make polyCub.exact.Gauss() defunct and drop gpclib xrefs (#2)

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: polyCub
 Title: Cubature over Polygonal Domains
-Version: 0.8.2
-Date: 2023-10-20
+Version: 0.9.0
+Date: 2023-10-25
 Authors@R: c(
     person("Sebastian", "Meyer",
            email = "[email protected]",
@@ -20,12 +20,10 @@ Description: Numerical integration of continuously differentiable
     product Gauss cubature (Sommariva and Vianello, 2007,
     <doi:10.1007/s10543-007-0131-2>),
     the simple two-dimensional midpoint rule
-    (wrapping 'spatstat.geom' functions),
+    (wrapping 'spatstat.geom' functions), and
     adaptive cubature for radially symmetric functions via line
     integrate() along the polygon boundary (Meyer and Held, 2014,
-    <doi:10.1214/14-AOAS743>, Supplement B),
-    and integration of the bivariate Gaussian density based on
-    polygon triangulation.
+    <doi:10.1214/14-AOAS743>, Supplement B).
     For simple integration along the axes, the 'cubature' package
     is more appropriate.
 License: GPL-2
@@ -44,7 +42,6 @@ Suggests:
     lattice,
     mvtnorm,
     statmod,
-    gpclib,
     sf,
     cubature,
     knitr,

Makefile

@@ -39,7 +39,7 @@ endef
 
 ## standard --as-cran check with remote checks disabled
 check: build
-	_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=2 $R CMD check --as-cran --run-dontrun --timings ${PKG}_${VERSION}.tar.gz
+	_R_CHECK_CRAN_INCOMING_REMOTE_=FALSE _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=2 $R CMD check --as-cran --timings ${PKG}_${VERSION}.tar.gz
 ## further option: --use-gct (for better detection of memory bugs/segfaults)
 	@$(check-report-warnings-in-examples)
 

NEWS.md

@@ -1,7 +1,12 @@
-polyCub 0.8.2 (UNRELEASED)
+polyCub 0.9.0 (2023-10-25)
 ==========================
 
-* Removed remaining references to archived package
+* `polyCub.exact.Gauss()` is defunct. It may be resurrected in future
+  versions, when a reliable replacement for `gpclib::tristrip()` is
+  implemented ([#2](https://github.com/bastistician/polyCub/issues/2)).
+
+* Removed remaining references to archived packages
+  [**gpclib**](https://CRAN.R-project.org/package=gpclib) and
   [**rgeos**](https://CRAN.R-project.org/package=rgeos).
 
 * **polyCub** now requires R >= 3.2.0.

R/coerce-gpc-methods.R

@@ -12,8 +12,8 @@
 #' Conversion between polygonal \code{"owin"} and \code{"gpc.poly"}
 #'
 #' Package \pkg{polyCub} implements converters between the classes
-#' \code{"\link[spatstat.geom:owin.object]{owin}"} of package \pkg{spatstat.geom} and
-#' \code{"\link[gpclib:gpc.poly-class]{gpc.poly}"} of package \pkg{gpclib}.
+#' \code{"\link[spatstat.geom:owin.object]{owin}"} of package \CRANpkg{spatstat.geom}
+#' and \code{"gpc.poly"} of package \CRANpkg{gpclib}.
 #'
 #' @param object an object of class \code{"gpc.poly"} or \code{"owin"},
 #' respectively.
@@ -33,18 +33,20 @@
 #' @keywords spatial methods
 #' @import methods
 #' @export
-#' @examples
-#' if (require("gpclib") && require("spatstat.geom")) {
-#'     ## use example polygons from
-#'     example(plotpolyf, ask = FALSE)
+#' @examplesIf requireNamespace("spatstat.geom")
+#' ## use example polygons from
+#' example(plotpolyf, ask = FALSE)
+#' letterR  # a simple "xylist"
 #'
-#'     letterR  # a simple "xylist"
-#'     letterR.owin <- owin(poly = letterR)
-#'     letterR.gpc_from_owin <- owin2gpc(letterR.owin)
-#'     letterR.xylist_from_gpc <- xylist(letterR.gpc_from_owin)
-#'     stopifnot(all.equal(letterR, lapply(letterR.xylist_from_gpc, "[", 1:2)))
-#'     letterR.owin_from_gpc <- as.owin(letterR.gpc_from_owin)
-#'     stopifnot(all.equal(letterR.owin, letterR.owin_from_gpc))
+#' letterR.owin <- spatstat.geom::owin(poly = letterR)
+#' letterR.gpc_from_owin <- owin2gpc(letterR.owin)
+#' ## warns if "gpclib" is unavailable
+#'
+#' if (is(letterR.gpc_from_owin, "gpc.poly")) {
+#'   letterR.xylist_from_gpc <- xylist(letterR.gpc_from_owin)
+#'   stopifnot(all.equal(letterR, lapply(letterR.xylist_from_gpc, `[`, 1:2)))
+#'   letterR.owin_from_gpc <- gpc2owin(letterR.gpc_from_owin)
+#'   stopifnot(all.equal(letterR.owin, letterR.owin_from_gpc))
 #' }
 owin2gpc <- function (object)
 {
@@ -110,10 +112,9 @@ as.owin.gpc.poly <- function (W, ...)
 }
 
 
-## check for the formal class "gpc.poly" (loading gpclib if necessary)
+## check for the formal class "gpc.poly"
 #' @import methods
 know_gpc.poly <- function ()
 {
-    isClass("gpc.poly") ||
-        requireNamespace("gpclib", quietly = TRUE)
+    isClass("gpc.poly") #|| requireNamespace("gpclib", quietly = TRUE)
 }

R/plotpolyf.R

@@ -18,7 +18,7 @@
 #' @param polyregion a polygonal domain.
 #' The following classes are supported:
 #' \code{"\link[spatstat.geom]{owin}"} from package \pkg{spatstat.geom},
-#' \code{"\link[gpclib:gpc.poly-class]{gpc.poly}"} from \pkg{gpclib},
+#' \code{"gpc.poly"} from \pkg{gpclib},
 #' \code{"\linkS4class{SpatialPolygons}"}, \code{"\linkS4class{Polygons}"},
 #' and \code{"\linkS4class{Polygon}"} from package \pkg{sp}, as well as
 #' \code{"\link[sf:st_polygon]{(MULTI)POLYGON}"} from package \pkg{sf}.

R/polyCub.exact.Gauss.R

@@ -9,23 +9,29 @@
 ################################################################################
 
 
-#' Quasi-Exact Cubature of the Bivariate Normal Density
+#' Quasi-Exact Cubature of the Bivariate Normal Density (DEFUNCT)
+#'
+#' This cubature method is defunct as of \pkg{polyCub} version 0.9.0.
+#' It relied on \code{tristrip()} from package \CRANpkg{gpclib} for polygon
+#' triangulation, but that package did not have a \acronym{FOSS} license and
+#' was no longer maintained on a mainstream repository.\cr
+#' Contributions to resurrect this cubature method are welcome: an alternative
+#' implementation for constrained polygon triangulation is needed, see
+#' \url{https://github.com/bastistician/polyCub/issues/2}.
 #'
 #' The bivariate Gaussian density can be integrated based on a triangulation of
 #' the (transformed) polygonal domain, using formulae from the
 #' Abramowitz and Stegun (1972) handbook (Section 26.9, Example 9, pp. 956f.).
 #' This method is quite cumbersome because the A&S formula is only for triangles
-#' where one vertex is the origin (0,0). For each triangle of the
-#' \code{\link[gpclib]{tristrip}} we have to check in which of the 6 outer
+#' where one vertex is the origin (0,0). For each triangle
+#' we have to check in which of the 6 outer
 #' regions of the triangle the origin (0,0) lies and adapt the signs in the
 #' formula appropriately: \eqn{(AOB+BOC-AOC)} or \eqn{(AOB-AOC-BOC)} or
 #' \eqn{(AOB+AOC-BOC)} or \eqn{(AOC+BOC-AOB)} or \ldots.
 #' However, the most time consuming step is the
 #' evaluation of \code{\link[mvtnorm]{pmvnorm}}.
 #'
-#' @note Package \pkg{gpclib} is required to produce the \code{tristrip}.
-#'
-#' @param polyregion a \code{"\link[gpclib:gpc.poly-class]{gpc.poly}"} polygon or
+#' @param polyregion a \code{"gpc.poly"} polygon or
 #' something that can be coerced to this class, e.g., an \code{"owin"} polygon
 #' (via \code{\link{owin2gpc}}), or an \code{"sfg"} polygon (via
 #' \code{\link{sfg2gpc}}).
@@ -74,6 +80,13 @@
 polyCub.exact.Gauss <- function (polyregion, mean = c(0,0), Sigma = diag(2),
                                  plot = FALSE)
 {
+    ## defunctify with a maintainer-level backdoor for building the vignette
+    if (!identical(Sys.getenv("R_GPCLIBPERMIT"), "true"))
+    .Defunct(msg = paste0(
+        "'polyCub.exact.Gauss' is currently unavailable.\n",
+        "Contributions are welcome: <https://github.com/bastistician/polyCub/issues/2>"
+        ))
+
     if (inherits(polyregion, "owin")) {
         polyregion <- owin2gpc(polyregion)
     } else if (inherits(polyregion, "sfg")) {
@@ -92,7 +105,8 @@ polyCub.exact.Gauss <- function (polyregion, mean = c(0,0), Sigma = diag(2),
 
     ## triangulation: tristrip() returns a list where each element is a
     ## coordinate matrix of vertices of triangles
-    triangleSets <- gpclib::tristrip(polyregion)
+    ## FIXME: need a reliable tristrip() alternative
+    triangleSets <- utils::getFromNamespace("tristrip", "gpclib")(polyregion)
 
 ### ILLUSTRATION ###
     if (plot) {

R/sfg2gpc.R

@@ -12,9 +12,9 @@
 #' Convert polygonal \code{"sfg"} to \code{"gpc.poly"}
 #'
 #' Package \pkg{polyCub} implements a converter from class
-#' \code{"\link[sf:st_polygon]{(MULTI)POLYGON}"} of package \pkg{sf} to
-#' \code{"\link[gpclib:gpc.poly-class]{gpc.poly}"} of package
-#' \pkg{gpclib} such that \code{\link{polyCub.exact.Gauss}}
+#' \code{"\link[sf:st_polygon]{(MULTI)POLYGON}"} of package \CRANpkg{sf}
+#' to \code{"gpc.poly"} of package \CRANpkg{gpclib}
+#' such that \code{\link{polyCub.exact.Gauss}}
 #' can be used with simple feature polygons.
 #'
 #' @param object a \code{"POLYGON"} or \code{"MULTIPOLYGON"} \code{"sfg"} object.
@@ -29,29 +29,27 @@
 #' @keywords spatial methods
 #' @import methods
 #' @export
-#' @examples
-#' if (require("gpclib") && require("sf")) withAutoprint({
+#' @examplesIf requireNamespace("sf")
+#' ## use example polygons from
+#' example(plotpolyf, ask = FALSE)
+#' letterR  # a simple "xylist"
 #'
-#'     ## use example polygons from
-#'     example(plotpolyf, ask = FALSE)
-#'
-#'     letterR  # a simple "xylist"
-#'     letterR.sfg <- st_polygon(lapply(letterR, function(xy)
-#'         rbind(cbind(xy$x, xy$y), c(xy$x[1], xy$y[1]))))
-#'     letterR.sfg
-#'     stopifnot(identical(letterR, xylist(letterR.sfg)))
-#'     \dontshow{
-#'     stopifnot(identical(rep(letterR, 2),
-#'         xylist(st_multipolygon(list(letterR.sfg, letterR.sfg)))))
-#'     }
-#'     ## convert sf "POLYGON" to a "gpc.poly"
-#'     letterR.gpc_from_sfg <- sfg2gpc(letterR.sfg)
-#'     letterR.gpc_from_sfg
-#'     \dontshow{if (requireNamespace("spatstat.geom")) {
-#'         letterR.xylist_from_gpc <- xylist(letterR.gpc_from_sfg) # with hole info
-#'         stopifnot(identical(letterR, lapply(letterR.xylist_from_gpc, "[", 1:2)))
-#'     }}
-#' })
+#' letterR.sfg <- sf::st_polygon(lapply(letterR, function(xy)
+#'     rbind(cbind(xy$x, xy$y), c(xy$x[1], xy$y[1]))))
+#' letterR.sfg
+#' stopifnot(identical(letterR, xylist(letterR.sfg)))
+#' \dontshow{
+#' stopifnot(identical(rep(letterR, 2),
+#'     xylist(sf::st_multipolygon(list(letterR.sfg, letterR.sfg)))))
+#' }
+#' ## convert sf "POLYGON" to a "gpc.poly"
+#' letterR.gpc_from_sfg <- sfg2gpc(letterR.sfg)
+#' letterR.gpc_from_sfg
+#' \dontshow{
+#' if (is(letterR.gpc_from_sfg, "gpc.poly") && requireNamespace("spatstat.geom")) {
+#'     letterR.xylist_from_gpc <- xylist(letterR.gpc_from_sfg) # with hole info
+#'     stopifnot(identical(letterR, lapply(letterR.xylist_from_gpc, `[`, 1:2)))
+#' }}
 sfg2gpc <- function (object)
 {
     assert_polygonal_sfg(object)

R/xylist.R

@@ -21,7 +21,7 @@
 #' following polygon classes:
 #' \itemize{
 #' \item \code{"\link[spatstat.geom:owin.object]{owin}"} from package \pkg{spatstat.geom}
-#' \item \code{"\link[gpclib:gpc.poly-class]{gpc.poly}"} from package \pkg{gpclib}
+#' \item \code{"gpc.poly"} from package \pkg{gpclib}
 #' \item \code{"\linkS4class{Polygons}"} from package \pkg{sp}
 #' (as well as \code{"\linkS4class{Polygon}"} and
 #' \code{"\linkS4class{SpatialPolygons}"})

R/zzz.R

@@ -1,7 +1,7 @@
 ################################################################################
 ### Package Setup
 ###
-### Copyright (C) 2009-2014,2018-2021 Sebastian Meyer
+### Copyright (C) 2009-2014,2018-2021,2023 Sebastian Meyer
 ###
 ### This file is part of the R package "polyCub",
 ### free software under the terms of the GNU General Public License, version 2,
@@ -33,25 +33,17 @@
 #' via line \code{\link{integrate}()} along the polygon boundary
 #' (Meyer and Held, 2014, Supplement B, Section 2.4).
 #' }
-#' \item{\code{\link{polyCub.exact.Gauss}}:}{
-#' Accurate (but slow) integration of the \emph{bivariate Gaussian density}
-#' based on polygon triangulation (via \code{\link[gpclib]{tristrip}} from
-#' \pkg{gpclib}) and (numerous) evaluations of cumulative densities (via
-#' \code{\link[mvtnorm]{pmvnorm}} from package \pkg{mvtnorm}).
-#' Note that there is also a function \code{\link{circleCub.Gauss}}
-#' to integrate the \emph{isotropic} Gaussian density over a
-#' \emph{circular domain}.
 #' }
-#' }
-#' A more detailed description and benchmark experiment of the above cubature
-#' methods can be found in the \code{vignette("polyCub")} and in
-#' Meyer (2010, Section 3.2).
+#' A brief description and benchmark experiment of the above cubature
+#' methods can be found in the \code{vignette("polyCub")}.
 #'
-#' @references
-#' Abramowitz, M. and Stegun, I. A. (1972).
-#' \emph{Handbook of Mathematical Functions with Formulas, Graphs, and
-#' Mathematical Tables}. New York: Dover Publications.
+#' There is also \code{\link{polyCub.exact.Gauss}}, intended to
+#' accurately (but slowly) integrate the \emph{bivariate Gaussian density};
+#' however, this implementation is disabled as of \pkg{polyCub} 0.9.0:
+#' it needs a reliable implementation of polygon triangulation.
+#' Meyer (2010, Section 3.2) discusses and compares some of these methods.
 #'
+#' @references
 #' Baddeley, A., Rubak, E. and Turner, R. (2015).
 #' \emph{Spatial Point Patterns: Methodology and Applications with R}.
 #' Chapman and Hall/CRC Press, London.