Support spell_check

DESCRIPTION

@@ -18,10 +18,12 @@ Imports:
         grDevices,
         matrixStats,
         Rdpack
-Suggests: extrafont,
-          testthat (>= 3.0.0),
-          withr,
-          viridisLite
+Suggests: 
+    extrafont,
+    testthat (>= 3.0.0),
+    withr,
+    viridisLite,
+    spelling
 License: GPL (>= 2)
 BugReports: https://github.com/MLopez-Ibanez/eaf/issues
 URL: https://mlopez-ibanez.github.io/eaf/, https://github.com/MLopez-Ibanez/eaf
@@ -33,3 +35,4 @@ Roxygen: list(markdown = TRUE)
 SystemRequirements: GNU make, Gnu Scientific Library
 RdMacros: Rdpack
 Config/testthat/edition: 3
+Language: en-GB

Makefile

@@ -78,9 +78,9 @@ releasebuild: clean
 	cd $(BINDIR) &&	R CMD build $(PACKAGEDIR) && tar -atvf $(PACKAGE)_$(PACKAGEVERSION).tar.gz
 
 releasecheck: cran
+	$(Reval) 'devtools::spell_check()'
 	$(Reval) 'urlchecker::url_check()'
-	$(MAKE) winbuild
-	$(MAKE) macbuild
+	$(MAKE) winbuild #$(MAKE) macbuild
 
 cran : build
 	cd $(BINDIR) && _R_CHECK_FORCE_SUGGESTS_=false _R_OPTIONS_STRINGS_AS_FACTORS_=false R CMD check --as-cran $(PACKAGE)_$(PACKAGEVERSION).tar.gz
@@ -144,8 +144,9 @@ submit:
 remotecran: releasebuild
 	$(Reval) "rhub::check_for_cran($(RHUB_COMMON_ARGS), show_status = TRUE)"
 
-macbuild: releasebuild
-	$(Reval) "rhub::check(platform='macos-highsierra-release-cran', $(RHUB_COMMON_ARGS))"
+# Stopped working
+# macbuild: releasebuild
+#	$(Reval) "rhub::check(platform='macos-highsierra-release-cran', $(RHUB_COMMON_ARGS))"
 
 winbuild: releasebuild
 	$(Reval) "devtools::check_win_release()"

NEWS.md

@@ -123,7 +123,7 @@
 
 # eaf 1.06
 
-* Fix bug when automatically generating a legend in eafplot with the
+* Fix bug when automatically generating a legend in `eafplot()` with the
   formula interface (Thanks to Bernd Bischl for reporting this)
 
 * Improve handling of various newline character formats.
@@ -132,7 +132,7 @@
 
 * `eafdiff.pl`: Mention option `--legendpos=none` to hide the legend.
 
-* eafplot.pl: Add options `--maximise` and `--xmaximise` and `--colors=`.
+* `eafplot.pl`: Add options `--maximise` and `--xmaximise` and `--colors=`.
   Fix bug with `--area`.
 
 * `eafplot.default()` now requires two colors when `type=="area"` and a
@@ -150,40 +150,40 @@
 
 * Attempt to deal with DOS/Unix newlines correctly.
 
-* eafplot.pl: Cleanups.
+* `eafplot.pl`: Cleanups.
   (`--single, --output, --legend`): New options.
   Default to PDF.
 
-* eafdiff.pl: Many cleanups.
+* `eafdiff.pl`: Many cleanups.
   EAF diff with `type="area"` is the default now.
   Parameter `--cex` replaced by `--scale`.
-  Do not require ps2eps.
-  Handle `--obj1=` better. Crop pdf before converting to png.
+  Do not require `ps2eps`.
+  Handle `--obj1=` better. Crop pdf before converting to `PNG`.
   (`--noattsurfs`): New option.
   (`--output-dir,--output`): New options.
   (`--eps`): New option. PDF is the default now.
 
-* Force eafdiff plots to use a square plotting region.
+* Force `eafdiffplot()` to use a square plotting region.
 
-* `read.data.sets()` normalizes paths, thus it works with files such as ~/file.
+* `read.data.sets()` normalizes paths, thus it works with files such as `~/file`.
 
 * Function `eafdiffplot()` handles `percentiles=NA` and grand.lines
   parameter.
 
 * Fix bug with ranges and `maximise=TRUE` in `eafdiffplot()`.
 
-* Fix points.steps to work correctly for all values of maximise.
+* Fix `points.steps` to work correctly for all values of `maximise`.
 
 * Fix bug in  `eafdiffplot(..., maximise=c(TRUE,FALSE), full.eaf = TRUE)`
 
-* Fix `"log"` parameter in eafplot and eafdiffplot.
+* Fix `"log"` parameter in `eafplot()` and `eafdiffplot()`.
 
 * Avoid that `eafplot.formula` modifies global options.
 
-* Add `'axes'` parameter to eafplot.
+* Add `'axes'` parameter to `eafplot()`.
 
 * To avoid confusion, the arguments `'xaxis.side'` and `'yaxis.side'` of
-  eafplot can only take values `c("below", "above")` and `c("left",
+  `eafplot()` can only take values `c("below", "above")` and `c("left",
   "right")`, respectively.
 
 * Add missing Makefile in `inst/scripts/eaf/`.
@@ -194,10 +194,10 @@
 
 # eaf 1.03
 
-* Handle maximise argument in eafdiffplot and `--maximise` command-line
+* Handle maximise argument in `eafdiffplot()` and `--maximise` command-line
   option in `eafdiff.pl`
 
-* R/calls.R (eafplot.data.frame): Fix problem with main parameter.
+* `R/calls.R` (`eafplot.data.frame`): Fix problem with main parameter.
 
 # eaf 1.00
 

R/eaf.R

@@ -375,7 +375,7 @@ points.steps <- function(x)
 #'  point. If groups is not `NULL`, then an additional column
 #'  indicates to which group the point belongs.
 #'
-#' @author  Manuel \enc{López-Ibáñez}{Lopez-Ibanez}
+#' @author  Manuel López-Ibáñez
 #'
 #'@note There are several examples of data sets in `system.file(package="eaf","extdata")`. The current implementation only supports two and three dimensional points.
 #'

R/eafplot.R

@@ -4,18 +4,18 @@
 #' attainment surfaces for certain percentiles or as points.
 #'
 #' This function can be used to plot random sets of points like those obtained
-#' by different runs of biobjective stochastic optimization algorithms.  An EAF
+#' by different runs of biobjective stochastic optimisation algorithms.  An EAF
 #' curve represents the boundary separating points that are known to be
 #' attainable (that is, dominated in Pareto sense) in at least a fraction
 #' (quantile) of the runs from those that are not. The median EAF represents
 #' the curve where the fraction of attainable points is 50%.  In single
-#' objective optimization the function can be used to plot the profile of
+#' objective optimisation the function can be used to plot the profile of
 #' solution quality over time of a collection of runs of a stochastic optimizer.
 #' 
 #' @param x Either a matrix of data values, or a data frame, or a list of
 #'     data frames of exactly three columns.
 #'
-#' @concept eafviz
+#' @concept visualisation
 #' @export
 eafplot <- function(x, ...) UseMethod("eafplot")
 
@@ -124,7 +124,7 @@ eafplot <- function(x, ...) UseMethod("eafplot")
 #'          las = 1, log = "y", main = "SPEA2 (Richmond)",
 #'          legend.pos = "bottomright")
 #' }
-#' @concept eafviz
+#' @concept visualisation
 #' @export
 eafplot.default <-
   function (x, sets = NULL, groups = NULL,
@@ -681,7 +681,7 @@ plot.eafdiff.side <- function (eafdiff, attsurfs = list(),
 #' #             file = "wrots_l100w10_dat-wrots_l10w100_dat-diff.txt",
 #' #             quote = FALSE, row.names = FALSE, col.names = FALSE)
 #'
-#' @concept eafviz
+#' @concept visualisation
 #'@export
 eafdiffplot <-
   function(data.left, data.right,
@@ -891,7 +891,7 @@ seq.intervals.labels <- function(s, first.open = FALSE, last.open = FALSE,
 #' 
 #'@param data Dataframe containing the fields mentioned in the formula and in groups.
 #'@export
-#'@concept eafviz
+#'@concept visualisation
 eafplot.formula <- function(formula, data, groups = NULL, subset = NULL, ...)
 {
   ## formula of type time+cost~run|inst, groups=alg
@@ -969,7 +969,7 @@ eafplot.formula <- function(formula, data, groups = NULL, subset = NULL, ...)
 #' @describeIn eafplot List interface for lists of data.frames or matrices
 #' 
 #'@export
-#'@concept eafviz
+#'@concept visualisation
 eafplot.list <- function(x, ...)
 {
   if (!is.list(x))

R/interactive.R

@@ -60,7 +60,7 @@
 #'
 #'@references
 #' \insertAllCited{}
-#' @concept eafviz
+#' @concept visualisation
 #' @export
 choose_eafdiffplot <- function(data.left, data.right, intervals = 5,
                                maximise = c(FALSE, FALSE),

R/read_datasets.R

@@ -89,7 +89,7 @@ read.data.sets <- function(file, col.names)
 #' @param x  The data set to write. The last column must be the set number.
 #' 
 #' @param file either a character string naming a file or a connection open for
-#'   writing. ‘""’ indicates output to the console.
+#'   writing. `""` indicates output to the console.
 #'
 #'@seealso \code{\link[utils]{write.table}}, [read_datasets()]
 #'

cran-comments.md

@@ -2,7 +2,7 @@ Dear CRAN maintainers,
 
 I would like to submit a new version of the 'eaf' package to CRAN.
 
-This fixes a -Wuse-after-free warning reported by Prof Brian Ripley.
+This fixes several warnings reported by CRAN.
 
 Regarding this NOTE:
 

inst/WORDLIST

@@ -0,0 +1,46 @@
+Bartz
+Beielstein
+Biobjective
+Bischl
+Cleanups
+Codecov
+Coloring
+DIMACS
+EAFs
+GD
+GPs
+Hausdorff
+Hypervolume
+IGD
+IGDX
+IRIDIA
+Ibáñez
+López
+Metaheuristics
+Mickael
+Molchanov
+ORCID
+Preuss
+Quemy
+Roxygen
+SPEA
+TR
+Tabu
+TabuCol
+TinyTeX
+Vanzyl's
+Vorob'ev
+behavior
+behaviors
+bibtex
+biobjective
+cleanups
+color
+colormap
+colors
+doi
+favor
+hypervolume
+libre
+metaheuristic
+nondominated

pkgdown/_pkgdown.yml

@@ -25,7 +25,7 @@ reference:
       - has_concept("eaf")
   - title: Visualizing the Empirical Attainment Function
     contents:
-      - has_concept("eafviz")
+      - has_concept("visualisation")
       - symDifPlot
   - title: Pareto dominance
     contents: has_concept("dominance")

tests/spelling.R

@@ -0,0 +1,3 @@
+if(requireNamespace('spelling', quietly = TRUE))
+  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                             skip_on_cran = TRUE)