' dt <- read.csv("http://datasets.flowingdata.com/ppg2008.csv")
 #'
 #' # Default output.
-#' ggcorr(dt[, -1])
+#' p_(ggcorr(dt[, -1]))
 #'
-#' # Labelled output, with coefficient transparency.
-#' ggcorr(dt[, -1],
+#' # Labeled output, with coefficient transparency.
+#' p_(ggcorr(dt[, -1],
 #'        label = TRUE,
-#'        label_alpha = TRUE)
+#'        label_alpha = TRUE))
 #'
 #' # Custom options.
-#' ggcorr(
+#' p_(ggcorr(
 #'   dt[, -1],
 #'   name = expression(rho),
 #'   geom = "circle",
@@ -122,13 +125,13 @@ if (getRversion() >= "2.15.1") {
 #'   nbreaks = 6,
 #'   angle = -45,
 #'   palette = "PuOr" # colorblind safe, photocopy-able
-#' )
+#' ))
 #'
 #' # Supply your own correlation matrix
-#' ggcorr(
+#' p_(ggcorr(
 #'   data = NULL,
 #'   cor_matrix = cor(dt[, -1], use = "pairwise")
-#' )
+#' ))
 ggcorr <- function(
   data,
   method = c("pairwise", "pearson"),
diff --git a/R/gglyph.R b/R/gglyph.R
index 9f967353d..a348625e7 100644
--- a/R/gglyph.R
+++ b/R/gglyph.R
@@ -19,21 +19,24 @@
 #' @export
 #' @author Di Cook, Heike Hofmann, Hadley Wickham
 #' @examples
-#'  data(nasa)
-#'  nasaLate <- nasa[
-#'    nasa$date >= as.POSIXct("1998-01-01") &
-#'    nasa$lat >= 20 &
-#'    nasa$lat <= 40 &
-#'    nasa$long >= -80 &
-#'    nasa$long <= -60
-#'  , ]
-#'  temp.gly <- glyphs(nasaLate, "long", "day", "lat", "surftemp", height=2.5)
-#'  ggplot2::ggplot(temp.gly, ggplot2::aes(gx, gy, group = gid)) +
-#'    add_ref_lines(temp.gly, color = "grey90") +
-#'    add_ref_boxes(temp.gly, color = "grey90") +
-#'    ggplot2::geom_path() +
-#'    ggplot2::theme_bw() +
-#'    ggplot2::labs(x = "", y = "")
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(nasa)
+#' nasaLate <- nasa[
+#'   nasa$date >= as.POSIXct("1998-01-01") &
+#'   nasa$lat >= 20 &
+#'   nasa$lat <= 40 &
+#'   nasa$long >= -80 &
+#'   nasa$long <= -60
+#' , ]
+#' temp.gly <- glyphs(nasaLate, "long", "day", "lat", "surftemp", height=2.5)
+#' p_(ggplot2::ggplot(temp.gly, ggplot2::aes(gx, gy, group = gid)) +
+#'   add_ref_lines(temp.gly, color = "grey90") +
+#'   add_ref_boxes(temp.gly, color = "grey90") +
+#'   ggplot2::geom_path() +
+#'   ggplot2::theme_bw() +
+#'   ggplot2::labs(x = "", y = ""))
 glyphs <- function(
   data,
   x_major, x_minor,
diff --git a/R/ggmatrix.R b/R/ggmatrix.R
index 3f868acd3..f836b72e9 100644
--- a/R/ggmatrix.R
+++ b/R/ggmatrix.R
@@ -25,7 +25,7 @@
 #' @importFrom rlang %||%
 #' @export
 #' @examples
-#' # small function to display plots only if it's interactive
+#' # Small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive
 #'
 #' plotList <- list()
@@ -50,7 +50,6 @@
 #'   showXAxisPlotLabels = FALSE
 #' )
 #' p_(pm)
-
 ggmatrix <- function(
   plots,
   nrow,
diff --git a/R/ggmatrix_legend.R b/R/ggmatrix_legend.R
index 42336654d..824820053 100644
--- a/R/ggmatrix_legend.R
+++ b/R/ggmatrix_legend.R
@@ -7,6 +7,9 @@
 #' @import ggplot2
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' library(ggplot2)
 #' histPlot <- qplot(
 #'   x = Sepal.Length,
@@ -20,10 +23,10 @@
 #' (top <- histPlot + theme(legend.position = "top"))
 #' (left <- histPlot + theme(legend.position = "left"))
 #'
-#' grab_legend(right)
-#' grab_legend(bottom)
-#' grab_legend(top)
-#' grab_legend(left)
+#' p_(grab_legend(right))
+#' p_(grab_legend(bottom))
+#' p_(grab_legend(top))
+#' p_(grab_legend(left))
 grab_legend <- function(p) {
   builtP <- ggplot_build(p)
   pTable <- ggplot_gtable(builtP)
@@ -63,12 +66,15 @@ print.legend_guide_box <- function(x, ..., plotNew = FALSE) {
 #' @return a function that when called with arguments will produce the legend of the plotting function supplied.
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' # display regular plot
-#' ggally_points(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species))
+#' p_(ggally_points(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species)))
 #'
 #' # Make a function that will only print the legend
 #' points_legend <- gglegend(ggally_points)
-#' points_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species))
+#' p_(points_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species)))
 #'
 #' # produce the sample legend plot, but supply a string that 'wrap' understands
 #' same_points_legend <- gglegend("points")
@@ -79,7 +85,7 @@ print.legend_guide_box <- function(x, ..., plotNew = FALSE) {
 #'
 #' # Complicated examples
 #' custom_legend <- wrap(gglegend("points"), size = 6)
-#' custom_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species))
+#' p_(custom_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species)))
 #'
 #' # Use within ggpairs
 #' pm <- ggpairs(
@@ -87,13 +93,13 @@ print.legend_guide_box <- function(x, ..., plotNew = FALSE) {
 #'   mapping = ggplot2::aes(color = Species),
 #'   upper = list(continuous = gglegend("points"))
 #' )
-#' # pm
+#' p_(pm)
 #'
 #' # Place a legend in a specific location
 #' pm <- ggpairs(iris, 1:2, mapping = ggplot2::aes(color = Species))
 #' # Make the legend
 #' pm[1,2] <- points_legend(iris, ggplot2::aes(Sepal.Width, Sepal.Length, color = Species))
-#' pm
+#' p_(pm)
 gglegend <- function(fn) {
 
   # allows users to supply a character just like in ggpairs
diff --git a/R/ggnet.R b/R/ggnet.R
index 5d75fffcb..d5fad81b5 100644
--- a/R/ggnet.R
+++ b/R/ggnet.R
@@ -136,6 +136,9 @@ if (getRversion() >= "2.15.1") {
 #' @importFrom utils head installed.packages
 #' @importFrom grDevices gray.colors
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' library(network)
 #'
 #' # random adjacency matrix
@@ -160,10 +163,10 @@ if (getRversion() >= "2.15.1") {
 #' # color palette
 #' p <- c("a" = "steelblue", "b" = "forestgreen", "c" = "tomato")
 #'
-#' ggnet(n, node.group = g, node.color = p, label = TRUE, color = "white")
+#' p_(ggnet(n, node.group = g, node.color = p, label = TRUE, color = "white"))
 #'
 #' # edge arrows on a directed network
-#' ggnet(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10)
+#' p_(ggnet(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10))
 ggnet <- function(
   net,
   mode             = "fruchtermanreingold",
diff --git a/R/ggnet2.R b/R/ggnet2.R
index 9358f987f..4cd05e382 100644
--- a/R/ggnet2.R
+++ b/R/ggnet2.R
@@ -199,6 +199,9 @@ if (getRversion() >= "2.15.1") {
 #' @importFrom utils installed.packages
 #' @importFrom grDevices gray.colors
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' library(network)
 #'
 #' # random adjacency matrix
@@ -214,42 +217,42 @@ if (getRversion() >= "2.15.1") {
 #' n <- network::network(m, directed = FALSE)
 #' n
 #'
-#' ggnet2(n, label = TRUE)
-#' ggnet2(n, label = TRUE, shape = 15)
-#' ggnet2(n, label = TRUE, shape = 15, color = "black", label.color = "white")
+#' p_(ggnet2(n, label = TRUE))
+#' p_(ggnet2(n, label = TRUE, shape = 15))
+#' p_(ggnet2(n, label = TRUE, shape = 15, color = "black", label.color = "white"))
 #'
 #' # add vertex attribute
 #' x = network.vertex.names(n)
 #' x = ifelse(x %in% c("a", "e", "i"), "vowel", "consonant")
 #' n %v% "phono" = x
 #'
-#' ggnet2(n, color = "phono")
-#' ggnet2(n, color = "phono", palette = c("vowel" = "gold", "consonant" = "grey"))
-#' ggnet2(n, shape = "phono", color = "phono")
+#' p_(ggnet2(n, color = "phono"))
+#' p_(ggnet2(n, color = "phono", palette = c("vowel" = "gold", "consonant" = "grey")))
+#' p_(ggnet2(n, shape = "phono", color = "phono"))
 #'
 #' if (require(RColorBrewer)) {
 #'
 #'   # random groups
 #'   n %v% "group" <- sample(LETTERS[1:3], 10, replace = TRUE)
 #'
-#'   ggnet2(n, color = "group", palette = "Set2")
+#'   p_(ggnet2(n, color = "group", palette = "Set2"))
 #'
 #' }
 #'
 #' # random weights
 #' n %e% "weight" <- sample(1:3, network.edgecount(n), replace = TRUE)
-#' ggnet2(n, edge.size = "weight", edge.label = "weight")
+#' p_(ggnet2(n, edge.size = "weight", edge.label = "weight"))
 #'
 #' # edge arrows on a directed network
-#' ggnet2(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10)
+#' p_(ggnet2(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10))
 #'
 #' # Padgett's Florentine wedding data
 #' data(flo, package = "network")
 #' flo
 #'
-#' ggnet2(flo, label = TRUE)
-#' ggnet2(flo, label = TRUE, label.trim = 4, vjust = -1, size = 3, color = 1)
-#' ggnet2(flo, label = TRUE, size = 12, color = "white")
+#' p_(ggnet2(flo, label = TRUE))
+#' p_(ggnet2(flo, label = TRUE, label.trim = 4, vjust = -1, size = 3, color = 1))
+#' p_(ggnet2(flo, label = TRUE, size = 12, color = "white"))
 ggnet2 <- function(
   net,
   mode             = "fruchtermanreingold",
diff --git a/R/ggnostic.R b/R/ggnostic.R
index 0adb2c4b7..effbebe4d 100644
--- a/R/ggnostic.R
+++ b/R/ggnostic.R
@@ -207,8 +207,11 @@ ggally_nostic_line <- function(
 #' @export
 #' @importFrom stats qnorm
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-#' ggally_nostic_resid(dt, ggplot2::aes(wt, .resid))
+#' p_(ggally_nostic_resid(dt, ggplot2::aes(wt, .resid)))
 ggally_nostic_resid <- function(
   data, mapping, ...,
   linePosition = 0,
@@ -271,8 +274,11 @@ ggally_nostic_resid <- function(
 #' @rdname ggally_nostic_std_resid
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-#' ggally_nostic_std_resid(dt, ggplot2::aes(wt, .std.resid))
+#' p_(ggally_nostic_std_resid(dt, ggplot2::aes(wt, .std.resid)))
 ggally_nostic_std_resid <- function(
   data, mapping, ...,
   sigma = 1
@@ -303,8 +309,11 @@ ggally_nostic_std_resid <- function(
 #' @return \pkg{ggplot2} plot object
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-#' ggally_nostic_se_fit(dt, ggplot2::aes(wt, .se.fit))
+#' p_(ggally_nostic_se_fit(dt, ggplot2::aes(wt, .se.fit)))
 ggally_nostic_se_fit <- function(
   data, mapping, ...,
   lineColor = brew_colors("grey"),
@@ -335,8 +344,11 @@ ggally_nostic_se_fit <- function(
 #' @return \pkg{ggplot2} plot object
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-#' ggally_nostic_sigma(dt, ggplot2::aes(wt, .sigma))
+#' p_(ggally_nostic_sigma(dt, ggplot2::aes(wt, .sigma)))
 ggally_nostic_sigma <- function(
   data, mapping, ...,
   lineColor = brew_colors("grey"),
@@ -367,8 +379,11 @@ ggally_nostic_sigma <- function(
 #' @export
 #' @importFrom stats pf
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-#' ggally_nostic_cooksd(dt, ggplot2::aes(wt, .cooksd))
+#' p_(ggally_nostic_cooksd(dt, ggplot2::aes(wt, .cooksd)))
 ggally_nostic_cooksd <- function(
   data, mapping, ...,
   linePosition = pf(0.5, length(attr(data, "var_x")), nrow(data) - length(attr(data, "var_x"))),
@@ -408,8 +423,11 @@ ggally_nostic_cooksd <- function(
 #' @return \pkg{ggplot2} plot object
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-#' ggally_nostic_hat(dt, ggplot2::aes(wt, .hat))
+#' p_(ggally_nostic_hat(dt, ggplot2::aes(wt, .hat)))
 ggally_nostic_hat <- function(
   data, mapping, ...,
   linePosition = 2 * sum(eval_data_col(data, mapping$y)) / nrow(data),
@@ -720,7 +738,10 @@ ggnostic <- function(
 #' @return \code{\link{ggmatrix}} object
 #' @export
 #' @examples
-#' ggts(pigs, "time", c("gilts", "profit", "s_per_herdsz", "production", "herdsz"))
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' p_(ggts(pigs, "time", c("gilts", "profit", "s_per_herdsz", "production", "herdsz")))
 ggts <- function(
   ...,
   columnLabelsX = NULL,
diff --git a/R/ggpairs.R b/R/ggpairs.R
index b92a3e60d..9c29fe90c 100644
--- a/R/ggpairs.R
+++ b/R/ggpairs.R
@@ -293,7 +293,7 @@ stop_if_high_cardinality <- function(data, columns, threshold) {
 #'      continuous = wrap("smooth_loess", alpha = 0.50, shape = "+")
 #'    ),
 #'    showStrips = FALSE
-#'  );
+#'  )
 #'
 #'  p_(pm)
 #'
@@ -655,8 +655,8 @@ ggduo <- function(
 #' @author Barret Schloerke, Jason Crowley, Di Cook, Heike Hofmann, Hadley Wickham
 #' @return \code{\link{ggmatrix}} object that if called, will print
 #' @examples
-#'  # small function to display plots only if it's interactive
-#'  p_ <- GGally::print_if_interactive
+#' # small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
 #'
 #'
 #' ## Quick example, with and without colour
diff --git a/R/ggpairs_add.R b/R/ggpairs_add.R
index 322ede97b..3b27c252b 100644
--- a/R/ggpairs_add.R
+++ b/R/ggpairs_add.R
@@ -235,7 +235,6 @@ add_to_ggmatrix <- function(
 #'
 #' # Use the output of a prior ggmatrix_location
 #' ggmatrix_location(pm, location = locs)
-#'
 ggmatrix_location <- function(
   pm,
   location = NULL,
diff --git a/R/ggpairs_getput.R b/R/ggpairs_getput.R
index 68eea4796..434a65be7 100644
--- a/R/ggpairs_getput.R
+++ b/R/ggpairs_getput.R
@@ -11,6 +11,9 @@
 #' @seealso \code{\link{getPlot}}
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' custom_car <- ggpairs(mtcars[, c("mpg", "wt", "cyl")], upper = "blank", title = "Custom Example")
 #' # ggplot example taken from example(geom_text)
 #'   plot <- ggplot2::ggplot(mtcars, ggplot2::aes(x=wt, y=mpg, label=rownames(mtcars)))
@@ -28,7 +31,7 @@
 #' custom_car[2,1] <- NULL
 #' custom_car[3,1] <- "blank" # the same as storing null
 #' custom_car[3,2] <- NULL
-#' custom_car
+#' p_(custom_car)
 putPlot <- function(pm, value, i, j){
   pos <- get_pos(pm, i, j)
   if (is.null(value)) {
@@ -59,9 +62,12 @@ putPlot <- function(pm, value, i, j){
 #' @seealso \code{\link{putPlot}}
 #' @export
 #' @examples
-#'  data(tips, package = "reshape")
-#'  plotMatrix2 <- ggpairs(tips[, 3:2], upper = list(combo = "denstrip"))
-#'  plotMatrix2[1, 2]
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
+#' data(tips, package = "reshape")
+#' plotMatrix2 <- ggpairs(tips[, 3:2], upper = list(combo = "denstrip"))
+#' p_(plotMatrix2[1, 2])
 getPlot <- function(pm, i, j){
   if (FALSE) {
     cat("i: ", i, " j: ", j, "\n")
diff --git a/R/ggscatmat.R b/R/ggscatmat.R
index ea9e6b608..e66c8bf83 100644
--- a/R/ggscatmat.R
+++ b/R/ggscatmat.R
@@ -216,7 +216,7 @@ uppertriangle <- function(data, columns=1:ncol(data), color=NULL, corMethod = "p
 #'
 #' data(flea)
 #'
-#' scatmat(flea, columns=2:4)
+#' p_(scatmat(flea, columns=2:4))
 #' p_(scatmat(flea, columns= 2:4, color="species"))
 scatmat <- function(data, columns=1:ncol(data), color=NULL, alpha=1) {
   data <- upgrade_scatmat_data(data)
@@ -302,7 +302,7 @@ scatmat <- function(data, columns=1:ncol(data), color=NULL, alpha=1) {
 #'
 #' data(flea)
 #'
-#' ggscatmat(flea, columns = 2:4)
+#' p_(ggscatmat(flea, columns = 2:4))
 #' p_(ggscatmat(flea, columns = 2:4, color = "species"))
 ggscatmat <- function(data, columns = 1:ncol(data), color = NULL, alpha = 1, corMethod = "pearson"){
   ## if 'color' is not a factor, mold it into one
diff --git a/R/ggsurv.R b/R/ggsurv.R
index 1fbb62c23..1b20ec7da 100644
--- a/R/ggsurv.R
+++ b/R/ggsurv.R
@@ -36,46 +36,48 @@ if(getRversion() >= "2.15.1") {
 #' @author Edwin Thoen
 #' @importFrom stats time
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
 #'
 #' if (require(survival) && require(scales)) {
 #'   data(lung, package = "survival")
 #'   sf.lung <- survival::survfit(Surv(time, status) ~ 1, data = lung)
-#'   ggsurv(sf.lung)
+#'   p_(ggsurv(sf.lung))
 #'
 #'   # Multiple strata examples
 #'   sf.sex <- survival::survfit(Surv(time, status) ~ sex, data = lung)
 #'   pl.sex <- ggsurv(sf.sex)
-#'   pl.sex
+#'   p_(pl.sex)
 #'
 #'   # Adjusting the legend of the ggsurv fit
-#'   pl.sex +
+#'   p_(pl.sex +
 #'     ggplot2::guides(linetype = FALSE) +
 #'     ggplot2::scale_colour_discrete(
 #'       name   = 'Sex',
 #'       breaks = c(1,2),
 #'       labels = c('Male', 'Female')
-#'     )
+#'     ))
 #'
 #'   # Multiple factors
 #'   lung2 <- plyr::mutate(lung, older = as.factor(age > 60))
 #'   sf.sex2 <- survival::survfit(Surv(time, status) ~ sex + older, data = lung2)
 #'   pl.sex2 <- ggsurv(sf.sex2)
-#'   pl.sex2
+#'   p_(pl.sex2)
 #'
 #'   # Change legend title
-#'   pl.sex2 + labs(color = "New Title", linetype = "New Title")
+#'   p_(pl.sex2 + labs(color = "New Title", linetype = "New Title"))
 #'
 #'   # We can still adjust the plot after fitting
 #'   data(kidney, package = "survival")
 #'   sf.kid <- survival::survfit(Surv(time, status) ~ disease, data = kidney)
 #'   pl.kid <- ggsurv(sf.kid, plot.cens = FALSE)
-#'   pl.kid
+#'   p_(pl.kid)
 #'
 #'   # Zoom in to first 80 days
-#'   pl.kid + ggplot2::coord_cartesian(xlim = c(0, 80), ylim = c(0.45, 1))
+#'   p_(pl.kid + ggplot2::coord_cartesian(xlim = c(0, 80), ylim = c(0.45, 1)))
 #'
 #'   # Add the diseases names to the plot and remove legend
-#'   pl.kid +
+#'   p_(pl.kid +
 #'     ggplot2::annotate(
 #'       "text",
 #'       label  = c("PKD", "Other", "GN", "AN"),
@@ -90,7 +92,7 @@ if(getRversion() >= "2.15.1") {
 #'         direction = 1
 #'       )(4)
 #'     ) +
-#'     ggplot2::guides(color = FALSE, linetype = FALSE)
+#'     ggplot2::guides(color = FALSE, linetype = FALSE))
 #' }
 ggsurv <- function(
   s,
diff --git a/R/ggtable.R b/R/ggtable.R
index 3d8c9b003..308c23e10 100644
--- a/R/ggtable.R
+++ b/R/ggtable.R
@@ -17,28 +17,30 @@
 #' # small function to display plots only if it's interactive
 #' p_ <- GGally::print_if_interactive
 #'
-#' data(tips, package = "reshape")
-#' ggtable(tips, "smoker", c("day", "time", "sex"))
+#' if (require(Hmisc)) {
+#'   data(tips, package = "reshape")
+#'   p_(ggtable(tips, "smoker", c("day", "time", "sex")))
 #'
-#' # displaying row proportions
-#' p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
+#'   # displaying row proportions
+#'   p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
 #'
-#' # filling cells with standardized residuals
-#' p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
+#'   # filling cells with standardized residuals
+#'   p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
 #'
-#' # if continuous variables are provided, just displaying some summary statistics
-#' p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))
+#'   # if continuous variables are provided, just displaying some summary statistics
+#'   p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))
 #'
-#' # specifying weights
-#' d <- as.data.frame(Titanic)
-#' p_(ggtable(
-#'   d,
-#'   "Survived",
-#'   c("Class", "Sex", "Age"),
-#'   mapping = aes(weight = Freq),
-#'   cells = "row.prop",
-#'   fill = "stdres"
-#' ))
+#'   # specifying weights
+#'   d <- as.data.frame(Titanic)
+#'   p_(ggtable(
+#'     d,
+#'     "Survived",
+#'     c("Class", "Sex", "Age"),
+#'     mapping = aes(weight = Freq),
+#'     cells = "row.prop",
+#'     fill = "stdres"
+#'   ))
+#' }
 ggtable <- function(
   data,
   columnsX = 1:ncol(data),
diff --git a/R/stat_cross.R b/R/stat_cross.R
index db37c1aee..636bd82c9 100644
--- a/R/stat_cross.R
+++ b/R/stat_cross.R
@@ -24,51 +24,54 @@
 #'
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' d <- as.data.frame(Titanic)
 #'
 #' # plot number of observations
-#' ggplot(d) +
-#'   aes(x = Class, y = Survived, weight = Freq, size = after_stat(observed)) +
-#'   stat_cross() +
-#'   scale_size_area(max_size = 20)
+#' p_(ggplot(d) +
+#'  aes(x = Class, y = Survived, weight = Freq, size = after_stat(observed)) +
+#'  stat_cross() +
+#'  scale_size_area(max_size = 20))
 #'
 #' # custom shape and fill colour based on chi-squared residuals
-#' ggplot(d) +
-#'   aes(
-#'     x = Class, y = Survived, weight = Freq,
-#'     size = after_stat(observed), fill = after_stat(stdres)
-#'   ) +
-#'   stat_cross(shape = 22) +
-#'   scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE) +
-#'   scale_size_area(max_size = 20)
+#' p_(ggplot(d) +
+#'  aes(
+#'    x = Class, y = Survived, weight = Freq,
+#'    size = after_stat(observed), fill = after_stat(stdres)
+#'  ) +
+#'  stat_cross(shape = 22) +
+#'  scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE) +
+#'  scale_size_area(max_size = 20))
 #'
 #' # plotting the number of observations as a table
-#' ggplot(d) +
-#'   aes(
-#'     x = Class, y = Survived, weight = Freq, label = after_stat(observed)
-#'   ) +
-#'   geom_text(stat = "cross")
+#' p_(ggplot(d) +
+#'  aes(
+#'    x = Class, y = Survived, weight = Freq, label = after_stat(observed)
+#'  ) +
+#'  geom_text(stat = "cross"))
 #'
 #' # Row proportions with standardized residuals
-#' ggplot(d) +
+#' p_(ggplot(d) +
 #'   aes(
 #'     x = Class, y = Survived, weight = Freq,
 #'     label = scales::percent(after_stat(row.prop)),
-#'      size = NULL, fill = after_stat(stdres)
+#'     size = NULL, fill = after_stat(stdres)
 #'   ) +
 #'   stat_cross(shape = 22, size = 30) +
 #'   geom_text(stat = "cross") +
 #'   scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE) +
 #'   facet_grid(Sex ~ .) +
 #'   labs(fill = "Standardized residuals") +
-#'   theme_minimal()
+#'   theme_minimal())
 #'
 #' # can work with continuous or character variables
 #' data(tips, package = "reshape")
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = tip, y = as.character(day), size = after_stat(observed)) +
 #'   stat_cross(alpha = .1, color = "blue") +
-#'   scale_size_area(max_size = 12)
+#'   scale_size_area(max_size = 12))
 stat_cross <- function(mapping = NULL, data = NULL,
                        geom = "point", position = "identity",
                        ...,
@@ -169,39 +172,42 @@ StatCross <- ggproto("StatCross", Stat,
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_cross(tips, mapping = aes(x = smoker, y = sex))
-#' ggally_cross(tips, mapping = aes(x = day, y = time))
+#' p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex)))
+#' p_(ggally_cross(tips, mapping = aes(x = day, y = time)))
 #'
 #' # Custom max size
-#' ggally_cross(tips, mapping = aes(x = smoker, y = sex)) +
-#'   scale_size_area(max_size = 40)
+#' p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex)) +
+#'   scale_size_area(max_size = 40))
 #'
 #' # Custom fill
-#' ggally_cross(tips, mapping = aes(x = smoker, y = sex), fill = "red")
+#' p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex), fill = "red"))
 #'
 #' # Custom shape
-#' ggally_cross(tips, mapping = aes(x = smoker, y = sex), shape = 21)
+#' p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex), shape = 21))
 #'
 #' # Fill squares according to standardized residuals
 #' d <- as.data.frame(Titanic)
-#' ggally_cross(
+#' p_(ggally_cross(
 #'   d,
 #'   mapping = aes(x = Class, y = Survived, weight = Freq, fill = after_stat(stdres))
 #' ) +
-#'   scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE)
+#'   scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE))
 #'
 #' # Add labels
-#' ggally_cross(
+#' p_(ggally_cross(
 #'   tips,
 #'   mapping = aes(
 #'     x = smoker, y = sex, colour = smoker,
 #'     label = scales::percent(after_stat(prop))
 #'   )
-#' )
+#' ))
 #'
 #' # Customize labels' appearance and same size for all squares
-#' ggally_cross(
+#' p_(ggally_cross(
 #'   tips,
 #'   mapping = aes(
 #'     x = smoker, y = sex,
@@ -211,7 +217,7 @@ StatCross <- ggproto("StatCross", Stat,
 #'   size = 40, # fix value for points size
 #'   fill = "darkblue",
 #'   geom_text_args = list(colour = "white", fontface = "bold", size = 6)
-#' )
+#' ))
 ggally_cross <- function(data, mapping, ..., scale_max_size = 20, geom_text_args = NULL){
   mapping <- remove_color_unless_equal(mapping, to = c("x", "y"))
   mapping <- mapping_color_to_fill(mapping)
@@ -265,32 +271,38 @@ ggally_cross <- function(data, mapping, ..., scale_max_size = 20, geom_text_args
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_table(tips, mapping = aes(x = smoker, y = sex))
-#' ggally_table(tips, mapping = aes(x = day, y = time))
-#' ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = smoker))
+#' p_(ggally_table(tips, mapping = aes(x = smoker, y = sex)))
+#' p_(ggally_table(tips, mapping = aes(x = day, y = time)))
+#' p_(ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = smoker)))
 #'
 #' # colour is kept only if equal to x or y
-#' ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = day))
+#' p_(ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = day)))
 #'
 #' # diagonal version
-#' ggally_tableDiag(tips, mapping = aes(x = smoker))
+#' p_(ggally_tableDiag(tips, mapping = aes(x = smoker)))
 #'
 #' # custom label size and color
-#' ggally_table(tips, mapping = aes(x = smoker, y = sex), size = 16, color = "red")
+#' p_(ggally_table(tips, mapping = aes(x = smoker, y = sex), size = 16, color = "red"))
 #'
 #' # display column proportions
-#' ggally_table(tips, mapping = aes(x = day, y = sex, label = scales::percent(after_stat(col.prop))))
+#' p_(ggally_table(
+#'   tips,
+#'   mapping = aes(x = day, y = sex, label = scales::percent(after_stat(col.prop)))
+#' ))
 #'
 #' # draw table cells
-#' ggally_table(
+#' p_(ggally_table(
 #'   tips,
 #'   mapping = aes(x = smoker, y = sex),
 #'   geom_tile_args = list(colour = "black", fill = "white")
-#' )
+#' ))
 #'
 #' # Use standardized residuals to fill table cells
-#' ggally_table(
+#' p_(ggally_table(
 #'   as.data.frame(Titanic),
 #'   mapping = aes(
 #'     x = Class, y = Survived, weight = Freq,
@@ -299,7 +311,7 @@ ggally_cross <- function(data, mapping, ..., scale_max_size = 20, geom_text_args
 #'   ),
 #'   geom_tile_args = list(colour = "black")
 #' ) +
-#' scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE)
+#' scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE))
 ggally_table <- function(data, mapping, keep.zero.cells = FALSE, ..., geom_tile_args = NULL){
   mapping <- remove_color_unless_equal(mapping, to = c("x", "y"))
 
@@ -347,29 +359,30 @@ ggally_tableDiag <- function(data, mapping, keep.zero.cells = FALSE, ..., geom_t
 #' @param geom_tile_args other arguments passed to \code{\link[ggplot2]{geom_tile}(...)}
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
 #'
 #' # differences with ggally_table()
-#' ggally_table(tips, mapping = aes(x = day, y = time))
-#' ggally_crosstable(tips, mapping = aes(x = day, y = time))
+#' p_(ggally_table(tips, mapping = aes(x = day, y = time)))
+#' p_(ggally_crosstable(tips, mapping = aes(x = day, y = time)))
 #'
 #' # display column proportions
-#' ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "col.prop")
+#' p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "col.prop"))
 #'
 #' # display row proportions
-#' ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "row.prop")
+#' p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "row.prop"))
 #'
 #' # change size of text
-#' ggally_crosstable(tips, mapping = aes(x = day, y = sex), size = 8)
+#' p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), size = 8))
 #'
 #' # fill cells with standardized residuals
-#' ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres")
+#' p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres"))
 #'
-#' \dontrun{
 #' # change scale for fill
-#' ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres") +
-#'   scale_fill_steps2(breaks = c(-2, 0, 2), show.limits = TRUE)
-#' }
+#' p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres") +
+#'   scale_fill_steps2(breaks = c(-2, 0, 2), show.limits = TRUE))
 ggally_crosstable <- function(
   data,
   mapping,
diff --git a/R/stat_prop.R b/R/stat_prop.R
index 8ce0f3c4b..f53a7ed6c 100644
--- a/R/stat_prop.R
+++ b/R/stat_prop.R
@@ -22,6 +22,8 @@
 #' @author Joseph Larmarange
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
 #'
 #' d <- as.data.frame(Titanic)
 #'
@@ -29,26 +31,25 @@
 #'   aes(x = Class, fill = Survived, weight = Freq, by = Class) +
 #'   geom_bar(position = "fill") +
 #'   geom_text(stat = "prop", position = position_fill(.5))
-#' p
-#' p + facet_grid(~ Sex)
+#' p_(p)
+#' p_(p + facet_grid(~ Sex))
 #'
-#' ggplot(d) +
+#' p_(ggplot(d) +
 #'   aes(x = Class, fill = Survived, weight = Freq) +
 #'   geom_bar(position = "dodge") +
 #'   geom_text(
 #'     aes(by = Survived), stat = "prop",
 #'     position = position_dodge(0.9), vjust = "bottom"
-#'  )
+#'  ))
 #'
-#' ggplot(d) +
+#' p_(ggplot(d) +
 #'   aes(x = Class, fill = Survived, weight = Freq, by = 1) +
 #'   geom_bar() +
 #'   geom_text(
 #'     aes(label = scales::percent(after_stat(prop), accuracy = 1)),
 #'     stat = "prop",
 #'     position = position_stack(.5)
-#'  )
-#'
+#'  ))
 stat_prop <- function(
   mapping = NULL,
   data = NULL,
@@ -142,32 +143,35 @@ StatProp <- ggproto("StatProp", Stat,
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
-#' ggally_colbar(tips, mapping = aes(x = smoker, y = sex))
-#' ggally_rowbar(tips, mapping = aes(x = smoker, y = sex))
+#' p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex)))
+#' p_(ggally_rowbar(tips, mapping = aes(x = smoker, y = sex)))
 #'
 #' # change labels' size
-#' ggally_colbar(tips, mapping = aes(x = smoker, y = sex), size = 8)
+#' p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex), size = 8))
 #'
 #' # change labels' colour and use bold
-#' ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
-#'               colour = "white", fontface = "bold")
+#' p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
+#'               colour = "white", fontface = "bold"))
 #'
 #' # custom bar width
-#' ggally_colbar(tips, mapping = aes(x = smoker, y = sex), geom_bar_args = list(width = .5))
+#' p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex), geom_bar_args = list(width = .5)))
 #'
 #' # change format of labels
-#' ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
-#'               label_format = scales::label_percent(accuracy = .01, decimal.mark = ","))
+#' p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
+#'               label_format = scales::label_percent(accuracy = .01, decimal.mark = ",")))
 #'
-#' ggduo(
+#' p_(ggduo(
 #'   data = as.data.frame(Titanic),
 #'   mapping = aes(weight = Freq),
 #'   columnsX = "Survived",
 #'   columnsY = c("Sex", "Class", "Age"),
 #'   types = list(discrete = "rowbar"),
 #'   legend = 1
-#' )
+#' ))
 ggally_colbar <- function(
   data,
   mapping,
diff --git a/R/stat_weighted_mean.R b/R/stat_weighted_mean.R
index 7b9a83245..0b7a4ad71 100644
--- a/R/stat_weighted_mean.R
+++ b/R/stat_weighted_mean.R
@@ -14,41 +14,44 @@
 #' @inheritParams ggplot2::stat_bin
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
 #'
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = day, y = total_bill) +
-#'   geom_point()
+#'   geom_point())
 #'
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = day, y = total_bill) +
-#'   stat_weighted_mean()
+#'   stat_weighted_mean())
 #'
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = day, y = total_bill, group = 1) +
-#'   stat_weighted_mean(geom = "line")
+#'   stat_weighted_mean(geom = "line"))
 #'
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = day, y = total_bill, colour = sex, group = sex) +
-#'   stat_weighted_mean(geom = "line")
+#'   stat_weighted_mean(geom = "line"))
 #'
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = day, y = total_bill, fill = sex) +
-#'   stat_weighted_mean(geom = "bar", position = "dodge")
+#'   stat_weighted_mean(geom = "bar", position = "dodge"))
 #'
 #' # computing a proportion on the fly
-#' ggplot(tips) +
+#' p_(ggplot(tips) +
 #'   aes(x = day, y = as.integer(smoker == "Yes"), fill = sex) +
 #'   stat_weighted_mean(geom = "bar", position = "dodge") +
-#'   scale_y_continuous(labels = scales::percent)
+#'   scale_y_continuous(labels = scales::percent))
 #'
 #' # taking into account some weights
 #' d <- as.data.frame(Titanic)
-#' ggplot(d) +
+#' p_(ggplot(d) +
 #'   aes(x = Class, y = as.integer(Survived == "Yes"), weight = Freq, fill = Sex) +
 #'   geom_bar(stat = "weighted_mean", position = "dodge") +
 #'   scale_y_continuous(labels = scales::percent) +
-#'   labs(y = "Survived")
+#'   labs(y = "Survived"))
 #'
 #'
 #' \dontrun{
@@ -147,37 +150,39 @@ StatWeightedMean <- ggproto(
 #' @keywords hplot
 #' @export
 #' @examples
+#' # Small function to display plots only if it's interactive
+#' p_ <- GGally::print_if_interactive
+#'
 #' data(tips, package = "reshape")
 #' tips_f <- tips
 #' tips_f$day <- factor(tips$day, c("Thur", "Fri", "Sat", "Sun"))
 #'
 #' # Numeric variable
-#' ggally_trends(tips_f, mapping = aes(x = day, y = total_bill))
-#' ggally_trends(tips_f, mapping = aes(x = day, y = total_bill, colour = time))
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = total_bill)))
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = total_bill, colour = time)))
 #'
 #' # Binary variable
-#' ggally_trends(tips_f, mapping = aes(x = day, y = smoker))
-#' ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex))
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker)))
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex)))
 #'
 #' # Discrete variable with 3 or more categories
-#' ggally_trends(tips_f, mapping = aes(x = smoker, y = day))
-#' ggally_trends(tips_f, mapping = aes(x = smoker, y = day, color = sex))
+#' p_(ggally_trends(tips_f, mapping = aes(x = smoker, y = day)))
+#' p_(ggally_trends(tips_f, mapping = aes(x = smoker, y = day, color = sex)))
 #'
 #' # Include zero on Y axis
-#' ggally_trends(tips_f, mapping = aes(x = day, y = total_bill), include_zero = TRUE)
-#' ggally_trends(tips_f, mapping = aes(x = day, y = smoker), include_zero = TRUE)
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = total_bill), include_zero = TRUE))
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker), include_zero = TRUE))
 #'
 #' # Change line size
-#' ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex), size = 3)
+#' p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex), size = 3))
 #'
 #' # Define weights with the appropriate aesthetic
 #' d <- as.data.frame(Titanic)
-#' ggally_trends(
+#' p_(ggally_trends(
 #'   d,
 #'   mapping = aes(x = Class, y = Survived, weight = Freq, color = Sex),
 #'   include_zero = TRUE
-#' )
-#'
+#' ))
 ggally_trends <- function(
   data,
   mapping,
diff --git a/R/vig_ggally.R b/R/vig_ggally.R
index d05df9715..a7513a540 100644
--- a/R/vig_ggally.R
+++ b/R/vig_ggally.R
@@ -7,11 +7,12 @@
 #' @param name Vignette name to open. If no name is provided, the vignette index will be opened
 #' @export
 #' @examples
+#' \donttest{
 #' # View `ggnostic` vignette
 #' vig_ggally("ggnostic")
 #'
 #' # View all vignettes by GGally
-#' vig_ggally()
+#' vig_ggally()}
 vig_ggally <- function(name) {
 
   vig_url <-
diff --git a/man/getPlot.Rd b/man/getPlot.Rd
index 2a1f4dbf0..f2bceed00 100644
--- a/man/getPlot.Rd
+++ b/man/getPlot.Rd
@@ -22,9 +22,12 @@ getPlot(pm, i, j)
 Retrieves the ggplot object at the desired location.
 }
 \examples{
- data(tips, package = "reshape")
- plotMatrix2 <- ggpairs(tips[, 3:2], upper = list(combo = "denstrip"))
- plotMatrix2[1, 2]
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+plotMatrix2 <- ggpairs(tips[, 3:2], upper = list(combo = "denstrip"))
+p_(plotMatrix2[1, 2])
 }
 \seealso{
 \code{\link{putPlot}}
diff --git a/man/ggally_autopoint.Rd b/man/ggally_autopoint.Rd
index 5b6394862..894da16fd 100644
--- a/man/ggally_autopoint.Rd
+++ b/man/ggally_autopoint.Rd
@@ -21,22 +21,23 @@ Make scatterplots compatible with both continuous and categorical variables
 using \code{\link[ggforce]{geom_autopoint}} from package \pkg{ggforce}.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_autopoint(tips, mapping = aes(x = tip, y = total_bill))
-ggally_autopoint(tips, mapping = aes(x = tip, y = sex))
-ggally_autopoint(tips, mapping = aes(x = smoker, y = sex))
-ggally_autopoint(tips, mapping = aes(x = smoker, y = sex, color = day))
-ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), size = 8)
-ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), alpha = .9)
+p_(ggally_autopoint(tips, mapping = aes(x = tip, y = total_bill)))
+p_(ggally_autopoint(tips, mapping = aes(x = tip, y = sex)))
+p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex)))
+p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex, color = day)))
+p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), size = 8))
+p_(ggally_autopoint(tips, mapping = aes(x = smoker, y = sex), alpha = .9))
 
-\dontrun{
-ggpairs(
+p_(ggpairs(
   tips,
   mapping = aes(colour = sex),
   upper = list(discrete = "autopoint", combo = "autopoint", continuous = "autopoint"),
   diag = list(discrete = "autopointDiag", continuous = "autopointDiag")
-)
-}
+))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggally_barDiag.Rd b/man/ggally_barDiag.Rd
index 263c75246..61bec4edb 100644
--- a/man/ggally_barDiag.Rd
+++ b/man/ggally_barDiag.Rd
@@ -19,9 +19,12 @@ ggally_barDiag(data, mapping, ..., rescale = FALSE)
 Displays a bar plot for the diagonal of a \code{\link{ggpairs}} plot matrix.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_barDiag(tips, mapping = ggplot2::aes(x = day))
-ggally_barDiag(tips, mapping = ggplot2::aes(x = tip), binwidth = 0.25)
+p_(ggally_barDiag(tips, mapping = ggplot2::aes(x = day)))
+p_(ggally_barDiag(tips, mapping = ggplot2::aes(x = tip), binwidth = 0.25))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_box.Rd b/man/ggally_box.Rd
index 7d5bb08f0..d743ba281 100644
--- a/man/ggally_box.Rd
+++ b/man/ggally_box.Rd
@@ -20,16 +20,19 @@ ggally_box_no_facet(data, mapping, ...)
 Make a box plot with a given data set. \code{ggally_box_no_facet} will be a single panel plot, while \code{ggally_box} will be a faceted plot
 }
 \examples{
- data(tips, package = "reshape")
- ggally_box(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
- ggally_box(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex"))
- ggally_box(
-   tips,
-   mapping        = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex"),
-   outlier.colour = "red",
-   outlier.shape  = 13,
-   outlier.size   = 8
- )
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_box(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+p_(ggally_box(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex")))
+p_(ggally_box(
+  tips,
+  mapping        = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex"),
+  outlier.colour = "red",
+  outlier.shape  = 13,
+  outlier.size   = 8
+))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_colbar.Rd b/man/ggally_colbar.Rd
index 386f9b75b..7b8de08d0 100644
--- a/man/ggally_colbar.Rd
+++ b/man/ggally_colbar.Rd
@@ -44,32 +44,35 @@ ggally_rowbar(
 Plot column or row percentage using bar plots.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_colbar(tips, mapping = aes(x = smoker, y = sex))
-ggally_rowbar(tips, mapping = aes(x = smoker, y = sex))
+p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex)))
+p_(ggally_rowbar(tips, mapping = aes(x = smoker, y = sex)))
 
 # change labels' size
-ggally_colbar(tips, mapping = aes(x = smoker, y = sex), size = 8)
+p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex), size = 8))
 
 # change labels' colour and use bold
-ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
-              colour = "white", fontface = "bold")
+p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
+              colour = "white", fontface = "bold"))
 
 # custom bar width
-ggally_colbar(tips, mapping = aes(x = smoker, y = sex), geom_bar_args = list(width = .5))
+p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex), geom_bar_args = list(width = .5)))
 
 # change format of labels
-ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
-              label_format = scales::label_percent(accuracy = .01, decimal.mark = ","))
+p_(ggally_colbar(tips, mapping = aes(x = smoker, y = sex),
+              label_format = scales::label_percent(accuracy = .01, decimal.mark = ",")))
 
-ggduo(
+p_(ggduo(
   data = as.data.frame(Titanic),
   mapping = aes(weight = Freq),
   columnsX = "Survived",
   columnsY = c("Sex", "Class", "Age"),
   types = list(discrete = "rowbar"),
   legend = 1
-)
+))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggally_cor.Rd b/man/ggally_cor.Rd
index 496ec2a56..97ab6e318 100644
--- a/man/ggally_cor.Rd
+++ b/man/ggally_cor.Rd
@@ -61,28 +61,31 @@ ggally_cor(
 Estimate correlation from the given data. If a color variable is supplied, the correlation will also be calculated per group.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_cor(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
- # display with grid
- ggally_cor(
-   tips,
-   mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
-   display_grid = TRUE
- )
- # change text attributes
- ggally_cor(
-   tips,
-   mapping = ggplot2::aes(x = total_bill, y = tip),
-   size = 15,
-   colour = I("red"),
-   title = "Correlation"
- )
- # split by a variable
- ggally_cor(
-   tips,
-   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
-   size = 5
- )
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_cor(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+# display with grid
+p_(ggally_cor(
+  tips,
+  mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
+  display_grid = TRUE
+))
+# change text attributes
+p_(ggally_cor(
+  tips,
+  mapping = ggplot2::aes(x = total_bill, y = tip),
+  size = 15,
+  colour = I("red"),
+  title = "Correlation"
+))
+# split by a variable
+p_(ggally_cor(
+  tips,
+  mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
+  size = 5
+))
 }
 \seealso{
 \code{\link{ggally_statistic}}, \code{\link{ggally_cor_v1_5}}
diff --git a/man/ggally_cor_v1_5.Rd b/man/ggally_cor_v1_5.Rd
index 33afb70b8..e25bd8c7f 100644
--- a/man/ggally_cor_v1_5.Rd
+++ b/man/ggally_cor_v1_5.Rd
@@ -45,27 +45,33 @@ ggally_cor_v1_5(
 Estimate correlation from the given data.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_cor_v1_5(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
- # display with no grid
- ggally_cor_v1_5(
-   tips,
-   mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
-   displayGrid = FALSE
- )
- # change text attributes
- ggally_cor_v1_5(
-   tips,
-   mapping = ggplot2::aes(x = total_bill, y = tip),
-   size = 15,
-   colour = I("red")
- )
- # split by a variable
- ggally_cor_v1_5(
-   tips,
-   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
-   size = 5
- )
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_cor_v1_5(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+
+# display with no grid
+p_(ggally_cor_v1_5(
+  tips,
+  mapping = ggplot2::aes_string(x = "total_bill", y = "tip"),
+  displayGrid = FALSE
+))
+
+# change text attributes
+p_(ggally_cor_v1_5(
+  tips,
+  mapping = ggplot2::aes(x = total_bill, y = tip),
+  size = 15,
+  colour = I("red")
+))
+
+# split by a variable
+p_(ggally_cor_v1_5(
+  tips,
+  mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"),
+  size = 5
+))
 }
 \seealso{
 \code{\link{ggally_cor}}
diff --git a/man/ggally_count.Rd b/man/ggally_count.Rd
index 912bf5ab1..a360a2672 100644
--- a/man/ggally_count.Rd
+++ b/man/ggally_count.Rd
@@ -27,22 +27,27 @@ with proportional areas.
 You can adjust the size of rectangles with the \code{x.width} argument.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex))
-ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex, fill = day))
+p_(ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex)))
+p_(ggally_count(tips, mapping = ggplot2::aes(x = smoker, y = sex, fill = day)))
 
-ggally_count(
+p_(ggally_count(
   as.data.frame(Titanic),
   mapping = ggplot2::aes(x = Class, y = Survived, weight = Freq)
-)
-ggally_count(
+))
+p_(ggally_count(
   as.data.frame(Titanic),
   mapping = ggplot2::aes(x = Class, y = Survived, weight = Freq),
   x.width = 0.5
-)
+))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 
-ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker))
-ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker, fill = sex))
+p_(ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker)))
+p_(ggally_countDiag(tips, mapping = ggplot2::aes(x = smoker, fill = sex)))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggally_cross.Rd b/man/ggally_cross.Rd
index 1b35eda30..8e7520b67 100644
--- a/man/ggally_cross.Rd
+++ b/man/ggally_cross.Rd
@@ -24,39 +24,42 @@ statistics computed by \code{\link{stat_cross}}. Labels could also
 be added (see examples).
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_cross(tips, mapping = aes(x = smoker, y = sex))
-ggally_cross(tips, mapping = aes(x = day, y = time))
+p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex)))
+p_(ggally_cross(tips, mapping = aes(x = day, y = time)))
 
 # Custom max size
-ggally_cross(tips, mapping = aes(x = smoker, y = sex)) +
-  scale_size_area(max_size = 40)
+p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex)) +
+  scale_size_area(max_size = 40))
 
 # Custom fill
-ggally_cross(tips, mapping = aes(x = smoker, y = sex), fill = "red")
+p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex), fill = "red"))
 
 # Custom shape
-ggally_cross(tips, mapping = aes(x = smoker, y = sex), shape = 21)
+p_(ggally_cross(tips, mapping = aes(x = smoker, y = sex), shape = 21))
 
 # Fill squares according to standardized residuals
 d <- as.data.frame(Titanic)
-ggally_cross(
+p_(ggally_cross(
   d,
   mapping = aes(x = Class, y = Survived, weight = Freq, fill = after_stat(stdres))
 ) +
-  scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE)
+  scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE))
 
 # Add labels
-ggally_cross(
+p_(ggally_cross(
   tips,
   mapping = aes(
     x = smoker, y = sex, colour = smoker,
     label = scales::percent(after_stat(prop))
   )
-)
+))
 
 # Customize labels' appearance and same size for all squares
-ggally_cross(
+p_(ggally_cross(
   tips,
   mapping = aes(
     x = smoker, y = sex,
@@ -66,7 +69,7 @@ ggally_cross(
   size = 40, # fix value for points size
   fill = "darkblue",
   geom_text_args = list(colour = "white", fontface = "bold", size = 6)
-)
+))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggally_crosstable.Rd b/man/ggally_crosstable.Rd
index c85dcefbc..3a28c2442 100644
--- a/man/ggally_crosstable.Rd
+++ b/man/ggally_crosstable.Rd
@@ -31,27 +31,28 @@ ggally_crosstable(
 \code{ggally_crosstable} is a variation of \code{\link{ggally_table}} with few modifications: (i) table cells are drawn; (ii) x and y axis are not expanded (and therefore are not aligned with other \code{ggally_*} plots); (iii) content and fill of cells can be easily controlled with dedicated arguments.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
 
 # differences with ggally_table()
-ggally_table(tips, mapping = aes(x = day, y = time))
-ggally_crosstable(tips, mapping = aes(x = day, y = time))
+p_(ggally_table(tips, mapping = aes(x = day, y = time)))
+p_(ggally_crosstable(tips, mapping = aes(x = day, y = time)))
 
 # display column proportions
-ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "col.prop")
+p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "col.prop"))
 
 # display row proportions
-ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "row.prop")
+p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), cells = "row.prop"))
 
 # change size of text
-ggally_crosstable(tips, mapping = aes(x = day, y = sex), size = 8)
+p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), size = 8))
 
 # fill cells with standardized residuals
-ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres")
+p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres"))
 
-\dontrun{
 # change scale for fill
-ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres") +
-  scale_fill_steps2(breaks = c(-2, 0, 2), show.limits = TRUE)
-}
+p_(ggally_crosstable(tips, mapping = aes(x = day, y = sex), fill = "stdres") +
+  scale_fill_steps2(breaks = c(-2, 0, 2), show.limits = TRUE))
 }
diff --git a/man/ggally_density.Rd b/man/ggally_density.Rd
index d885008d3..ca20999d2 100644
--- a/man/ggally_density.Rd
+++ b/man/ggally_density.Rd
@@ -20,17 +20,20 @@ Make a 2D density plot from a given data.
 The aesthetic "fill" determines whether or not \code{stat_density2d} (filled) or \code{geom_density2d} (lines) is used.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_density(tips, mapping = ggplot2::aes(x = total_bill, y = tip))
- ggally_density(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
- ggally_density(
-   tips,
-   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
- )
- ggally_density(
-   tips,
-   mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
- ) + ggplot2::scale_fill_gradient(breaks = c(0.05, 0.1, 0.15, 0.2))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_density(tips, mapping = ggplot2::aes(x = total_bill, y = tip)))
+p_(ggally_density(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+p_(ggally_density(
+  tips,
+  mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
+))
+p_(ggally_density(
+  tips,
+  mapping = ggplot2::aes_string(x = "total_bill", y = "tip", fill = "..level..")
+) + ggplot2::scale_fill_gradient(breaks = c(0.05, 0.1, 0.15, 0.2)))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_densityDiag.Rd b/man/ggally_densityDiag.Rd
index cbedf583c..0f8d975af 100644
--- a/man/ggally_densityDiag.Rd
+++ b/man/ggally_densityDiag.Rd
@@ -19,9 +19,12 @@ ggally_densityDiag(data, mapping, ..., rescale = FALSE)
 Displays a density plot for the diagonal of a \code{\link{ggpairs}} plot matrix.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill))
- ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill, color = day))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill)))
+p_(ggally_densityDiag(tips, mapping = ggplot2::aes(x = total_bill, color = day)))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_denstrip.Rd b/man/ggally_denstrip.Rd
index 8c3023fdd..48b5ca2f9 100644
--- a/man/ggally_denstrip.Rd
+++ b/man/ggally_denstrip.Rd
@@ -17,13 +17,16 @@ ggally_denstrip(data, mapping, ...)
 Displays a Tile Plot as densely as possible.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_denstrip(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
- ggally_denstrip(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex"))
- ggally_denstrip(
-   tips,
-   mapping = ggplot2::aes_string(x = "sex", y = "tip", binwidth = "0.2")
- ) + ggplot2::scale_fill_gradient(low = "grey80", high = "black")
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_denstrip(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+p_(ggally_denstrip(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex")))
+p_(ggally_denstrip(
+  tips,
+  mapping = ggplot2::aes_string(x = "sex", y = "tip", binwidth = "0.2")
+) + ggplot2::scale_fill_gradient(low = "grey80", high = "black"))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_diagAxis.Rd b/man/ggally_diagAxis.Rd
index 93b533f39..c3a38a8e0 100644
--- a/man/ggally_diagAxis.Rd
+++ b/man/ggally_diagAxis.Rd
@@ -42,9 +42,12 @@ ggally_diagAxis(
 This function is used when \code{axisLabels == "internal"}.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_diagAxis(tips, ggplot2::aes(x=tip))
- ggally_diagAxis(tips, ggplot2::aes(x=sex))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_diagAxis(tips, ggplot2::aes(x=tip)))
+p_(ggally_diagAxis(tips, ggplot2::aes(x=sex)))
 }
 \author{
 Jason Crowley and Barret Schloerke
diff --git a/man/ggally_dot.Rd b/man/ggally_dot.Rd
index 7044d0ac7..1693e45f0 100644
--- a/man/ggally_dot.Rd
+++ b/man/ggally_dot.Rd
@@ -20,17 +20,20 @@ ggally_dot_no_facet(data, mapping, ...)
 Add jittering with the box plot. \code{ggally_dot_no_facet} will be a single panel plot, while \code{ggally_dot} will be a faceted plot
 }
 \examples{
- data(tips, package = "reshape")
- ggally_dot(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
- ggally_dot(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex"))
- ggally_dot(
-   tips,
-   mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
- )
- ggally_dot(
-   tips,
-   mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex", shape = "sex")
- ) + ggplot2::scale_shape(solid=FALSE)
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_dot(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+p_(ggally_dot(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "sex")))
+p_(ggally_dot(
+  tips,
+  mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
+))
+p_(ggally_dot(
+  tips,
+  mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex", shape = "sex")
+) + ggplot2::scale_shape(solid=FALSE))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_dot_and_box.Rd b/man/ggally_dot_and_box.Rd
index 9ac823f25..bfedf0bd9 100644
--- a/man/ggally_dot_and_box.Rd
+++ b/man/ggally_dot_and_box.Rd
@@ -19,17 +19,20 @@ ggally_dot_and_box(data, mapping, ..., boxPlot = TRUE)
 Place box plots or dot plots on the graph
 }
 \examples{
- data(tips, package = "reshape")
- ggally_dot_and_box(
-   tips,
-   mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
-   boxPlot = TRUE
- )
- ggally_dot_and_box(
-   tips,
-   mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
-   boxPlot = FALSE
- )
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_dot_and_box(
+  tips,
+  mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
+  boxPlot = TRUE
+))
+p_(ggally_dot_and_box(
+  tips,
+  mapping = ggplot2::aes(x = total_bill, y = sex, color = sex),
+  boxPlot = FALSE
+))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_facetbar.Rd b/man/ggally_facetbar.Rd
index 80962a879..cef320886 100644
--- a/man/ggally_facetbar.Rd
+++ b/man/ggally_facetbar.Rd
@@ -17,9 +17,12 @@ ggally_facetbar(data, mapping, ...)
 X variables are plotted using \code{geom_bar} and are faceted by the Y variable.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_facetbar(tips, ggplot2::aes(x = sex, y = smoker, fill = time))
- ggally_facetbar(tips, ggplot2::aes(x = smoker, y = sex, fill = time))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_facetbar(tips, ggplot2::aes(x = sex, y = smoker, fill = time)))
+p_(ggally_facetbar(tips, ggplot2::aes(x = smoker, y = sex, fill = time)))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_facetdensity.Rd b/man/ggally_facetdensity.Rd
index 1966df305..3228a510d 100644
--- a/man/ggally_facetdensity.Rd
+++ b/man/ggally_facetdensity.Rd
@@ -17,12 +17,15 @@ ggally_facetdensity(data, mapping, ...)
 Make density plots by displaying subsets of the data in different panels.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_facetdensity(tips, mapping = ggplot2::aes(x = total_bill, y = sex))
- ggally_facetdensity(
-   tips,
-   mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
- )
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_facetdensity(tips, mapping = ggplot2::aes(x = total_bill, y = sex)))
+p_(ggally_facetdensity(
+  tips,
+  mapping = ggplot2::aes_string(y = "total_bill", x = "sex", color = "sex")
+))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_facethist.Rd b/man/ggally_facethist.Rd
index 1c3605170..3e8903a74 100644
--- a/man/ggally_facethist.Rd
+++ b/man/ggally_facethist.Rd
@@ -17,9 +17,12 @@ ggally_facethist(data, mapping, ...)
 Display subsetted histograms of the data in different panels.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_facethist(tips, mapping = ggplot2::aes(x = tip, y = sex))
- ggally_facethist(tips, mapping = ggplot2::aes_string(x = "tip", y = "sex"), binwidth = 0.1)
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_facethist(tips, mapping = ggplot2::aes(x = tip, y = sex)))
+p_(ggally_facethist(tips, mapping = ggplot2::aes_string(x = "tip", y = "sex"), binwidth = 0.1))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_nostic_cooksd.Rd b/man/ggally_nostic_cooksd.Rd
index 81224702c..33a204c8e 100644
--- a/man/ggally_nostic_cooksd.Rd
+++ b/man/ggally_nostic_cooksd.Rd
@@ -31,8 +31,11 @@ A line is added at F_{p, n - p}(0.5) to display the general cutoff point for Coo
 Reference: Michael H. Kutner, Christopher J. Nachtsheim, John Neter, and William Li. Applied linear statistical models. The McGraw-Hill / Irwin series operations and decision sciences. McGraw-Hill Irwin, 2005, p. 403
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-ggally_nostic_cooksd(dt, ggplot2::aes(wt, .cooksd))
+p_(ggally_nostic_cooksd(dt, ggplot2::aes(wt, .cooksd)))
 }
 \seealso{
 \code{stats::\link[stats]{cooks.distance}}
diff --git a/man/ggally_nostic_hat.Rd b/man/ggally_nostic_hat.Rd
index acaf4d396..b347b5faa 100644
--- a/man/ggally_nostic_hat.Rd
+++ b/man/ggally_nostic_hat.Rd
@@ -44,8 +44,11 @@ A suggested "cutoff" line is added to the plot at a height of 2 * p / n and an e
 If either \code{linePosition} or \code{avgLinePosition} is \code{NULL}, the respective line will not be drawn.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-ggally_nostic_hat(dt, ggplot2::aes(wt, .hat))
+p_(ggally_nostic_hat(dt, ggplot2::aes(wt, .hat)))
 }
 \seealso{
 \code{stats::\link[stats]{influence}}
diff --git a/man/ggally_nostic_resid.Rd b/man/ggally_nostic_resid.Rd
index fea5f9391..a6d811f0d 100644
--- a/man/ggally_nostic_resid.Rd
+++ b/man/ggally_nostic_resid.Rd
@@ -46,8 +46,11 @@ ggally_nostic_resid(
 If non-null \code{pVal} and \code{sigma} values are given, confidence interval lines will be added to the plot at the specified \code{pVal} percentiles of a N(0, sigma) distribution.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-ggally_nostic_resid(dt, ggplot2::aes(wt, .resid))
+p_(ggally_nostic_resid(dt, ggplot2::aes(wt, .resid)))
 }
 \seealso{
 \code{stats::\link[stats]{residuals}}
diff --git a/man/ggally_nostic_se_fit.Rd b/man/ggally_nostic_se_fit.Rd
index c3af9c402..4ea776256 100644
--- a/man/ggally_nostic_se_fit.Rd
+++ b/man/ggally_nostic_se_fit.Rd
@@ -33,8 +33,11 @@ Since the se.fit is \code{TRUE} and scale is unset by default, the standard erro
 A base line of 0 is added to give reference to a perfect fit.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-ggally_nostic_se_fit(dt, ggplot2::aes(wt, .se.fit))
+p_(ggally_nostic_se_fit(dt, ggplot2::aes(wt, .se.fit)))
 }
 \seealso{
 \code{stats::\link[stats]{influence}}
diff --git a/man/ggally_nostic_sigma.Rd b/man/ggally_nostic_sigma.Rd
index 6623fafcc..824e4ebff 100644
--- a/man/ggally_nostic_sigma.Rd
+++ b/man/ggally_nostic_sigma.Rd
@@ -31,8 +31,11 @@ sigma: a vector whose i-th element contains the estimate of the residual standar
 A line is added to display the overall model's sigma value. This gives a baseline for comparison
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-ggally_nostic_sigma(dt, ggplot2::aes(wt, .sigma))
+p_(ggally_nostic_sigma(dt, ggplot2::aes(wt, .sigma)))
 }
 \seealso{
 \code{stats::\link[stats]{influence}}
diff --git a/man/ggally_nostic_std_resid.Rd b/man/ggally_nostic_std_resid.Rd
index 53a1c97d9..33e19b25d 100644
--- a/man/ggally_nostic_std_resid.Rd
+++ b/man/ggally_nostic_std_resid.Rd
@@ -18,8 +18,11 @@ ggally_nostic_std_resid(data, mapping, ..., sigma = 1)
 If non-null \code{pVal} and \code{sigma} values are given, confidence interval lines will be added to the plot at the specified \code{pVal} locations of a N(0, 1) distribution.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 dt <- broomify(stats::lm(mpg ~ wt + qsec + am, data = mtcars))
-ggally_nostic_std_resid(dt, ggplot2::aes(wt, .std.resid))
+p_(ggally_nostic_std_resid(dt, ggplot2::aes(wt, .std.resid)))
 }
 \seealso{
 \code{stats::\link[stats]{rstandard}}
diff --git a/man/ggally_points.Rd b/man/ggally_points.Rd
index 4759ef647..6c410f092 100644
--- a/man/ggally_points.Rd
+++ b/man/ggally_points.Rd
@@ -17,10 +17,13 @@ ggally_points(data, mapping, ...)
 Make a scatter plot with a given data set.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(mtcars)
-ggally_points(mtcars, mapping = ggplot2::aes(x = disp, y = hp))
-ggally_points(mtcars, mapping = ggplot2::aes_string(x = "disp", y = "hp"))
-ggally_points(
+p_(ggally_points(mtcars, mapping = ggplot2::aes(x = disp, y = hp)))
+p_(ggally_points(mtcars, mapping = ggplot2::aes_string(x = "disp", y = "hp")))
+p_(ggally_points(
   mtcars,
   mapping = ggplot2::aes_string(
     x     = "disp",
@@ -28,7 +31,7 @@ ggally_points(
     color = "as.factor(cyl)",
     size  = "gear"
   )
-)
+))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_ratio.Rd b/man/ggally_ratio.Rd
index 43c004733..d8eff8348 100644
--- a/man/ggally_ratio.Rd
+++ b/man/ggally_ratio.Rd
@@ -27,14 +27,17 @@ ggally_ratio(
 Plots the mosaic plot by using fluctuation.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_ratio(tips, ggplot2::aes(sex, day))
-ggally_ratio(tips, ggplot2::aes(sex, day)) + ggplot2::coord_equal()
+p_(ggally_ratio(tips, ggplot2::aes(sex, day)))
+p_(ggally_ratio(tips, ggplot2::aes(sex, day)) + ggplot2::coord_equal())
 # only plot tiles greater or equal to 20 and scale to a max of 50
-ggally_ratio(
+p_(ggally_ratio(
   tips, ggplot2::aes(sex, day),
   floor = 20, ceiling = 50
-) + ggplot2::theme(aspect.ratio = 4/2)
+) + ggplot2::theme(aspect.ratio = 4/2))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_smooth.Rd b/man/ggally_smooth.Rd
index 03360c2a4..e4582e890 100644
--- a/man/ggally_smooth.Rd
+++ b/man/ggally_smooth.Rd
@@ -38,10 +38,13 @@ Add a smoothed condition mean with a given scatter plot.
 Y limits are reduced to match original Y range with the goal of keeping the Y axis the same across plots.
 }
 \examples{
- data(tips, package = "reshape")
- ggally_smooth(tips, mapping = ggplot2::aes(x = total_bill, y = tip))
- ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip"))
- ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex"))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(tips, package = "reshape")
+p_(ggally_smooth(tips, mapping = ggplot2::aes(x = total_bill, y = tip)))
+p_(ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip")))
+p_(ggally_smooth(tips, mapping = ggplot2::aes_string(x = "total_bill", y = "tip", color = "sex")))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_summarise_by.Rd b/man/ggally_summarise_by.Rd
index e483dde69..0835fe5b7 100644
--- a/man/ggally_summarise_by.Rd
+++ b/man/ggally_summarise_by.Rd
@@ -42,27 +42,32 @@ Display summary statistics of a continuous variable for each value of a discrete
 \code{mean_sd} computes mean and standard deviation.
 }
 \examples{
-data(tips, package = "reshape")
-ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day))
-ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 
-# colour is kept only if equal to the discrete variable
-ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = day))
-ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = sex))
-ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill, color = day))
+if (require(Hmisc)) {
+  data(tips, package = "reshape")
+  p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day)))
+  p_(ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill)))
 
-# custom text size
-ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), size = 6)
+  # colour is kept only if equal to the discrete variable
+  p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = day)))
+  p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day, color = sex)))
+  p_(ggally_summarise_by(tips, mapping = aes(x = day, y = total_bill, color = day)))
 
-# change statistic to display
-ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = mean_sd)
+  # custom text size
+  p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), size = 6))
 
-# custom stat function
-weighted_sum <- function(x, weights = NULL) {
-  if (is.null(weights)) weights <- 1
-  paste0("Total : ", round(sum(x * weights, na.rm = TRUE), digits = 1))
+  # change statistic to display
+  p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = mean_sd))
+
+  # custom stat function
+  weighted_sum <- function(x, weights = NULL) {
+    if (is.null(weights)) weights <- 1
+    paste0("Total : ", round(sum(x * weights, na.rm = TRUE), digits = 1))
+  }
+  p_(ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = weighted_sum))
 }
-ggally_summarise_by(tips, mapping = aes(x = total_bill, y = day), text_fn = weighted_sum)
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggally_table.Rd b/man/ggally_table.Rd
index aeb290366..5967c675f 100644
--- a/man/ggally_table.Rd
+++ b/man/ggally_table.Rd
@@ -41,32 +41,38 @@ The \strong{colour} aesthetic is taken into account only if equal to
   \strong{x} or \strong{y}.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggally_table(tips, mapping = aes(x = smoker, y = sex))
-ggally_table(tips, mapping = aes(x = day, y = time))
-ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = smoker))
+p_(ggally_table(tips, mapping = aes(x = smoker, y = sex)))
+p_(ggally_table(tips, mapping = aes(x = day, y = time)))
+p_(ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = smoker)))
 
 # colour is kept only if equal to x or y
-ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = day))
+p_(ggally_table(tips, mapping = aes(x = smoker, y = sex, colour = day)))
 
 # diagonal version
-ggally_tableDiag(tips, mapping = aes(x = smoker))
+p_(ggally_tableDiag(tips, mapping = aes(x = smoker)))
 
 # custom label size and color
-ggally_table(tips, mapping = aes(x = smoker, y = sex), size = 16, color = "red")
+p_(ggally_table(tips, mapping = aes(x = smoker, y = sex), size = 16, color = "red"))
 
 # display column proportions
-ggally_table(tips, mapping = aes(x = day, y = sex, label = scales::percent(after_stat(col.prop))))
+p_(ggally_table(
+  tips,
+  mapping = aes(x = day, y = sex, label = scales::percent(after_stat(col.prop)))
+))
 
 # draw table cells
-ggally_table(
+p_(ggally_table(
   tips,
   mapping = aes(x = smoker, y = sex),
   geom_tile_args = list(colour = "black", fill = "white")
-)
+))
 
 # Use standardized residuals to fill table cells
-ggally_table(
+p_(ggally_table(
   as.data.frame(Titanic),
   mapping = aes(
     x = Class, y = Survived, weight = Freq,
@@ -75,7 +81,7 @@ ggally_table(
   ),
   geom_tile_args = list(colour = "black")
 ) +
-scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE)
+scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggally_text.Rd b/man/ggally_text.Rd
index 57dada971..22a55ae2b 100644
--- a/man/ggally_text.Rd
+++ b/man/ggally_text.Rd
@@ -33,8 +33,11 @@ ggally_text(
 Plot text for a plot.
 }
 \examples{
-ggally_text("Example 1")
-ggally_text("Example\nTwo", mapping = ggplot2::aes(size = 15), color = I("red"))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+p_(ggally_text("Example 1"))
+p_(ggally_text("Example\nTwo", mapping = ggplot2::aes(size = 15), color = I("red")))
 }
 \author{
 Barret Schloerke
diff --git a/man/ggally_trends.Rd b/man/ggally_trends.Rd
index 8d90bd500..a73126639 100644
--- a/man/ggally_trends.Rd
+++ b/man/ggally_trends.Rd
@@ -21,37 +21,39 @@ For continuous y variables, plot the evolution of the mean.
 For binary y variables, plot the evolution of the proportion.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
 tips_f <- tips
 tips_f$day <- factor(tips$day, c("Thur", "Fri", "Sat", "Sun"))
 
 # Numeric variable
-ggally_trends(tips_f, mapping = aes(x = day, y = total_bill))
-ggally_trends(tips_f, mapping = aes(x = day, y = total_bill, colour = time))
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = total_bill)))
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = total_bill, colour = time)))
 
 # Binary variable
-ggally_trends(tips_f, mapping = aes(x = day, y = smoker))
-ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex))
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker)))
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex)))
 
 # Discrete variable with 3 or more categories
-ggally_trends(tips_f, mapping = aes(x = smoker, y = day))
-ggally_trends(tips_f, mapping = aes(x = smoker, y = day, color = sex))
+p_(ggally_trends(tips_f, mapping = aes(x = smoker, y = day)))
+p_(ggally_trends(tips_f, mapping = aes(x = smoker, y = day, color = sex)))
 
 # Include zero on Y axis
-ggally_trends(tips_f, mapping = aes(x = day, y = total_bill), include_zero = TRUE)
-ggally_trends(tips_f, mapping = aes(x = day, y = smoker), include_zero = TRUE)
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = total_bill), include_zero = TRUE))
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker), include_zero = TRUE))
 
 # Change line size
-ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex), size = 3)
+p_(ggally_trends(tips_f, mapping = aes(x = day, y = smoker, colour = sex), size = 3))
 
 # Define weights with the appropriate aesthetic
 d <- as.data.frame(Titanic)
-ggally_trends(
+p_(ggally_trends(
   d,
   mapping = aes(x = Class, y = Survived, weight = Freq, color = Sex),
   include_zero = TRUE
-)
-
+))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggbivariate.Rd b/man/ggbivariate.Rd
index 656dc74ec..5d3d0397e 100644
--- a/man/ggbivariate.Rd
+++ b/man/ggbivariate.Rd
@@ -38,23 +38,25 @@ weights (see examples)}
 an outcome variable with several potential explanatory variables.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
-ggbivariate(tips, "smoker", c("day", "time", "sex", "tip"))
+p_(ggbivariate(tips, "smoker", c("day", "time", "sex", "tip")))
 
-\dontrun{
 # Personalize plot title and legend title
-ggbivariate(
+p_(ggbivariate(
   tips, "smoker", c("day", "time", "sex", "tip"),
   title = "Custom title"
 ) +
-  labs(fill = "Smoker ?")
+  labs(fill = "Smoker ?"))
 
 # Customize fill colour scale
-ggbivariate(tips, "smoker", c("day", "time", "sex", "tip")) +
-  scale_fill_brewer(type = "qual")
+p_(ggbivariate(tips, "smoker", c("day", "time", "sex", "tip")) +
+  scale_fill_brewer(type = "qual"))
 
 # Customize labels
-ggbivariate(
+p_(ggbivariate(
   tips, "smoker", c("day", "time", "sex", "tip"),
   rowbar_args = list(
     colour = "white",
@@ -62,19 +64,18 @@ ggbivariate(
     fontface = "bold",
     label_format = scales::label_percent(accurary = 1)
   )
-)
+))
 
 # Choose the sub-plot from which get legend
-ggbivariate(tips, "smoker")
-ggbivariate(tips, "smoker", legend = 3)
+p_(ggbivariate(tips, "smoker"))
+p_(ggbivariate(tips, "smoker", legend = 3))
 
 # Use mapping to indicate weights
 d <- as.data.frame(Titanic)
-ggbivariate(d, "Survived", mapping = aes(weight = Freq))
+p_(ggbivariate(d, "Survived", mapping = aes(weight = Freq)))
 
 # outcome can be numerical
-ggbivariate(tips, outcome = "tip", title = "tip")
-}
+p_(ggbivariate(tips, outcome = "tip", title = "tip"))
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggcoef.Rd b/man/ggcoef.Rd
index dc6c8d2d0..c6bd578cc 100644
--- a/man/ggcoef.Rd
+++ b/man/ggcoef.Rd
@@ -66,9 +66,12 @@ if \code{x} is not a data frame)}
 Plot the coefficients of a model with \pkg{broom} and \pkg{ggplot2}.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 library(broom)
 reg <- lm(Sepal.Length ~ Sepal.Width + Petal.Length + Petal.Width, data = iris)
-ggcoef(reg)
+p_(ggcoef(reg))
 \donttest{d <- as.data.frame(Titanic)
 reg2 <- glm(Survived ~ Sex + Age + Class, family = binomial, data = d, weights = d$Freq)
 ggcoef(reg2, exponentiate = TRUE)
diff --git a/man/ggcorr.Rd b/man/ggcorr.Rd
index 564ed50ef..f8aa556eb 100644
--- a/man/ggcorr.Rd
+++ b/man/ggcorr.Rd
@@ -147,19 +147,22 @@ Recommended values for the \code{nbreaks} argument are \code{3} to
 supported by diverging ColorBrewer palettes.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 # Basketball statistics provided by Nathan Yau at Flowing Data.
 dt <- read.csv("http://datasets.flowingdata.com/ppg2008.csv")
 
 # Default output.
-ggcorr(dt[, -1])
+p_(ggcorr(dt[, -1]))
 
-# Labelled output, with coefficient transparency.
-ggcorr(dt[, -1],
+# Labeled output, with coefficient transparency.
+p_(ggcorr(dt[, -1],
        label = TRUE,
-       label_alpha = TRUE)
+       label_alpha = TRUE))
 
 # Custom options.
-ggcorr(
+p_(ggcorr(
   dt[, -1],
   name = expression(rho),
   geom = "circle",
@@ -170,13 +173,13 @@ ggcorr(
   nbreaks = 6,
   angle = -45,
   palette = "PuOr" # colorblind safe, photocopy-able
-)
+))
 
 # Supply your own correlation matrix
-ggcorr(
+p_(ggcorr(
   data = NULL,
   cor_matrix = cor(dt[, -1], use = "pairwise")
-)
+))
 }
 \seealso{
 \code{\link[stats]{cor}} and \code{corrplot} in the
diff --git a/man/ggduo.Rd b/man/ggduo.Rd
index e111ad5f3..718f303b6 100644
--- a/man/ggduo.Rd
+++ b/man/ggduo.Rd
@@ -130,7 +130,7 @@ If a function is supplied as an option, it should implement the function api of
      continuous = wrap("smooth_loess", alpha = 0.50, shape = "+")
    ),
    showStrips = FALSE
- );
+ )
 
  p_(pm)
 
diff --git a/man/gglegend.Rd b/man/gglegend.Rd
index 6a9be51d8..639c977e6 100644
--- a/man/gglegend.Rd
+++ b/man/gglegend.Rd
@@ -16,12 +16,15 @@ a function that when called with arguments will produce the legend of the plotti
 Plot only legend of plot function
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 # display regular plot
-ggally_points(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species))
+p_(ggally_points(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species)))
 
 # Make a function that will only print the legend
 points_legend <- gglegend(ggally_points)
-points_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species))
+p_(points_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species)))
 
 # produce the sample legend plot, but supply a string that 'wrap' understands
 same_points_legend <- gglegend("points")
@@ -32,7 +35,7 @@ identical(
 
 # Complicated examples
 custom_legend <- wrap(gglegend("points"), size = 6)
-custom_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species))
+p_(custom_legend(iris, ggplot2::aes(Sepal.Length, Sepal.Width, color = Species)))
 
 # Use within ggpairs
 pm <- ggpairs(
@@ -40,11 +43,11 @@ pm <- ggpairs(
   mapping = ggplot2::aes(color = Species),
   upper = list(continuous = gglegend("points"))
 )
-# pm
+p_(pm)
 
 # Place a legend in a specific location
 pm <- ggpairs(iris, 1:2, mapping = ggplot2::aes(color = Species))
 # Make the legend
 pm[1,2] <- points_legend(iris, ggplot2::aes(Sepal.Width, Sepal.Length, color = Species))
-pm
+p_(pm)
 }
diff --git a/man/ggmatrix.Rd b/man/ggmatrix.Rd
index d31cc37be..a5f17412f 100644
--- a/man/ggmatrix.Rd
+++ b/man/ggmatrix.Rd
@@ -66,7 +66,7 @@ Now that the \code{\link{print.ggmatrix}} method uses a large \pkg{gtable} objec
 }
 
 \examples{
-# small function to display plots only if it's interactive
+# Small function to display plots only if it's interactive
 p_ <- GGally::print_if_interactive
 
 plotList <- list()
diff --git a/man/ggmatrix_location.Rd b/man/ggmatrix_location.Rd
index af24d9c65..567103609 100644
--- a/man/ggmatrix_location.Rd
+++ b/man/ggmatrix_location.Rd
@@ -74,5 +74,4 @@ locs
 
 # Use the output of a prior ggmatrix_location
 ggmatrix_location(pm, location = locs)
-
 }
diff --git a/man/ggnet.Rd b/man/ggnet.Rd
index a0820d992..ef25384de 100644
--- a/man/ggnet.Rd
+++ b/man/ggnet.Rd
@@ -205,6 +205,9 @@ but will be unweighted. To compute weighted network measures, see the
 \code{tnet} package by Tore Opsahl (\code{help("tnet", package = "tnet")}).
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 library(network)
 
 # random adjacency matrix
@@ -229,10 +232,10 @@ g
 # color palette
 p <- c("a" = "steelblue", "b" = "forestgreen", "c" = "tomato")
 
-ggnet(n, node.group = g, node.color = p, label = TRUE, color = "white")
+p_(ggnet(n, node.group = g, node.color = p, label = TRUE, color = "white"))
 
 # edge arrows on a directed network
-ggnet(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10)
+p_(ggnet(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10))
 }
 \seealso{
 \code{\link{ggnet2}} in this package,
diff --git a/man/ggnet2.Rd b/man/ggnet2.Rd
index 23fcc4268..2da339861 100644
--- a/man/ggnet2.Rd
+++ b/man/ggnet2.Rd
@@ -293,6 +293,9 @@ The nodes of bipartite networks can be mapped to their mode by passing the
 \code{"event"}.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 library(network)
 
 # random adjacency matrix
@@ -308,42 +311,42 @@ m
 n <- network::network(m, directed = FALSE)
 n
 
-ggnet2(n, label = TRUE)
-ggnet2(n, label = TRUE, shape = 15)
-ggnet2(n, label = TRUE, shape = 15, color = "black", label.color = "white")
+p_(ggnet2(n, label = TRUE))
+p_(ggnet2(n, label = TRUE, shape = 15))
+p_(ggnet2(n, label = TRUE, shape = 15, color = "black", label.color = "white"))
 
 # add vertex attribute
 x = network.vertex.names(n)
 x = ifelse(x \%in\% c("a", "e", "i"), "vowel", "consonant")
 n \%v\% "phono" = x
 
-ggnet2(n, color = "phono")
-ggnet2(n, color = "phono", palette = c("vowel" = "gold", "consonant" = "grey"))
-ggnet2(n, shape = "phono", color = "phono")
+p_(ggnet2(n, color = "phono"))
+p_(ggnet2(n, color = "phono", palette = c("vowel" = "gold", "consonant" = "grey")))
+p_(ggnet2(n, shape = "phono", color = "phono"))
 
 if (require(RColorBrewer)) {
 
   # random groups
   n \%v\% "group" <- sample(LETTERS[1:3], 10, replace = TRUE)
 
-  ggnet2(n, color = "group", palette = "Set2")
+  p_(ggnet2(n, color = "group", palette = "Set2"))
 
 }
 
 # random weights
 n \%e\% "weight" <- sample(1:3, network.edgecount(n), replace = TRUE)
-ggnet2(n, edge.size = "weight", edge.label = "weight")
+p_(ggnet2(n, edge.size = "weight", edge.label = "weight"))
 
 # edge arrows on a directed network
-ggnet2(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10)
+p_(ggnet2(network(m, directed = TRUE), arrow.gap = 0.05, arrow.size = 10))
 
 # Padgett's Florentine wedding data
 data(flo, package = "network")
 flo
 
-ggnet2(flo, label = TRUE)
-ggnet2(flo, label = TRUE, label.trim = 4, vjust = -1, size = 3, color = 1)
-ggnet2(flo, label = TRUE, size = 12, color = "white")
+p_(ggnet2(flo, label = TRUE))
+p_(ggnet2(flo, label = TRUE, label.trim = 4, vjust = -1, size = 3, color = 1))
+p_(ggnet2(flo, label = TRUE, size = 12, color = "white"))
 }
 \seealso{
 \code{\link{ggnet}} in this package,
diff --git a/man/ggpairs.Rd b/man/ggpairs.Rd
index 2db4c03ec..e3117da21 100644
--- a/man/ggpairs.Rd
+++ b/man/ggpairs.Rd
@@ -97,8 +97,8 @@ If 'blank' is ever chosen as an option, then ggpairs will produce an empty plot.
 If a function is supplied as an option to \code{upper}, \code{lower}, or \code{diag}, it should implement the function api of \code{function(data, mapping, ...){#make ggplot2 plot}}.  If a specific function needs its parameters set, \code{\link{wrap}(fn, param1 = val1, param2 = val2)} the function with its parameters.
 }
 \examples{
- # small function to display plots only if it's interactive
- p_ <- GGally::print_if_interactive
+# small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 
 
 ## Quick example, with and without colour
diff --git a/man/ggscatmat.Rd b/man/ggscatmat.Rd
index a5dfc7281..04d92b9ea 100644
--- a/man/ggscatmat.Rd
+++ b/man/ggscatmat.Rd
@@ -34,7 +34,7 @@ p_ <- GGally::print_if_interactive
 
 data(flea)
 
-ggscatmat(flea, columns = 2:4)
+p_(ggscatmat(flea, columns = 2:4))
 p_(ggscatmat(flea, columns = 2:4, color = "species"))
 }
 \author{
diff --git a/man/ggsurv.Rd b/man/ggsurv.Rd
index 0aedfb611..4d29759e3 100644
--- a/man/ggsurv.Rd
+++ b/man/ggsurv.Rd
@@ -72,46 +72,48 @@ As a first argument it needs a \code{survfit} object, created by the
 multiple strata objects.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 
 if (require(survival) && require(scales)) {
   data(lung, package = "survival")
   sf.lung <- survival::survfit(Surv(time, status) ~ 1, data = lung)
-  ggsurv(sf.lung)
+  p_(ggsurv(sf.lung))
 
   # Multiple strata examples
   sf.sex <- survival::survfit(Surv(time, status) ~ sex, data = lung)
   pl.sex <- ggsurv(sf.sex)
-  pl.sex
+  p_(pl.sex)
 
   # Adjusting the legend of the ggsurv fit
-  pl.sex +
+  p_(pl.sex +
     ggplot2::guides(linetype = FALSE) +
     ggplot2::scale_colour_discrete(
       name   = 'Sex',
       breaks = c(1,2),
       labels = c('Male', 'Female')
-    )
+    ))
 
   # Multiple factors
   lung2 <- plyr::mutate(lung, older = as.factor(age > 60))
   sf.sex2 <- survival::survfit(Surv(time, status) ~ sex + older, data = lung2)
   pl.sex2 <- ggsurv(sf.sex2)
-  pl.sex2
+  p_(pl.sex2)
 
   # Change legend title
-  pl.sex2 + labs(color = "New Title", linetype = "New Title")
+  p_(pl.sex2 + labs(color = "New Title", linetype = "New Title"))
 
   # We can still adjust the plot after fitting
   data(kidney, package = "survival")
   sf.kid <- survival::survfit(Surv(time, status) ~ disease, data = kidney)
   pl.kid <- ggsurv(sf.kid, plot.cens = FALSE)
-  pl.kid
+  p_(pl.kid)
 
   # Zoom in to first 80 days
-  pl.kid + ggplot2::coord_cartesian(xlim = c(0, 80), ylim = c(0.45, 1))
+  p_(pl.kid + ggplot2::coord_cartesian(xlim = c(0, 80), ylim = c(0.45, 1)))
 
   # Add the diseases names to the plot and remove legend
-  pl.kid +
+  p_(pl.kid +
     ggplot2::annotate(
       "text",
       label  = c("PKD", "Other", "GN", "AN"),
@@ -126,7 +128,7 @@ if (require(survival) && require(scales)) {
         direction = 1
       )(4)
     ) +
-    ggplot2::guides(color = FALSE, linetype = FALSE)
+    ggplot2::guides(color = FALSE, linetype = FALSE))
 }
 }
 \author{
diff --git a/man/ggtable.Rd b/man/ggtable.Rd
index 427612c2f..0819d5271 100644
--- a/man/ggtable.Rd
+++ b/man/ggtable.Rd
@@ -38,28 +38,30 @@ cross-tabulated tables of discrete variables.
 # small function to display plots only if it's interactive
 p_ <- GGally::print_if_interactive
 
-data(tips, package = "reshape")
-ggtable(tips, "smoker", c("day", "time", "sex"))
+if (require(Hmisc)) {
+  data(tips, package = "reshape")
+  p_(ggtable(tips, "smoker", c("day", "time", "sex")))
 
-# displaying row proportions
-p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
+  # displaying row proportions
+  p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
 
-# filling cells with standardized residuals
-p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
+  # filling cells with standardized residuals
+  p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
 
-# if continuous variables are provided, just displaying some summary statistics
-p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))
+  # if continuous variables are provided, just displaying some summary statistics
+  p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))
 
-# specifying weights
-d <- as.data.frame(Titanic)
-p_(ggtable(
-  d,
-  "Survived",
-  c("Class", "Sex", "Age"),
-  mapping = aes(weight = Freq),
-  cells = "row.prop",
-  fill = "stdres"
-))
+  # specifying weights
+  d <- as.data.frame(Titanic)
+  p_(ggtable(
+    d,
+    "Survived",
+    c("Class", "Sex", "Age"),
+    mapping = aes(weight = Freq),
+    cells = "row.prop",
+    fill = "stdres"
+  ))
+}
 }
 \author{
 Joseph Larmarange
diff --git a/man/ggts.Rd b/man/ggts.Rd
index fbf3496b0..d7e6621e8 100644
--- a/man/ggts.Rd
+++ b/man/ggts.Rd
@@ -20,5 +20,8 @@ ggts(..., columnLabelsX = NULL, xlab = "time")
 GGally implementation of ts.plot. Wraps around the ggduo function and removes the column strips
 }
 \examples{
-ggts(pigs, "time", c("gilts", "profit", "s_per_herdsz", "production", "herdsz"))
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+p_(ggts(pigs, "time", c("gilts", "profit", "s_per_herdsz", "production", "herdsz")))
 }
diff --git a/man/glyphs.Rd b/man/glyphs.Rd
index f37917f7d..e2534f74a 100644
--- a/man/glyphs.Rd
+++ b/man/glyphs.Rd
@@ -39,21 +39,24 @@ that no scaling is performed.}
 Create the data needed to generate a glyph plot.
 }
 \examples{
- data(nasa)
- nasaLate <- nasa[
-   nasa$date >= as.POSIXct("1998-01-01") &
-   nasa$lat >= 20 &
-   nasa$lat <= 40 &
-   nasa$long >= -80 &
-   nasa$long <= -60
- , ]
- temp.gly <- glyphs(nasaLate, "long", "day", "lat", "surftemp", height=2.5)
- ggplot2::ggplot(temp.gly, ggplot2::aes(gx, gy, group = gid)) +
-   add_ref_lines(temp.gly, color = "grey90") +
-   add_ref_boxes(temp.gly, color = "grey90") +
-   ggplot2::geom_path() +
-   ggplot2::theme_bw() +
-   ggplot2::labs(x = "", y = "")
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
+data(nasa)
+nasaLate <- nasa[
+  nasa$date >= as.POSIXct("1998-01-01") &
+  nasa$lat >= 20 &
+  nasa$lat <= 40 &
+  nasa$long >= -80 &
+  nasa$long <= -60
+, ]
+temp.gly <- glyphs(nasaLate, "long", "day", "lat", "surftemp", height=2.5)
+p_(ggplot2::ggplot(temp.gly, ggplot2::aes(gx, gy, group = gid)) +
+  add_ref_lines(temp.gly, color = "grey90") +
+  add_ref_boxes(temp.gly, color = "grey90") +
+  ggplot2::geom_path() +
+  ggplot2::theme_bw() +
+  ggplot2::labs(x = "", y = ""))
 }
 \author{
 Di Cook, Heike Hofmann, Hadley Wickham
diff --git a/man/grab_legend.Rd b/man/grab_legend.Rd
index 398cd0de0..297c6ce20 100644
--- a/man/grab_legend.Rd
+++ b/man/grab_legend.Rd
@@ -22,6 +22,9 @@ grab_legend(p)
 Grab the legend and print it as a plot
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 library(ggplot2)
 histPlot <- qplot(
   x = Sepal.Length,
@@ -35,8 +38,8 @@ histPlot <- qplot(
 (top <- histPlot + theme(legend.position = "top"))
 (left <- histPlot + theme(legend.position = "left"))
 
-grab_legend(right)
-grab_legend(bottom)
-grab_legend(top)
-grab_legend(left)
+p_(grab_legend(right))
+p_(grab_legend(bottom))
+p_(grab_legend(top))
+p_(grab_legend(left))
 }
diff --git a/man/putPlot.Rd b/man/putPlot.Rd
index 025e86000..1bbfaf183 100644
--- a/man/putPlot.Rd
+++ b/man/putPlot.Rd
@@ -24,6 +24,9 @@ putPlot(pm, value, i, j)
 Function to place your own plot in the layout.
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 custom_car <- ggpairs(mtcars[, c("mpg", "wt", "cyl")], upper = "blank", title = "Custom Example")
 # ggplot example taken from example(geom_text)
   plot <- ggplot2::ggplot(mtcars, ggplot2::aes(x=wt, y=mpg, label=rownames(mtcars)))
@@ -41,7 +44,7 @@ custom_car[1, 3] <- personal_plot
 custom_car[2,1] <- NULL
 custom_car[3,1] <- "blank" # the same as storing null
 custom_car[3,2] <- NULL
-custom_car
+p_(custom_car)
 }
 \seealso{
 \code{\link{getPlot}}
diff --git a/man/scatmat.Rd b/man/scatmat.Rd
index 3c07815be..6f498aa78 100644
--- a/man/scatmat.Rd
+++ b/man/scatmat.Rd
@@ -24,7 +24,7 @@ p_ <- GGally::print_if_interactive
 
 data(flea)
 
-scatmat(flea, columns=2:4)
+p_(scatmat(flea, columns=2:4))
 p_(scatmat(flea, columns= 2:4, color="species"))
 }
 \author{
diff --git a/man/stat_cross.Rd b/man/stat_cross.Rd
index e54912a1f..8e8fae41d 100644
--- a/man/stat_cross.Rd
+++ b/man/stat_cross.Rd
@@ -89,50 +89,53 @@ from \pkg{broom}.
 }
 
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 d <- as.data.frame(Titanic)
 
 # plot number of observations
-ggplot(d) +
-  aes(x = Class, y = Survived, weight = Freq, size = after_stat(observed)) +
-  stat_cross() +
-  scale_size_area(max_size = 20)
+p_(ggplot(d) +
+ aes(x = Class, y = Survived, weight = Freq, size = after_stat(observed)) +
+ stat_cross() +
+ scale_size_area(max_size = 20))
 
 # custom shape and fill colour based on chi-squared residuals
-ggplot(d) +
-  aes(
-    x = Class, y = Survived, weight = Freq,
-    size = after_stat(observed), fill = after_stat(stdres)
-  ) +
-  stat_cross(shape = 22) +
-  scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE) +
-  scale_size_area(max_size = 20)
+p_(ggplot(d) +
+ aes(
+   x = Class, y = Survived, weight = Freq,
+   size = after_stat(observed), fill = after_stat(stdres)
+ ) +
+ stat_cross(shape = 22) +
+ scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE) +
+ scale_size_area(max_size = 20))
 
 # plotting the number of observations as a table
-ggplot(d) +
-  aes(
-    x = Class, y = Survived, weight = Freq, label = after_stat(observed)
-  ) +
-  geom_text(stat = "cross")
+p_(ggplot(d) +
+ aes(
+   x = Class, y = Survived, weight = Freq, label = after_stat(observed)
+ ) +
+ geom_text(stat = "cross"))
 
 # Row proportions with standardized residuals
-ggplot(d) +
+p_(ggplot(d) +
   aes(
     x = Class, y = Survived, weight = Freq,
     label = scales::percent(after_stat(row.prop)),
-     size = NULL, fill = after_stat(stdres)
+    size = NULL, fill = after_stat(stdres)
   ) +
   stat_cross(shape = 22, size = 30) +
   geom_text(stat = "cross") +
   scale_fill_steps2(breaks = c(-3, -2, 2, 3), show.limits = TRUE) +
   facet_grid(Sex ~ .) +
   labs(fill = "Standardized residuals") +
-  theme_minimal()
+  theme_minimal())
 
 # can work with continuous or character variables
 data(tips, package = "reshape")
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = tip, y = as.character(day), size = after_stat(observed)) +
   stat_cross(alpha = .1, color = "blue") +
-  scale_size_area(max_size = 12)
+  scale_size_area(max_size = 12))
 }
 \keyword{datasets}
diff --git a/man/stat_prop.Rd b/man/stat_prop.Rd
index dc66ca32a..d8d4c93c5 100644
--- a/man/stat_prop.Rd
+++ b/man/stat_prop.Rd
@@ -87,6 +87,8 @@ should be a factor.
 }
 
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 
 d <- as.data.frame(Titanic)
 
@@ -94,26 +96,25 @@ p <- ggplot(d) +
   aes(x = Class, fill = Survived, weight = Freq, by = Class) +
   geom_bar(position = "fill") +
   geom_text(stat = "prop", position = position_fill(.5))
-p
-p + facet_grid(~ Sex)
+p_(p)
+p_(p + facet_grid(~ Sex))
 
-ggplot(d) +
+p_(ggplot(d) +
   aes(x = Class, fill = Survived, weight = Freq) +
   geom_bar(position = "dodge") +
   geom_text(
     aes(by = Survived), stat = "prop",
     position = position_dodge(0.9), vjust = "bottom"
- )
+ ))
 
-ggplot(d) +
+p_(ggplot(d) +
   aes(x = Class, fill = Survived, weight = Freq, by = 1) +
   geom_bar() +
   geom_text(
     aes(label = scales::percent(after_stat(prop), accuracy = 1)),
     stat = "prop",
     position = position_stack(.5)
- )
-
+ ))
 }
 \seealso{
 \code{\link[ggplot2]{stat_count}}
diff --git a/man/stat_weighted_mean.Rd b/man/stat_weighted_mean.Rd
index 32b810fd2..5ca6bc2b4 100644
--- a/man/stat_weighted_mean.Rd
+++ b/man/stat_weighted_mean.Rd
@@ -84,41 +84,44 @@ aesthetic if provided.
 }
 
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
+
 data(tips, package = "reshape")
 
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = day, y = total_bill) +
-  geom_point()
+  geom_point())
 
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = day, y = total_bill) +
-  stat_weighted_mean()
+  stat_weighted_mean())
 
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = day, y = total_bill, group = 1) +
-  stat_weighted_mean(geom = "line")
+  stat_weighted_mean(geom = "line"))
 
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = day, y = total_bill, colour = sex, group = sex) +
-  stat_weighted_mean(geom = "line")
+  stat_weighted_mean(geom = "line"))
 
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = day, y = total_bill, fill = sex) +
-  stat_weighted_mean(geom = "bar", position = "dodge")
+  stat_weighted_mean(geom = "bar", position = "dodge"))
 
 # computing a proportion on the fly
-ggplot(tips) +
+p_(ggplot(tips) +
   aes(x = day, y = as.integer(smoker == "Yes"), fill = sex) +
   stat_weighted_mean(geom = "bar", position = "dodge") +
-  scale_y_continuous(labels = scales::percent)
+  scale_y_continuous(labels = scales::percent))
 
 # taking into account some weights
 d <- as.data.frame(Titanic)
-ggplot(d) +
+p_(ggplot(d) +
   aes(x = Class, y = as.integer(Survived == "Yes"), weight = Freq, fill = Sex) +
   geom_bar(stat = "weighted_mean", position = "dodge") +
   scale_y_continuous(labels = scales::percent) +
-  labs(y = "Survived")
+  labs(y = "Survived"))
 
 
 \dontrun{
diff --git a/man/v1_ggmatrix_theme.Rd b/man/v1_ggmatrix_theme.Rd
index 8ae8693c8..87e8ed474 100644
--- a/man/v1_ggmatrix_theme.Rd
+++ b/man/v1_ggmatrix_theme.Rd
@@ -10,8 +10,10 @@ v1_ggmatrix_theme()
 Modify a \code{\link{ggmatrix}} object by adding an \pkg{ggplot2} object to all
 }
 \examples{
+# Small function to display plots only if it's interactive
+p_ <- GGally::print_if_interactive
 
-ggpairs(iris, 1:2) + v1_ggmatrix_theme()
+p_(ggpairs(iris, 1:2) + v1_ggmatrix_theme())
 # move the column names to the left and bottom
-ggpairs(iris, 1:2, switch = "both") + v1_ggmatrix_theme()
+p_(ggpairs(iris, 1:2, switch = "both") + v1_ggmatrix_theme())
 }
diff --git a/man/vig_ggally.Rd b/man/vig_ggally.Rd
index 9cdffc327..bae47dfed 100644
--- a/man/vig_ggally.Rd
+++ b/man/vig_ggally.Rd
@@ -16,9 +16,10 @@ This function will open the directly to the vignette requested. If no \code{name
 This method allows for vignettes to be hosted remotely, reducing \pkg{GGally}'s package size, and installation time.
 }
 \examples{
+\donttest{
 # View `ggnostic` vignette
 vig_ggally("ggnostic")
 
 # View all vignettes by GGally
-vig_ggally()
+vig_ggally()}
 }
diff --git a/tests/testthat/test-zzz_ggpairs.R b/tests/testthat/test-zzz_ggpairs.R
index 6648ce830..19735eee3 100644
--- a/tests/testthat/test-zzz_ggpairs.R
+++ b/tests/testthat/test-zzz_ggpairs.R
@@ -558,6 +558,7 @@ test_that("strip-top and strip-right", {
 test_that("subtypes", {
 
   testthat::skip_on_cran()
+  testthat::skip_if_not_installed("Hmisc")
 
 # list of the different plot types to check
 # continuous

From ffd39898d4ec6191c3464d9842bdf08b521d9724 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 01:21:50 -0400
Subject: [PATCH 14/22] Run revdep

---
 revdep/README.md   |   6 +-
 revdep/problems.md | 136 ++++++++++++++++++---------------------------
 2 files changed, 56 insertions(+), 86 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index 6b70bd723..1f92d0b0f 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -10,7 +10,7 @@
 |collate  |en_US.UTF-8                  |
 |ctype    |en_US.UTF-8                  |
 |tz       |America/New_York             |
-|date     |2020-06-04                   |
+|date     |2020-06-05                   |
 
 # Dependencies
 
@@ -68,10 +68,10 @@
 |[httk](problems.md#httk)                         |2.0.1   |      |        |1    |
 |[ICtest](problems.md#ictest)                     |0.3-2   |      |        |1    |
 |imageData                                        |0.1-60  |      |        |     |
-|[isomiRs](problems.md#isomirs)                   |1.16.1  |2     |        |3    |
+|[isomiRs](problems.md#isomirs)                   |1.16.2  |1     |        |3    |
 |ITNr                                             |0.6.0   |      |        |     |
 |[jmv](problems.md#jmv)                           |1.2.5   |      |        |1    |
-|[jsmodule](problems.md#jsmodule)                 |1.0.7   |      |        |1    |
+|[jsmodule](problems.md#jsmodule)                 |1.0.8   |      |        |1    |
 |[LANDD](problems.md#landd)                       |1.1.0   |      |        |1    |
 |[MAINT.Data](problems.md#maintdata)              |2.3.1   |      |        |1    |
 |[MAST](problems.md#mast)                         |1.14.0  |      |        |2    |
diff --git a/revdep/problems.md b/revdep/problems.md
index 4af15d300..a0ee16b38 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -289,20 +289,20 @@ Run `revdep_details(,"finalfit")` for more info
     1    Alive            1 511
     2     Died            2 404
     3     <NA>           NA  14
-
+    
     $counts[[19]]
       sex.factor2 age.factor2   n
     1           M   <60 years 204
     2           M   60+ years 241
     3           F   <60 years 210
     4           F   60+ years 274
-
-
-    >
+    
+    
+    > 
     > # Select a tibble and expand
     > out$counts[[9]] %>%
     +   print(n = Inf)
-    Error in print.default(m, ..., quote = quote, right = right, max = max) :
+    Error in print.default(m, ..., quote = quote, right = right, max = max) : 
       invalid 'na.print' specification
     Calls: %>% ... print -> print.data.frame -> print -> print.default
     Execution halted
@@ -392,7 +392,7 @@ Run `revdep_details(,"ggbio")` for more info
 *   checking examples ... WARNING
     ```
     Found the following significant warnings:
-
+    
       Warning: 'GenenameFilter' is deprecated.
     Deprecated functions may be defunct as soon as of the next release of
     R.
@@ -464,11 +464,11 @@ Run `revdep_details(,"GGPA")` for more info
     File ‘GGPA/libs/GGPA.so’:
       Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
         Object: ‘3_Param.o’
-
+    
     Compiled code should not call entry points which might terminate R nor
     write to stdout/stderr instead of to the console, nor use Fortran I/O
     nor system RNGs.
-
+    
     See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
     ```
 
@@ -548,10 +548,10 @@ Run `revdep_details(,"ICtest")` for more info
 
 <details>
 
-* Version: 1.16.1
+* Version: 1.16.2
 * Source code: https://github.com/cran/isomiRs
 * BugReports: https://github.com/lpantano/isomiRs/issues
-* Date/Publication: 2020-05-26
+* Date/Publication: 2020-06-03
 * Number of recursive dependencies: 149
 
 Run `revdep_details(,"isomiRs")` for more info
@@ -562,52 +562,21 @@ Run `revdep_details(,"isomiRs")` for more info
 
 *   checking examples ... ERROR
     ```
-    ...
-    Joining, by = "merge"
-    Error: Problem with `summarise()` input `n_genes`.
-    ✖ could not find function "n"
-    ℹ Input `n_genes` is `n()`.
-    ℹ The error occured in group 1: merge = "one_groupcontrol", cluster = 1, xaxis = "control", colored = "one_group".
-    Backtrace:
-         █
-      1. └─isomiRs::isoNetwork(...)
-      2.   └─isomiRs:::.viz_mirna_gene_enrichment(...)
-      3.     └─isomiRs:::.cluster_exp(...)
-      4.       └─DEGreport::degPatterns(ma, meta, time = "xaxis", minc = 0, plot = FALSE)
-      5.         └─`%>%`(...)
-      6.           ├─base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
-      7.           └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
-      8.             └─base::eval(quote(`_fseq`(`_lhs`)), env, env)
-      9.               └─DEGreport:::`_fseq`(`_lhs`)
-     10.                 └─magrittr::freduce(value, `_function_list`)
-     11.                   └─function_list[[i]](value)
-     12.                     ├─dplyr::summarise(., abundance = median(value), n_genes = n())
-     13.
+    Running examples in ‘isomiRs-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: mirna2targetscan
+    > ### Title: Find targets in targetscan database
+    > ### Aliases: mirna2targetscan
+    > 
+    > ### ** Examples
+    > 
+    > library(targetscan.Hs.eg.db)
+    Error in library(targetscan.Hs.eg.db) : 
+      there is no package called ‘targetscan.Hs.eg.db’
     Execution halted
     ```
 
-*   checking tests ...
-    ```
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 13 lines of output:
-      ℹ The error occured in group 1: merge = "one_groupcontrol_1", cluster = 1, xaxis = "control_1", colored = "one_group".
-      Backtrace:
-        1. testthat::expect_equal(unique(.cluster_exp(gene)), c(1, 2))
-        5. isomiRs:::.cluster_exp(gene)
-        6. DEGreport::degPatterns(ma, meta, time = "xaxis", minc = 0, plot = FALSE)
-        4. dplyr::group_by(...)
-       11. dplyr::summarise(., abundance = median(value), n_genes = n())
-       16. dplyr:::summarise_cols(.data, ...)
-
-      ══ testthat results  ═══════════════════════════════════════════════════════════
-      [ OK: 27 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
-      1. Error: matrix (@test_calculus.R#23)
-
-      Error: testthat unit tests failed
-      Execution halted
-    ```
-
 *   checking package dependencies ... NOTE
     ```
     Package suggested but not available for checking: ‘targetscan.Hs.eg.db’
@@ -675,11 +644,11 @@ Run `revdep_details(,"jmv")` for more info
 
 <details>
 
-* Version: 1.0.7
+* Version: 1.0.8
 * Source code: https://github.com/cran/jsmodule
 * URL: https://github.com/jinseob2kim/jsmodule
 * BugReports: https://github.com/jinseob2kim/jsmodule/issues
-* Date/Publication: 2020-04-29 17:20:09 UTC
+* Date/Publication: 2020-06-04 17:00:02 UTC
 * Number of recursive dependencies: 188
 
 Run `revdep_details(,"jsmodule")` for more info
@@ -843,24 +812,24 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 
 *   checking S3 generic/method consistency ... WARNING
     ```
-
-    (R:15348): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:49914): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     See section ‘Generic functions and methods’ in the ‘Writing R
     Extensions’ manual.
     ```
 
 *   checking replacement functions ... WARNING
     ```
-
-    (R:15410): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50079): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     The argument of a replacement function which corresponds to the right
     hand side must be named ‘value’.
     ```
 
 *   checking for missing documentation entries ... WARNING
     ```
-
-    (R:15967): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50734): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     All user-level objects in a package should have documentation entries.
     See chapter ‘Writing R documentation files’ in the ‘Writing R
     Extensions’ manual.
@@ -868,38 +837,38 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 
 *   checking for code/documentation mismatches ... WARNING
     ```
-
-    (R:16060): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
-
-    (R:16138): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
-
-    (R:16267): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50780): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50817): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50949): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     ```
 
 *   checking dependencies in R code ... NOTE
     ```
-
-    (R:15208): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:49828): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     ```
 
 *   checking foreign function calls ... NOTE
     ```
-
-    (R:15441): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50140): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     See chapter ‘System and foreign language interfaces’ in the ‘Writing R
     Extensions’ manual.
     ```
 
 *   checking R code for possible problems ... NOTE
     ```
-
-    (R:15653): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:50408): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     ```
 
 *   checking Rd \usage sections ... NOTE
     ```
-
-    (R:16367): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    
+    (R:51056): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     The \usage entries for S3 methods should use the \method markup and not
     their full name.
     See chapter ‘Writing R documentation files’ in the ‘Writing R
@@ -947,18 +916,18 @@ Run `revdep_details(,"MOFA")` for more info
     ```
     Running examples in ‘MOFA-Ex.R’ failed
     The error most likely occurred in:
-
+    
     > ### Name: DataOptions
     > ### Title: DataOptions: set and retrieve data options
     > ### Aliases: DataOptions DataOptions<- DataOptions,MOFAmodel-method
     > ###   DataOptions<-,MOFAmodel,list-method
-    >
+    > 
     > ### ** Examples
-    >
+    > 
     > # load a trained MOFAmodel object
     > filepath <- system.file("extdata", "scMT_model.hdf5", package = "MOFAdata")
     > MOFAobject <- loadModel(filepath)
-    Error in h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) :
+    Error in h5checktypeOrOpenLoc(file, readonly = TRUE, native = native) : 
       Error in h5checktypeOrOpenLoc(). Cannot open file. File '' does not exist.
     Calls: loadModel -> h5read -> h5checktypeOrOpenLoc
     Execution halted
@@ -1495,10 +1464,10 @@ Run `revdep_details(,"tidybulk")` for more info
       Getting the 5 most variable genes
       ══ testthat results  ═══════════════════════════════════════════════════════════
       [ OK: 139 | SKIPPED: 0 | WARNINGS: 18 | FAILED: 3 ]
-      1. Error: Only scaled counts - no object (@test-bulk_methods.R#65)
-      2. Error: tidybulk SummarizedExperiment normalisation manual (@test-bulk_methods_SummarizedExperiment.R#29)
-      3. Error: tidybulk SummarizedExperiment normalisation (@test-bulk_methods_SummarizedExperiment.R#50)
-
+      1. Error: Only scaled counts - no object (@test-bulk_methods.R#65) 
+      2. Error: tidybulk SummarizedExperiment normalisation manual (@test-bulk_methods_SummarizedExperiment.R#29) 
+      3. Error: tidybulk SummarizedExperiment normalisation (@test-bulk_methods_SummarizedExperiment.R#50) 
+      
       Error: testthat unit tests failed
       Execution halted
     ```
@@ -1644,3 +1613,4 @@ Run `revdep_details(,"vidger")` for more info
         data   4.7Mb
         doc    6.1Mb
     ```
+

From 1d7c1ef9f128cf7592dd00c117697739ba9fac73 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 01:31:36 -0400
Subject: [PATCH 15/22] Do not error on warning

aka error that scagnostics can't be found
---
 .github/workflows/R-CMD-check.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index eca13d31e..242dda789 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -97,7 +97,7 @@ jobs:
       - name: Check as CRAN
         env:
           _R_CHECK_CRAN_INCOMING_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "note", check_dir = "check")
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
       - name: Show testthat output

From 8d0de8c788cb849246bd0939272ef0459509d52a Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 01:55:18 -0400
Subject: [PATCH 16/22] Test less things on CRAN for timing purposes

---
 tests/testthat/test-gg-plots.R    | 2 ++
 tests/testthat/test-zzz_ggpairs.R | 4 +++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-gg-plots.R b/tests/testthat/test-gg-plots.R
index f99e53b5f..400b600e9 100644
--- a/tests/testthat/test-gg-plots.R
+++ b/tests/testthat/test-gg-plots.R
@@ -1,5 +1,7 @@
 
 context("gg-plots")
+# This file takes too long
+testthat::skip_on_cran()
 
 data(tips, package = "reshape")
 data(nasa)
diff --git a/tests/testthat/test-zzz_ggpairs.R b/tests/testthat/test-zzz_ggpairs.R
index 19735eee3..63467dc10 100644
--- a/tests/testthat/test-zzz_ggpairs.R
+++ b/tests/testthat/test-zzz_ggpairs.R
@@ -1,5 +1,7 @@
-
 context("ggpairs")
+# This file takes too long
+testthat::skip_on_cran()
+
 data(tips, package = "reshape")
 
 expect_print <- function(p) {

From cc766e3c0e9f949c323c183b3fe0834b33269e1e Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 02:08:23 -0400
Subject: [PATCH 17/22] Update cran-comments.md

---
 cran-comments.md | 60 +++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 47 insertions(+), 13 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index 0724be103..a8200149a 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,6 +1,46 @@
 
 ## Comments
 
+### 2020-6-4
+
+Changes since last submission:
+* I removed the package vignettes (and will only host them on the package's website). 
+* I have altered the examples to only print the ggplot2 images if they are in an interactive session.
+* I have made some of the longer running tests to be CI only. (On a weekly schedule)
+
+The package size should be smaller (I did not receive any warnings) and the check time should be faster.
+
+I have rerun package checks and revdep checks and updated the final results below.
+
+Please let me know if there is anything else I can do.
+
+Best,
+Barret
+
+
+### 2020-6-4
+
+Thanks, we see:
+
+
+   Size of tarball: 5726242 bytes
+
+This is more than the 5MB CRAN threshhold and more than ever before?
+
+
+Flavor: r-devel-windows-ix86+x86_64
+Check: Overall checktime, Result: NOTE
+   Overall checktime 14 min > 10 min
+
+This is also rather extensive.
+
+
+Can these be reduced?
+
+Best,
+Uwe Ligges
+
+
 ### 2020-6-3
 
 I have removed `packagedocs` as a dependency.  This fixes the errors on CRAN check.
@@ -48,27 +88,21 @@ Brian D. Ripley
 * win-builder
   * oldrelease
   * release
-  * devel
+  * devel - Could not test. `Failed FTP upload: 550`
 
 #### R CMD check results
 
-win-builder
-* 0 errors | 0 warnings | 0 notes
-
-
-Local & GitHub Actions
-* 0 errors | 0 warnings | 1 notes
-
-N  checking installed package size ...
-     installed size is  7.8Mb
-     sub-directories of 1Mb or more:
-       doc   6.1Mb
+win-builder - release:
+* checking files in 'vignettes' ... NOTE
+Package has no Sweave vignette sources and no VignetteBuilder field.
 
+Everywhere else:
+* 0 errors | 0 warnings | 0 notes
 
 
 ## revdepcheck results
 
-Link: https://github.com/ggobi/ggally/commit/8a6b8ffbf6f7187dc9503ac51c3f5f48b3f72a1c
+Link: https://github.com/ggobi/ggally/blob/rc-v2.0.0/revdep/README.md
 
 We checked 98 reverse dependencies (77 from CRAN + 21 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
 

From abc207c8e572e760ce645e72f47be95df57d2086 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 02:10:46 -0400
Subject: [PATCH 18/22] Update CRAN-RELEASE

---
 CRAN-RELEASE | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/CRAN-RELEASE b/CRAN-RELEASE
index 8fe858a41..46e3d4786 100644
--- a/CRAN-RELEASE
+++ b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-06-04.
-Once it is accepted, delete this file and tag the release (commit 415e109e64).
+This package was submitted to CRAN on 2020-06-05.
+Once it is accepted, delete this file and tag the release (commit cc766e3c0e).

From daf5a9fe82c1395f3cd1de2e1b832f8389003ca2 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 12:41:24 -0400
Subject: [PATCH 19/22] Update ggtable.Rd

---
 man/ggtable.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/ggtable.Rd b/man/ggtable.Rd
index 0819d5271..aa348f3af 100644
--- a/man/ggtable.Rd
+++ b/man/ggtable.Rd
@@ -46,7 +46,7 @@ if (require(Hmisc)) {
   p_(ggtable(tips, "smoker", c("day", "time", "sex"), cells = "row.prop"))
 
   # filling cells with standardized residuals
-  p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres"))
+  p_(ggtable(tips, "smoker", c("day", "time", "sex"), fill = "stdres", legend = 1))
 
   # if continuous variables are provided, just displaying some summary statistics
   p_(ggtable(tips, c("smoker", "total_bill"), c("day", "time", "sex", "tip")))

From 1dd3322e8746595fa3d1184f1dbc6f86984f4f47 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 14:34:47 -0400
Subject: [PATCH 20/22] Run revdep

---
 revdep/README.md      | 206 ++++++++++++++++++++----------------------
 revdep/problems.md    |  44 ++-------
 revdep/revdep_cran.md |  10 +-
 3 files changed, 111 insertions(+), 149 deletions(-)

diff --git a/revdep/README.md b/revdep/README.md
index 1f92d0b0f..06c0e8074 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -20,112 +20,106 @@
 
 # Revdeps
 
-## New problems (1)
-
-|package                                          |version |error |warning |note |
-|:------------------------------------------------|:-------|:-----|:-------|:----|
-|[robustSingleCell](problems.md#robustsinglecell) |0.1.1   |      |__+1__  |     |
-
 ## All (98)
 
-|package                                          |version |error |warning |note |
-|:------------------------------------------------|:-------|:-----|:-------|:----|
-|[adventr](problems.md#adventr)                   |0.1.8   |      |        |2    |
-|[alevinQC](problems.md#alevinqc)                 |1.4.0   |      |        |1    |
-|[ALPS](problems.md#alps)                         |1.2.0   |      |        |1    |
-|BAS                                              |1.5.5   |      |        |     |
-|bayestestR                                       |0.6.0   |      |        |     |
-|[BGGM](problems.md#bggm)                         |2.0.0   |      |        |2    |
-|[bigPint](problems.md#bigpint)                   |1.4.0   |      |        |1    |
-|brinton                                          |0.1.7   |      |        |     |
-|CARBayes                                         |5.2     |      |        |     |
-|CARBayesST                                       |3.1     |      |        |     |
-|[CeTF](problems.md#cetf)                         |1.0.2   |      |        |1    |
-|[CINNA](problems.md#cinna)                       |1.1.53  |      |        |1    |
-|[CluMSID](problems.md#clumsid)                   |1.4.0   |      |        |2    |
-|clustrd                                          |1.3.7-2 |      |        |     |
-|[ctsem](problems.md#ctsem)                       |3.2.1   |      |        |3    |
-|DescribeDisplay                                  |0.2.7   |      |        |     |
-|discourseGT                                      |1.0.0   |      |        |     |
-|eechidna                                         |1.4.0   |      |        |     |
-|egoTERGM                                         |2.1.1   |      |        |     |
-|EMMIXmfa                                         |2.0.11  |      |        |     |
-|[fic](problems.md#fic)                           |1.0.0   |      |        |1    |
-|[finalfit](problems.md#finalfit)                 |1.0.1   |1     |        |     |
-|[fingerPro](problems.md#fingerpro)               |1.1     |      |        |1    |
-|fpp2                                             |2.3     |      |        |     |
-|freqparcoord                                     |1.0.1   |      |        |     |
-|[GENESIS](problems.md#genesis)                   |2.18.0  |      |        |3    |
-|[ggbio](problems.md#ggbio)                       |1.36.0  |      |1       |2    |
-|ggmcmc                                           |1.4.1   |      |        |     |
-|[GGPA](problems.md#ggpa)                         |1.0.0   |      |        |2    |
-|ggPMX                                            |1.1.1   |      |        |     |
-|[ggquickeda](problems.md#ggquickeda)             |0.1.6   |      |        |1    |
-|glancedata                                       |1.0.1   |      |        |     |
-|growthPheno                                      |1.0-22  |      |        |     |
-|gsynth                                           |1.0.9   |      |        |     |
-|HierDpart                                        |0.5.0   |      |        |     |
-|[httk](problems.md#httk)                         |2.0.1   |      |        |1    |
-|[ICtest](problems.md#ictest)                     |0.3-2   |      |        |1    |
-|imageData                                        |0.1-60  |      |        |     |
-|[isomiRs](problems.md#isomirs)                   |1.16.2  |1     |        |3    |
-|ITNr                                             |0.6.0   |      |        |     |
-|[jmv](problems.md#jmv)                           |1.2.5   |      |        |1    |
-|[jsmodule](problems.md#jsmodule)                 |1.0.8   |      |        |1    |
-|[LANDD](problems.md#landd)                       |1.1.0   |      |        |1    |
-|[MAINT.Data](problems.md#maintdata)              |2.3.1   |      |        |1    |
-|[MAST](problems.md#mast)                         |1.14.0  |      |        |2    |
-|[MCbiclust](problems.md#mcbiclust)               |1.12.0  |      |        |1    |
-|metan                                            |1.6.0   |      |        |     |
-|[mgcViz](problems.md#mgcviz)                     |0.1.6   |      |        |1    |
-|[MissingDataGUI](problems.md#missingdatagui)     |0.2-5   |      |4       |4    |
-|mitch                                            |1.0.4   |      |        |     |
-|miWQS                                            |0.2.0   |      |        |     |
-|mlergm                                           |0.5     |      |        |     |
-|mlr3viz                                          |0.1.1   |      |        |     |
-|[mlrMBO](problems.md#mlrmbo)                     |1.1.4   |      |        |1    |
-|[MOFA](problems.md#mofa)                         |1.4.0   |1     |        |5    |
-|MRPC                                             |2.2.0   |      |        |     |
-|[NetworkChange](problems.md#networkchange)       |0.6     |      |        |1    |
-|[nzelect](problems.md#nzelect)                   |0.4.0   |      |        |2    |
-|[ORFik](problems.md#orfik)                       |1.8.1   |      |        |2    |
-|OutliersO3                                       |0.6.3   |      |        |     |
-|[PAFway](problems.md#pafway)                     |0.1.3   |      |        |1    |
-|ParamHelpers                                     |1.14    |      |        |     |
-|Pi                                               |2.0.0   |      |        |     |
-|[plotly](problems.md#plotly)                     |4.9.2.1 |      |        |1    |
-|[PopGenReport](problems.md#popgenreport)         |3.0.4   |      |        |1    |
-|PPforest                                         |0.1.1   |      |        |     |
-|[pubh](problems.md#pubh)                         |1.1.14  |      |        |1    |
-|qualvar                                          |0.2.0   |      |        |     |
-|QuantNorm                                        |1.0.5   |      |        |     |
-|randomForestExplainer                            |0.10.0  |      |        |     |
-|RHMS                                             |1.6     |      |        |     |
-|[robCompositions](problems.md#robcompositions)   |2.2.1   |      |        |1    |
-|[robustbase](problems.md#robustbase)             |0.93-6  |      |        |1    |
-|[robustSingleCell](problems.md#robustsinglecell) |0.1.1   |      |__+1__  |     |
-|[rrr](problems.md#rrr)                           |1.0.0   |      |        |1    |
-|rwty                                             |1.0.2   |      |        |     |
-|[scPipe](problems.md#scpipe)                     |1.10.0  |      |        |4    |
-|[SeqSQC](problems.md#seqsqc)                     |1.10.0  |      |        |1    |
-|SHELF                                            |1.7.0   |      |        |     |
-|SimBIID                                          |0.2.0   |      |        |     |
-|simplexdesign                                    |0.1.0   |      |        |     |
-|[SmartEDA](problems.md#smarteda)                 |0.3.5   |      |        |1    |
-|[spinifex](problems.md#spinifex)                 |0.1.0   |      |        |1    |
-|[spup](problems.md#spup)                         |1.3-2   |      |        |1    |
-|staRdom                                          |1.1.11  |      |        |     |
-|[statVisual](problems.md#statvisual)             |1.2.1   |      |        |1    |
-|[tidybulk](problems.md#tidybulk)                 |1.0.0   |2     |        |3    |
-|TNBC.CMS                                         |1.4.0   |      |        |     |
-|tsfeatures                                       |1.0.1   |      |        |     |
-|[TVTB](problems.md#tvtb)                         |1.14.0  |      |        |1    |
-|[ubiquity](problems.md#ubiquity)                 |1.0.1   |      |        |1    |
-|[ufs](problems.md#ufs)                           |0.3.1   |      |        |2    |
-|userfriendlyscience                              |0.7.2   |      |        |     |
-|ushr                                             |0.2.3   |      |        |     |
-|[vidger](problems.md#vidger)                     |1.8.0   |      |        |1    |
-|vortexR                                          |1.1.7   |      |        |     |
-|WRS2                                             |1.0-0   |      |        |     |
-|WRSS                                             |3.0     |      |        |     |
+|package                                        |version |error |warning |note |
+|:----------------------------------------------|:-------|:-----|:-------|:----|
+|[adventr](problems.md#adventr)                 |0.1.8   |      |        |2    |
+|[alevinQC](problems.md#alevinqc)               |1.4.0   |      |        |1    |
+|[ALPS](problems.md#alps)                       |1.2.0   |      |        |1    |
+|BAS                                            |1.5.5   |      |        |     |
+|bayestestR                                     |0.6.0   |      |        |     |
+|[BGGM](problems.md#bggm)                       |2.0.0   |      |        |2    |
+|[bigPint](problems.md#bigpint)                 |1.4.0   |      |        |1    |
+|brinton                                        |0.1.7   |      |        |     |
+|CARBayes                                       |5.2     |      |        |     |
+|CARBayesST                                     |3.1     |      |        |     |
+|[CeTF](problems.md#cetf)                       |1.0.2   |      |        |1    |
+|[CINNA](problems.md#cinna)                     |1.1.53  |      |        |1    |
+|[CluMSID](problems.md#clumsid)                 |1.4.0   |      |        |2    |
+|clustrd                                        |1.3.7-2 |      |        |     |
+|[ctsem](problems.md#ctsem)                     |3.2.1   |      |        |3    |
+|DescribeDisplay                                |0.2.7   |      |        |     |
+|discourseGT                                    |1.0.0   |      |        |     |
+|eechidna                                       |1.4.0   |      |        |     |
+|egoTERGM                                       |2.1.1   |      |        |     |
+|EMMIXmfa                                       |2.0.11  |      |        |     |
+|[fic](problems.md#fic)                         |1.0.0   |      |        |1    |
+|[finalfit](problems.md#finalfit)               |1.0.1   |1     |        |     |
+|[fingerPro](problems.md#fingerpro)             |1.1     |      |        |1    |
+|fpp2                                           |2.3     |      |        |     |
+|freqparcoord                                   |1.0.1   |      |        |     |
+|[GENESIS](problems.md#genesis)                 |2.18.0  |      |        |3    |
+|[ggbio](problems.md#ggbio)                     |1.36.0  |      |1       |2    |
+|ggmcmc                                         |1.4.1   |      |        |     |
+|[GGPA](problems.md#ggpa)                       |1.0.0   |      |        |2    |
+|ggPMX                                          |1.1.1   |      |        |     |
+|[ggquickeda](problems.md#ggquickeda)           |0.1.6   |      |        |1    |
+|glancedata                                     |1.0.1   |      |        |     |
+|growthPheno                                    |1.0-22  |      |        |     |
+|gsynth                                         |1.0.9   |      |        |     |
+|HierDpart                                      |0.5.0   |      |        |     |
+|[httk](problems.md#httk)                       |2.0.1   |      |        |1    |
+|[ICtest](problems.md#ictest)                   |0.3-2   |      |        |1    |
+|imageData                                      |0.1-60  |      |        |     |
+|[isomiRs](problems.md#isomirs)                 |1.16.2  |1     |        |3    |
+|ITNr                                           |0.6.0   |      |        |     |
+|[jmv](problems.md#jmv)                         |1.2.5   |      |        |1    |
+|[jsmodule](problems.md#jsmodule)               |1.0.8   |      |        |1    |
+|[LANDD](problems.md#landd)                     |1.1.0   |      |        |1    |
+|[MAINT.Data](problems.md#maintdata)            |2.3.1   |      |        |1    |
+|[MAST](problems.md#mast)                       |1.14.0  |      |        |2    |
+|[MCbiclust](problems.md#mcbiclust)             |1.12.0  |      |        |1    |
+|metan                                          |1.6.0   |      |        |     |
+|[mgcViz](problems.md#mgcviz)                   |0.1.6   |      |        |1    |
+|[MissingDataGUI](problems.md#missingdatagui)   |0.2-5   |      |4       |4    |
+|mitch                                          |1.0.4   |      |        |     |
+|miWQS                                          |0.2.0   |      |        |     |
+|mlergm                                         |0.5     |      |        |     |
+|mlr3viz                                        |0.1.1   |      |        |     |
+|[mlrMBO](problems.md#mlrmbo)                   |1.1.4   |      |        |1    |
+|[MOFA](problems.md#mofa)                       |1.4.0   |1     |        |5    |
+|MRPC                                           |2.2.0   |      |        |     |
+|[NetworkChange](problems.md#networkchange)     |0.6     |      |        |1    |
+|[nzelect](problems.md#nzelect)                 |0.4.0   |      |        |2    |
+|[ORFik](problems.md#orfik)                     |1.8.1   |      |        |2    |
+|OutliersO3                                     |0.6.3   |      |        |     |
+|[PAFway](problems.md#pafway)                   |0.1.3   |      |        |1    |
+|ParamHelpers                                   |1.14    |      |        |     |
+|Pi                                             |2.0.0   |      |        |     |
+|[plotly](problems.md#plotly)                   |4.9.2.1 |      |        |1    |
+|[PopGenReport](problems.md#popgenreport)       |3.0.4   |      |        |1    |
+|PPforest                                       |0.1.1   |      |        |     |
+|[pubh](problems.md#pubh)                       |1.1.14  |      |        |1    |
+|qualvar                                        |0.2.0   |      |        |     |
+|QuantNorm                                      |1.0.5   |      |        |     |
+|randomForestExplainer                          |0.10.0  |      |        |     |
+|RHMS                                           |1.6     |      |        |     |
+|[robCompositions](problems.md#robcompositions) |2.2.1   |      |        |1    |
+|[robustbase](problems.md#robustbase)           |0.93-6  |      |        |1    |
+|robustSingleCell                               |0.1.1   |      |        |     |
+|[rrr](problems.md#rrr)                         |1.0.0   |      |        |1    |
+|rwty                                           |1.0.2   |      |        |     |
+|[scPipe](problems.md#scpipe)                   |1.10.0  |      |        |4    |
+|[SeqSQC](problems.md#seqsqc)                   |1.10.0  |      |        |1    |
+|SHELF                                          |1.7.0   |      |        |     |
+|SimBIID                                        |0.2.0   |      |        |     |
+|simplexdesign                                  |0.1.0   |      |        |     |
+|[SmartEDA](problems.md#smarteda)               |0.3.5   |      |        |1    |
+|[spinifex](problems.md#spinifex)               |0.1.0   |      |        |1    |
+|[spup](problems.md#spup)                       |1.3-2   |      |        |1    |
+|staRdom                                        |1.1.11  |      |        |     |
+|[statVisual](problems.md#statvisual)           |1.2.1   |      |        |1    |
+|[tidybulk](problems.md#tidybulk)               |1.0.0   |2     |        |3    |
+|TNBC.CMS                                       |1.4.0   |      |        |     |
+|tsfeatures                                     |1.0.1   |      |        |     |
+|[TVTB](problems.md#tvtb)                       |1.14.0  |      |        |1    |
+|[ubiquity](problems.md#ubiquity)               |1.0.1   |      |        |1    |
+|[ufs](problems.md#ufs)                         |0.3.1   |      |        |2    |
+|userfriendlyscience                            |0.7.2   |      |        |     |
+|ushr                                           |0.2.3   |      |        |     |
+|[vidger](problems.md#vidger)                   |1.8.0   |      |        |1    |
+|vortexR                                        |1.1.7   |      |        |     |
+|WRS2                                           |1.0-0   |      |        |     |
+|WRSS                                           |3.0     |      |        |     |
 
diff --git a/revdep/problems.md b/revdep/problems.md
index a0ee16b38..27dbc1f6e 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -813,7 +813,7 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 *   checking S3 generic/method consistency ... WARNING
     ```
     
-    (R:49914): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:34676): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     See section ‘Generic functions and methods’ in the ‘Writing R
     Extensions’ manual.
     ```
@@ -821,7 +821,7 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 *   checking replacement functions ... WARNING
     ```
     
-    (R:50079): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:34834): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     The argument of a replacement function which corresponds to the right
     hand side must be named ‘value’.
     ```
@@ -829,7 +829,7 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 *   checking for missing documentation entries ... WARNING
     ```
     
-    (R:50734): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:35294): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     All user-level objects in a package should have documentation entries.
     See chapter ‘Writing R documentation files’ in the ‘Writing R
     Extensions’ manual.
@@ -838,23 +838,23 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 *   checking for code/documentation mismatches ... WARNING
     ```
     
-    (R:50780): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:35454): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     
-    (R:50817): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:35517): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     
-    (R:50949): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:35576): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     ```
 
 *   checking dependencies in R code ... NOTE
     ```
     
-    (R:49828): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:34374): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     ```
 
 *   checking foreign function calls ... NOTE
     ```
     
-    (R:50140): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:34960): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     See chapter ‘System and foreign language interfaces’ in the ‘Writing R
     Extensions’ manual.
     ```
@@ -862,13 +862,13 @@ Run `revdep_details(,"MissingDataGUI")` for more info
 *   checking R code for possible problems ... NOTE
     ```
     
-    (R:50408): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:35057): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     ```
 
 *   checking Rd \usage sections ... NOTE
     ```
     
-    (R:51056): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
+    (R:35671): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
     The \usage entries for S3 methods should use the \method markup and not
     their full name.
     See chapter ‘Writing R documentation files’ in the ‘Writing R
@@ -1198,30 +1198,6 @@ Run `revdep_details(,"robustbase")` for more info
     Package unavailable to check Rd xrefs: ‘robustX’
     ```
 
-# robustSingleCell
-
-<details>
-
-* Version: 0.1.1
-* Source code: https://github.com/cran/robustSingleCell
-* URL: https://github.com/asmagen/robustSingleCell
-* BugReports: https://github.com/asmagen/robustSingleCell/issues
-* Date/Publication: 2019-04-23 22:00:02 UTC
-* Number of recursive dependencies: 149
-
-Run `revdep_details(,"robustSingleCell")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking whether package ‘robustSingleCell’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: replacing previous import ‘GGally::mean_sd’ by ‘ggpubr::mean_sd’ when loading ‘robustSingleCell’
-      Warning: replacing previous import ‘GGally::median_iqr’ by ‘ggpubr::median_iqr’ when loading ‘robustSingleCell’
-    ```
-
 # rrr
 
 <details>
diff --git a/revdep/revdep_cran.md b/revdep/revdep_cran.md
index cca947750..78b22edab 100644
--- a/revdep/revdep_cran.md
+++ b/revdep/revdep_cran.md
@@ -2,13 +2,5 @@
 
 We checked 98 reverse dependencies (77 from CRAN + 21 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 1 new problems
+ * We saw 0 new problems
  * We failed to check 0 packages
-
-Issues with CRAN packages are summarised below.
-
-### New problems
-(This reports the first line of each new failure)
-
-* robustSingleCell
-  checking whether package ‘robustSingleCell’ can be installed ... WARNING

From 11d821418bef6e29e26b073f948c576551b27b24 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 14:36:44 -0400
Subject: [PATCH 21/22] Update cran-comments.md

---
 cran-comments.md | 60 ++++++++++++++++++++++++++++++++----------------
 1 file changed, 40 insertions(+), 20 deletions(-)

diff --git a/cran-comments.md b/cran-comments.md
index a8200149a..abccb3ce8 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,10 +1,48 @@
 
 ## Comments
 
+### 2020-6-5
+
+I have renamed the offending functions.
+
+I have rerun package checks and revdep checks and updated the final results below. (tl/dr 0 revdep problems & 0 errors | 0 warnings | 0 notes)
+
+Please let me know if there is anything else I can do.
+
+Best,
+Barret
+
+
+### 2020-6-5
+
+I talked with Joseph (co-author and author of the conflicting function names).  We are going to change our function names and resubmit.  This seems like the safest approach all around.
+
+Thank you for your time and patience.
+
+Best,
+Barret
+
+
+### 2020-6-5
+
+Changes to worse in reverse depends:
+
+Package: robustSingleCell
+Check: whether package can be installed
+New result: WARNING
+
+
+  Found the following significant warnings:
+    Warning: replacing previous import ‘GGally::mean_sd’ by ‘ggpubr::mean_sd’ when loading ‘robustSingleCell’
+    Warning: replacing previous import ‘GGally::median_iqr’ by ‘ggpubr::median_iqr’ when loading ‘robustSingleCell’
+
+- CRAN teams' auto-check service
+
+
 ### 2020-6-4
 
 Changes since last submission:
-* I removed the package vignettes (and will only host them on the package's website). 
+* I removed the package vignettes (and will only host them on the package's website).
 * I have altered the examples to only print the ggplot2 images if they are in an interactive session.
 * I have made some of the longer running tests to be CI only. (On a weekly schedule)
 
@@ -92,11 +130,6 @@ Brian D. Ripley
 
 #### R CMD check results
 
-win-builder - release:
-* checking files in 'vignettes' ... NOTE
-Package has no Sweave vignette sources and no VignetteBuilder field.
-
-Everywhere else:
 * 0 errors | 0 warnings | 0 notes
 
 
@@ -106,18 +139,5 @@ Link: https://github.com/ggobi/ggally/blob/rc-v2.0.0/revdep/README.md
 
 We checked 98 reverse dependencies (77 from CRAN + 21 from BioConductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 1 new problems
+ * We saw 0 new problems
  * We failed to check 0 packages
-
-#### New revdepcheck problems
-
-One package had an extra warning produced due to a import clash. A PR was made here: https://github.com/asmagen/robustSingleCell/pull/34
-This is not a breaking change, so I did not deem it necessary to wait two weeks before submitting to CRAN (delaying a CRAN deadline).
-
-* robustSingleCell
-  * checking whether package ‘robustSingleCell’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: replacing previous import ‘GGally::mean_sd’ by ‘ggpubr::mean_sd’ when loading ‘robustSingleCell’
-      Warning: replacing previous import ‘GGally::median_iqr’ by ‘ggpubr::median_iqr’ when loading ‘robustSingleCell’
-    ```

From ea372b12f1bbebaa6b9fc89dc661c6df394665b4 Mon Sep 17 00:00:00 2001
From: Barret Schloerke <schloerke@gmail.com>
Date: Fri, 5 Jun 2020 14:41:29 -0400
Subject: [PATCH 22/22] Update CRAN-RELEASE

---
 CRAN-RELEASE | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CRAN-RELEASE b/CRAN-RELEASE
index 46e3d4786..4d759fbe8 100644
--- a/CRAN-RELEASE
+++ b/CRAN-RELEASE
@@ -1,2 +1,2 @@
 This package was submitted to CRAN on 2020-06-05.
-Once it is accepted, delete this file and tag the release (commit cc766e3c0e).
+Once it is accepted, delete this file and tag the release (commit 11d821418b).