Fix Clang warnings

.github/workflows/R-CMD-check.yaml

@@ -96,7 +96,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@main
+        uses: actions/upload-artifact@mv4
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: eaf
 Type: Package
 Title: Plots of the Empirical Attainment Function
-Version: 2.5.0.9000
+Version: 2.5.1
 Authors@R: c(person("Manuel", "López-Ibáñez", role = c("aut", "cre"),
                               email = "manuel.lopez-ibanez@manchester.ac.uk",
                               comment = c(ORCID = "0000-0001-9974-1295")),
@@ -30,7 +30,7 @@ URL: https://mlopez-ibanez.github.io/eaf/, https://github.com/MLopez-Ibanez/eaf
 LazyLoad: true
 LazyData: true
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
 SystemRequirements: GNU make, Gnu Scientific Library
 RdMacros: Rdpack

NEWS.md

@@ -1,4 +1,6 @@
-# eaf (development version)
+# eaf 2.5.1
+
+ * Fix Clang warning.
 
 # eaf 2.5
 

R/eafplot.R

@@ -55,11 +55,11 @@ eafplot <- function(x, ...) UseMethod("eafplot")
 #' 
 #' @template arg_maximise
 #' 
-#' @param xaxis.side On which side that xaxis is drawn. Valid values are
-#'   "below" and "above". See [axis()].
+#' @param xaxis.side On which side that x-axis is drawn. Valid values are
+#'   `"below"` and `"above"`. See [axis()].
 #' 
-#' @param yaxis.side On which side that yaxis is drawn. Valid values are "left"
-#'   and "right". See [axis()].
+#' @param yaxis.side On which side that y-axis is drawn. Valid values are `"left"`
+#'   and `"right"`. See [axis()].
 #'   
 #' @param axes A logical value indicating whether both axes should be drawn
 #'   on the plot.
@@ -70,7 +70,7 @@ eafplot <- function(x, ...) UseMethod("eafplot")
 #' 
 #' @return Return (invisibly) the attainment surfaces computed.
 #' 
-#' @seealso   [read_datasets()] [eafdiffplot()] [pdf_crop()]
+#' @seealso   [eafdiffplot()] [pdf_crop()]
 #'
 #'@examples
 #' data(gcp2x2)
@@ -157,8 +157,8 @@ eafplot.default <-
 {
   type <- match.arg (type, c("point", "area"))
   maximise <- as.logical(maximise)
-  xaxis.side <- match.arg(xaxis.side, c("below", "above"))
-  yaxis.side <- match.arg(yaxis.side, c("left", "right"))
+  xaxis_side <- match.arg(xaxis.side, c("below", "above"))
+  yaxis_side <- match.arg(yaxis.side, c("left", "right"))
 
   if (is.null(col)) {
     if (type == "point") {
@@ -241,8 +241,8 @@ eafplot.default <-
        xlim = xlim, ylim = ylim, log = log, axes = FALSE, las = las,
        panel.first = ({
          if (axes) {
-           plot_eaf_axis(xaxis.side, xlab, las = las, sci.notation = sci.notation)
-           plot_eaf_axis(yaxis.side, ylab, las = las, sci.notation = sci.notation,
+           plot_eaf_axis(xaxis_side, xlab, las = las, sci.notation = sci.notation)
+           plot_eaf_axis(yaxis_side, ylab, las = las, sci.notation = sci.notation,
                          # FIXME: eafplot uses 2.2, why the difference?
                          line = 2.75)
          }
@@ -368,11 +368,11 @@ prettySciNotation <- function(x, digits = 1L)
 axis_side <- function(side)
 {
   if (!is.character(side)) return(side)
-  return(switch(side,
-                below = 1,
-                left = 2,
-                above = 3,
-                right = 4))
+  switch(side,
+    below = 1,
+    left = 2,
+    above = 3,
+    right = 4)
 }
 
 plot_eaf_axis <- function(side, lab, las,
@@ -396,8 +396,8 @@ plot_eaf_axis <- function(side, lab, las,
   ##   ## Now do the minor ticks, at 1/10 of each power of 10 interval
   ##   ##at.minor <- 2:9 * rep(c(10^c(1:max.pow)) / 10, each = length(2:9))
   ##   at.minor <- 1:10 * rep(c(10^c(1:max.pow)) / 10, each = length(1:10))
-  ##   axis (yaxis.side, at = at.minor, tcl = -0.25, labels = FALSE, las=las)
-  ##   axis (yaxis.side, at = at.minor, labels = FALSE, tck=1,
+  ##   axis (yaxis_side, at = at.minor, tcl = -0.25, labels = FALSE, las=las)
+  ##   axis (yaxis_side, at = at.minor, labels = FALSE, tck=1,
   ##         col='lightgray', lty='dotted', lwd=par("lwd"))
   ## }
 
@@ -454,8 +454,8 @@ plot_eafdiff_side <- function (eafdiff, attsurfs = list(),
   type <- match.arg (type, c("point", "area"))
   maximise <- as.logical(maximise)
   side <- match.arg (side, c("left", "right"))
-  xaxis.side <- if (side == "left") "below" else "above"
-  yaxis.side <- if (side == "left") "left" else "right"
+  xaxis_side <- if (side == "left") "below" else "above"
+  yaxis_side <- if (side == "left") "left" else "right"
 
   # For !full.eaf && type == "area", str(eafdiff) is a polygon:
   ##  $  num [, 1:2]
@@ -497,8 +497,8 @@ plot_eafdiff_side <- function (eafdiff, attsurfs = list(),
   plot(xlim, ylim, type = "n", xlab = "", ylab = "",
        xlim = xlim, ylim = ylim, log = log, axes = FALSE, las = las,
        panel.first = ({
-         plot_eaf_axis (xaxis.side, xlab, las = las, sci.notation = sci.notation)
-         plot_eaf_axis (yaxis.side, ylab, las = las, sci.notation = sci.notation,
+         plot_eaf_axis (xaxis_side, xlab, las = las, sci.notation = sci.notation)
+         plot_eaf_axis (yaxis_side, ylab, las = las, sci.notation = sci.notation,
                         line = 2.2)
 
          if (nrow(eafdiff)) {
@@ -585,10 +585,10 @@ plot_eafdiff_side <- function (eafdiff, attsurfs = list(),
 #'   (\samp{points}) or whether to color the areas that have at least a
 #'   certain value (\samp{area}).
 #' 
-#'@param legend.pos The position of the legend. See [legend()].  A value of
+#' @param legend.pos The position of the legend. See [legend()].  A value of
 #'   `"none"` hides the legend.
 #' 
-#'@param title.left,title.right Title for left and right panels, respectively.
+#' @param title.left,title.right Title for left and right panels, respectively.
 #'  
 #' @param xlim,ylim,cex,cex.lab,cex.axis Graphical parameters, see
 #'   [plot.default()].
@@ -647,7 +647,7 @@ plot_eafdiff_side <- function (eafdiff, attsurfs = list(),
 #' 
 #' @return Returns a representation of the EAF differences (invisibly).
 #' 
-#' @seealso    [read_datasets()] [eafplot()] [pdf_crop()]
+#' @seealso    [eafplot()] [pdf_crop()]
 #' 
 #' @examples
 #' ## NOTE: The plots in the website look squashed because of how pkgdown

cleanup

@@ -1,6 +1,12 @@
 #!/bin/sh
 rm -f  config.* confdefs.h tests/testthat/*.pdf \
        src/*.o src/*.so src/Makevars src/config.h src/symbols.rds \
-       inst/doc/*.blg inst/doc/*.bbl *-Ex.R
+       inst/doc/*.blg inst/doc/*.bbl *-Ex.R \
+       src/eaf/eaf \
+       src/mo-tools/dominatedsets \
+       src/mo-tools/epsilon \
+       src/mo-tools/igd \
+       src/mo-tools/ndsort \
+       src/mo-tools/nondominated
 
 rm -rf autom4te.cache

src/Makevars.in

@@ -15,24 +15,12 @@ OBJECTS = $(SOURCES:.c=.o)
 
 export GSL_CFLAGS GSL_LIBS
 
-eaf = eaf/eaf$(EXEEXT)
-igd = mo-tools/igd$(EXEEXT)
-epsilon = mo-tools/epsilon$(EXEEXT)
-dominatedsets = mo-tools/dominatedsets$(EXEEXT)
-nondominated = mo-tools/nondominated$(EXEEXT)
-ndsort = mo-tools/ndsort$(EXEEXT)
-
 .PHONY: all clean
 
 all: $(SHLIB)
-	$(MAKE) -C eaf all march=none CC="$(CC)" CFLAGS="$(CFLAGS) $(LTO)" OPT_CFLAGS="" WARN_CFLAGS="" DEBUG=$(DEBUG) EXE=$(EXEEXT)
-	$(MAKE) -C mo-tools all march=none CC="$(CC)" CFLAGS="$(CFLAGS) $(LTO)" OPT_CFLAGS="" WARN_CFLAGS="" DEBUG=$(DEBUG) EXE=$(EXEEXT)
 
 $(SHLIB): $(OBJECTS) 
 
 clean:
-	@-rm -f *.o *.so *.dll \
-	eaf/*.o $(eaf) \
-	$(igd) $(epsilon) $(dominatedsets) $(nondominated) $(ndsort) \
-	mo-tools/*.o 
+	@-rm -f *.o *.so *.dll eaf/*.o mo-tools/*.o 
 

src/Makevars.win

@@ -14,30 +14,16 @@ MOTOOLS_SRC_FILES = hv_contrib.c hv.c pareto.c whv.c whv_hype.c
 SOURCES = $(EAF_SRC_FILES:%=eaf/%) $(MOTOOLS_SRC_FILES:%=mo-tools/%) init.c  Reaf.c  Repsilon.c  Rhv.c  Rnondominated.c
 OBJECTS = $(SOURCES:.c=.o)
 
-EXEEXT=.exe
-
 export GSL_CFLAGS GSL_LIBS
 
-eaf = eaf/eaf$(EXEEXT)
-igd = mo-tools/igd$(EXEEXT)
-epsilon = mo-tools/epsilon$(EXEEXT)
-dominatedsets = mo-tools/dominatedsets$(EXEEXT)
-nondominated = mo-tools/nondominated$(EXEEXT)
-ndsort = mo-tools/ndsort$(EXEEXT)
-
 .PHONY: all clean winlibs
 
 all: $(SHLIB)
-	$(MAKE) -C eaf all march=none CC="$(CC)" CFLAGS="$(CFLAGS)" OPT_CFLAGS="" WARN_CFLAGS="" DEBUG=$(DEBUG) EXE=$(EXEEXT)
-	$(MAKE) -C mo-tools all march=none CC="$(CC)" CFLAGS="$(CFLAGS)" OPT_CFLAGS="" WARN_CFLAGS="" DEBUG=$(DEBUG) EXE=$(EXEEXT)
 
 $(SHLIB): $(OBJECTS)
 
 clean:
-	@-rm -f *.o *.so *.dll \
-	eaf/*.o $(eaf) \
-	$(igd) $(epsilon) $(dominatedsets) $(nondominated) $(ndsort) \
-	mo-tools/*.o
+	@-rm -f *.o *.so *.dll eaf/*.o	mo-tools/*.o
 
 $(OBJECTS): winlibs
 

src/eaf/eaf_main.c

@@ -81,14 +81,16 @@ static void usage(void)
 
 static void version(void)
 {
-    printf("%s version %s"
-#ifdef MARCH
-           " (optimised for "MARCH")"
-#endif
 #ifndef VERSION
 #define VERSION "unknown"
 #endif
-           "\n\n", program_invocation_short_name, VERSION);
+#ifdef MARCH
+#define OPTIMISED_FOR_STR " (optimised for "MARCH")"
+#else
+#define OPTIMISED_FOR_STR ""
+#endif
+    printf("%s version " VERSION OPTIMISED_FOR_STR
+           "\n\n", program_invocation_short_name);
     printf(
 "Copyright (C) 2009\n"
 "Carlos Fonseca <cmfonsec@ualg.pt>\n"

src/eaf/svn_version

@@ -1 +1 @@
-292
+292M

src/install.libs.R

@@ -1,17 +1,8 @@
-execs <- c(file.path("eaf", "eaf"),
-           file.path("mo-tools", c("epsilon","igd","dominatedsets","nondominated","ndsort")))
-
-if (WINDOWS) execs <- paste0(execs, ".exe")
-if (any(file.exists(execs))) {
-  dest <- file.path(R_PACKAGE_DIR,  paste0('bin', R_ARCH))
+files <- Sys.glob(paste0("*", SHLIB_EXT))
+if (any(file.exists(files))) {
+  dest <- file.path(R_PACKAGE_DIR, paste0('libs', R_ARCH))
   dir.create(dest, recursive = TRUE, showWarnings = FALSE)
-  file.copy(execs, dest, overwrite = TRUE)
+  file.copy(files, dest, overwrite = TRUE)
 }
-
-files <- Sys.glob(paste0("*", SHLIB_EXT))
-dest <- file.path(R_PACKAGE_DIR, paste0('libs', R_ARCH))
-dir.create(dest, recursive = TRUE, showWarnings = FALSE)
-file.copy(files, dest, overwrite = TRUE)
-if (file.exists("symbols.rds")) {
+if (file.exists("symbols.rds"))
   file.copy("symbols.rds", dest, overwrite = TRUE)
-}