ggobi · schloerke · Aug 3, 2017 · Jun 2, 2017 · Jul 20, 2017 · Jul 20, 2017
diff --git a/.helper_functions b/.helper_functions
@@ -50,7 +50,8 @@ reverse_depends:
   do_check <- function() {
     devtools::revdep_check(
       bioconductor = TRUE,
-      ignore = c("nzelect"),
+      # ignore = c("nzelect"),
+      ignore = c(),
       libpath = .libPaths()[1],
       srcpath = normalizePath(file.path("revdep", "lib"))
     )

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: GGally
-Version: 1.3.1
+Version: 1.3.2
 License: GPL (>= 2.0)
 Title: Extension to 'ggplot2'
 Type: Package
@@ -29,6 +29,7 @@ Depends:
     R (>= 3.1)
 Imports:
     ggplot2 (>= 2.2.0),
+    grDevices,
     grid,
     gtable (>= 0.2.0),
     plyr (>= 1.8.3),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,20 @@
+GGally 1.3.2
+-----------------
+
+`ggpairs` and `ggduo`
+
+* Removed warning where pure numeric names gave a warning (#238, @lepennec)
+* Fixed ordering issue with horizontal boxplots (#239)
+
+`ggparcoord`
+
+* Fixed missing `x` aes requirement when shadebox is provided (#237, @treysp)
+
+Package
+
+* Made igraph a non required dependency for tests (#240)
+
+
 GGally 1.3.1
 -----------------
 

diff --git a/R/gg-plots.R b/R/gg-plots.R
@@ -577,7 +577,7 @@ ggally_dot_and_box_no_facet <- function(data, mapping, ..., boxPlot = TRUE) {
   if (horizontal) {
     p <- p +
       scale_x_discrete(
-        breaks = rev(levels(eval_data_col(data, mapping$x)))
+        limits = rev(levels(eval_data_col(data, mapping$x)))
       ) +
       coord_flip()
   }
@@ -844,7 +844,7 @@ ggally_barDiag <- function(data, mapping, ..., rescale = FALSE){
 }
 
 
-#' GGplot Text
+#' Text Plot
 #'
 #' Plot text for a plot.
 #'

diff --git a/R/ggnetworkmap.R b/R/ggnetworkmap.R
@@ -39,7 +39,7 @@ if(getRversion() >= "2.15.1") {
 #' @param label.size size of the labels.  Defaults to \code{size / 2}.
 #' @param ... other arguments supplied to geom_text for the node labels. Arguments pertaining to the title or other items can be achieved through ggplot2 methods.
 #' @author Amos Elberg \email{amos.elberg@@gmail.com}. Original by Moritz Marbach \email{mmarbach@@mail.uni-mannheim.de}, Francois Briatte \email{f.briatte@@gmail.com}
-#' @details This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet.  The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart.  Segments can be straight lines, or plotted as great circles.  Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a gglot2 limitation and cannot yet be fixed.  Nodes can have two color schemes, which are then plotted as the center and ring around the node.  The color schemes are selected by adding scale_fill_ or scale_color_ just like any other ggplot2 plot. If there are no rings, scale_color sets the color of the nodes.  If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers.  Note that additional arguments in the ... are passed to geom_text for plotting labels.
+#' @details This is a function for plotting graphs generated by \code{network} or \code{igraph} in a more flexible and elegant manner than permitted by ggnet.  The function does not need to be the first plot in the ggplot chain, so the graph can be plotted on top of a map or other chart.  Segments can be straight lines, or plotted as great circles.  Note that the great circles feature can produce odd results with arrows and with vertices beyond the plot edges; this is a ggplot2 limitation and cannot yet be fixed.  Nodes can have two color schemes, which are then plotted as the center and ring around the node.  The color schemes are selected by adding scale_fill_ or scale_color_ just like any other ggplot2 plot. If there are no rings, scale_color sets the color of the nodes.  If there are rings, scale_color sets the color of the rings, and scale_fill sets the color of the centers.  Note that additional arguments in the ... are passed to geom_text for plotting labels.
 #' @importFrom utils installed.packages
 #' @examples
 #' # small function to display plots only if it's interactive

diff --git a/R/ggpairs.R b/R/ggpairs.R
@@ -127,18 +127,6 @@ fix_column_values <- function(
     }
   }
 
-  colnamesUsed <- colnamesData[columns]
-  nameIsOnlyNumber <- ! str_detect(colnamesUsed, "[^0-9]")
-  if (any(nameIsOnlyNumber)) {
-    badColumns <- colnamesUsed[nameIsOnlyNumber]
-    names(badColumns) <- paste("column =", columns[nameIsOnlyNumber])
-    warning(paste(
-      "Data column name is numeric.  Desired behavior may not be as expected.\n\n",
-      "c(", paste("'", names(badColumns), "' = '", badColumns, "'", collapse = "", sep = ""), ")",
-      sep = ""
-    ))
-  }
-
   columns
 }
 
@@ -518,7 +506,7 @@ ggduo <- function(
 
     sectionAes <- add_and_overwrite_aes(
       add_and_overwrite_aes(
-        aes_string(x = xColName, y = yColName),
+        aes_(x = as.name(xColName), y = as.name(yColName)),
         mapping
       ),
       types$mapping
@@ -819,7 +807,7 @@ ggpairs <- function(
 
     sectionAes <- add_and_overwrite_aes(
       add_and_overwrite_aes(
-        aes_string(x = xColName, y = yColName),
+        aes_(x = as.name(xColName), y = as.name(yColName)),
         mapping
       ),
       types$mapping
@@ -867,7 +855,7 @@ ggpairs <- function(
 #'
 #' @keywords internal
 #' @author Barret Schloerke \email{schloerke@@gmail.com}
-#' @return aes_string output
+#' @return aes_ output
 #' @import ggplot2
 #' @rdname add_and_overwrite_aes
 #' @examples

diff --git a/R/ggparcoord.R b/R/ggparcoord.R
@@ -249,6 +249,17 @@ ggparcoord <- function(
     stop("invalid value for 'boxplot'; must be a logical operator")
   }
 
+  if (!is.null(shadeBox) && length(shadeBox) != 1) {
+    stop("invalid value for 'shadeBox'; must be a single color")
+  } else {
+    valid_color <- tryCatch(is.matrix(grDevices::col2rgb(shadeBox)),
+                            error = function(e) FALSE)
+
+    if (!valid_color) {
+      stop("invalid value for 'shadeBox'; must be a valid R color")
+    }
+  }
+
   if (is.logical(splineFactor)) {
     if (splineFactor) {
       splineFactor <- 3
@@ -498,6 +509,7 @@ ggparcoord <- function(
         data = d.sum, size = I(10), col = shadeBox,
         inherit.aes = FALSE,
         mapping = aes_string(
+          x = "variable",
           ymin = "min",
           ymax = "max",
           group = "variable"

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,82 +1,75 @@
 
 ## Comments
 
-### 2017-6-7
+### 2017-8-2
 
-vortexR has been updated to handle the new version of GGally.  From my reverse dependency checks, there were no other affected packages.  <https://github.com/ggobi/ggally/blob/master/revdep/problem-diff.txt>
+No revdep authors were emailed as it is only small bug fixes or 'Suggest' dependency change for Brian.
+
+Please let me know if there is anything I can do.  Thank you for your time.
 
 Best,
 Barret
 
 
-### 2017-6-7
-
-On CRAN
-- @carlopacioni vortexR maintainer
-
-
-### 2017-6-4
-
-vortexR maintainer contacted.
-
+### 2017-7-18
 
-### 2017-6-4
+As §1.1.3.1 of the manual told you, packages in Suggests: should be used
+conditionally.  The latest version of igraph will not install on Solaris
+(hence packages strictly depending on it), and as you can see from its
+CRAN checks page, your package now fails its check.
 
-~ Please give two weeks notice to affected packages.
-- Uwe
+Please correct ASAP and definitely within a month.
 
+--
+Brian D. Ripley,
 
-### 2017-6-2
-
-No revdep authors were emailed as it is only small bug fixes, url link fixes, and new functions.
-
-Please let me know if there is anything I can do.  Thank you for your time.
-
-Best,
-Barret
 
 
 #### Test environments and R CMD check results
 
 * local OS X install
-  * R version 3.4.0 (2017-04-21)
+  * R version 3.4.1 (2017-06-30)
     Platform: x86_64-apple-darwin15.6.0 (64-bit)
-    Running under: macOS Sierra 10.12.4
+    Running under: macOS Sierra 10.12.5
     * 0 errors | 0 warnings | 0 notes
 
 * travis-ci
-  * R version 3.4.0 (2017-04-21)
+  * R version 3.4.1 (2017-06-30)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Ubuntu precise (12.04.5 LTS)
     * 0 errors | 0 warnings | 0 notes
 
-  * R Under development (unstable) (2017-05-24 r72734)
+  * R Under development (unstable) (2017-08-01 r73010)
     Platform: x86_64-pc-linux-gnu (64-bit)
     Running under: Ubuntu precise (12.04.5 LTS)
     * 0 errors | 0 warnings | 0 notes
 
 * win-builder (devel and release)
-  * R version 3.4.0 (2017-04-21)
+  * R version 3.4.1 (2017-06-30)
     * 0 errors | 0 warnings | 0 notes
-  * R Under development (unstable) (2017-06-01 r72753)
+  * R Under development (unstable) (2017-07-31 r73003)
     * 0 errors | 0 warnings | 0 notes
 
 
 ## Reverse dependencies
 
 Checked on
-  * R version 3.4.0 (2017-04-21)
+  * R version 3.4.1 (2017-06-30)
     Platform: x86_64-apple-darwin15.6.0 (64-bit)
-    Running under: macOS Sierra 10.12.4
+    Running under: macOS Sierra 10.12.5
 
 No difference in test results due to GGally upgrade: <https://github.com/ggobi/ggally/blob/master/revdep/problem-diff.txt>
 
 
 Errors not related to GGally upgrade:
-* Failed to install dependencies for: MissingDataGUI, specmine
-* ggbio: checking examples ... ERROR
-* POUMM: checking re-building of vignette outputs ... WARNING
-* TVTB: checking tests ... ERROR
 
-* Check failed to finish in 20 minutes, so ignored
-  * nzelect
+|package        |version | errors| warnings| notes|
+|:--------------|:-------|------:|--------:|-----:|
+|eechidna       |1.1     |      0|        1|     1| - vignette building
+|nzelect        |0.3.3   |      0|        1|     0| - vignette building
+|PopGenReport   |3.0.0   |      0|        1|     1| - due to missing package dependencies
+|POUMM          |1.3.2   |      1|        0|     0| - can not install source package
+|MissingDataGUI |0.2-5   |      1|        0|     0| - can not install dependencies
+|specmine       |1.0     |      1|        0|     0| - can not install dependencies
+
+* Side note, package 'Pi' took over 4 hours to check.
diff --git a/man/add_and_overwrite_aes.Rd b/man/add_and_overwrite_aes.Rd
diff --git a/man/ggally_text.Rd b/man/ggally_text.Rd
diff --git a/man/ggnetworkmap.Rd b/man/ggnetworkmap.Rd