CRS cache and updated CRS print method

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: sp
-Version: 1.4-5
+Version: 1.4-6
 Title: Classes and Methods for Spatial Data
 Authors@R: c(person("Edzer", "Pebesma", role = c("aut", "cre"),
 				email = "edzer.pebesma@uni-muenster.de"),
@@ -16,7 +16,7 @@ Authors@R: c(person("Edzer", "Pebesma", role = c("aut", "cre"),
 			person("Joseph", "O'Rourke", role = "ctb"))
 Depends: R (>= 3.0.0), methods
 Imports: utils, stats, graphics, grDevices, lattice, grid
-Suggests: RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat, maptools, deldir
+Suggests: RColorBrewer, rgdal (>= 1.2-3), rgeos (>= 0.3-13), gstat, maptools, deldir, knitr, rmarkdown
 Description: Classes and methods for spatial
   data; the classes document where the spatial location information
   resides, for 2D or 3D data. Utility functions are provided, e.g. for
@@ -44,3 +44,5 @@ Collate: bpy.colors.R AAA.R Class-CRS.R CRS-methods.R
 	recenter.R dms.R gridlines.R spdists.R rbind.R flipSGDF.R
 	chfids.R loadmeuse.R compassRose.R surfaceArea.R spOptions.R
 	subset.R disaggregate.R sp_spat1.R merge.R aggregate.R
+VignetteBuilder: knitr
+

R/AAA.R

@@ -11,6 +11,10 @@ assign("col.regions", bpy.colors(), envir = .spOptions)
 assign("thin_PROJ6_warnings", FALSE, envir=.spOptions)
 assign("PROJ6_warnings_count", 0L, envir=.spOptions)
 
+#.sp_CRS_cache <- new.env(FALSE, globalenv())
+#assign("CRS_CACHE", list(), envir=.sp_CRS_cache)
+.sp_CRS_cache <- new.env(hash=TRUE, globalenv())
+
 .onLoad <- function(lib, pkg) {
   load_stuff()
 }

R/CRS-methods.R

@@ -1,4 +1,4 @@
-# Copyright (c) 2003-20 by Barry Rowlingson and Roger Bivand
+# Copyright (c) 2003-21 by Barry Rowlingson and Roger Bivand
 
 if (!is.R()) {
   strsplit <- function(a,b) {
@@ -35,15 +35,42 @@ setMethod("rebuild_CRS", signature(obj = "CRS"),
     stopifnot(is.logical(get_source_if_boundcrs))
     stopifnot(length(get_source_if_boundcrs) == 1L)
     stopifnot(is.character(projargs))
+#    CRS_CACHE <- get("CRS_CACHE", envir=.sp_CRS_cache)
+    input_projargs <- projargs
+    if (!is.na(input_projargs)) {
+        res <- .sp_CRS_cache[[input_projargs]]
+        if (!is.null(res)) {
+            return(res)
+        }
+    }
+    if (doCheckCRSArgs && requireNamespace("rgdal", quietly = TRUE)) {
+       if (packageVersion("rgdal") >= "1.5.1" && !rgdal::new_proj_and_gdal()) {
+           if (is.na(projargs) && !is.null(SRS_string)) {
+               if (substring(SRS_string, 1, 4) == "EPSG") {
+                   pa0 <- strsplit(SRS_string, ":")[[1]]
+                   projargs <- paste0("+init=epsg:", pa0[2])
+               }
+           }
+        }
+    }
     if (!is.na(projargs)) {
         if (length(grep("^[ ]*\\+", projargs)) == 0) {
             if (is.null(SRS_string)) {
                 if (doCheckCRSArgs && 
                     requireNamespace("rgdal", quietly = TRUE)) {
-                    if (packageVersion("rgdal") >= "1.5.1" && 
-                        rgdal::new_proj_and_gdal()) {
-                        SRS_string <- projargs
-                        projargs <- NA_character_
+                    if (packageVersion("rgdal") >= "1.5.1") { 
+                        if (rgdal::new_proj_and_gdal()) {
+                            SRS_string <- projargs
+                            projargs <- NA_character_
+                        } else {
+                            if (substring(projargs, 1, 4) == "EPSG") {
+                                pa0 <- strsplit(projargs, ":")[[1]]
+                                projargs <- paste0("+init=epsg:", pa0[2])
+                            } else {
+                                stop("Cannot revert", projargs,
+                                    "to +init=epsg:")
+                            }
+                        }
                     }
                 }
             } else {
@@ -96,15 +123,21 @@ setMethod("rebuild_CRS", signature(obj = "CRS"),
                     uprojargs <- res[[2]]
                     comm <- res[[3]]
                 } else { #stop("rgdal version mismatch")
-                    res <- rgdal::checkCRSArgs(uprojargs)
-                    if (!res[[1]]) stop(res[[2]])
-                    uprojargs <- res[[2]]
+                    if (!is.na(uprojargs)) {
+                        res <- rgdal::checkCRSArgs(uprojargs)
+                        if (!res[[1]]) stop(res[[2]])
+                        uprojargs <- res[[2]]
+                    }
                 }
             } else stop("rgdal version mismatch")
         }
     }
     res <- new("CRS", projargs=uprojargs)
     if (!is.null(comm)) comment(res) <- comm
+    if (!is.na(slot(res, "projargs"))) .sp_CRS_cache[[input_projargs]] <- res
+#    CRS_CACHE[[input_projargs]] <- res
+#    assign("CRS_CACHE", CRS_CACHE, envir=.sp_CRS_cache)
+
     res
 }
 if (!isGeneric("wkt"))
@@ -137,9 +170,15 @@ setMethod("wkt", signature(obj = "CRS"),
 
 "print.CRS" <- function(x, ...)
 {
+    cat("Coordinate Reference System:\n")
     pst <- paste(strwrap(x@projargs), collapse="\n")
-    if (nchar(pst) < 40) cat(paste("CRS arguments:", pst, "\n"))
-    else cat(paste("CRS arguments:\n", pst, "\n"))
+    if (nchar(pst) < 40) cat(paste("Deprecated Proj.4 representation:", pst, "\n"))
+    else cat(paste("Deprecated Proj.4 representation:\n", pst, "\n"))
+    wkt <- wkt(x)
+    if (!is.null(wkt)) {
+        cat("WKT2 2019 representation:\n")
+        cat(wkt, "\n")
+    }
     invisible(pst)
 }
 

R/projected.R

@@ -4,7 +4,7 @@ setMethod("proj4string", signature(obj = "Spatial"),
                   if (get("rgdal_show_exportToProj4_warnings",
                     envir=.spOptions)) {
                     if (!get("thin_PROJ6_warnings", envir=.spOptions)) {
-                      warning("CRS object has comment, which is lost in output")
+                      warning("CRS object has comment, which is lost in output; in tests, see\nhttps://cran.r-project.org/web/packages/sp/vignettes/CRS_warnings.html")
                     } else {
                       if (get("PROJ6_warnings_count",
                         envir=.spOptions) == 0L) {

inst/NEWS.Rd

@@ -39,7 +39,7 @@
   \itemize{
 	\item update sp gallery, see \url{https://edzer.github.io/sp/}
 	\item move \code{methods} from Imports: to Depends:
-    \item improve base plot methods for \code{SpatialGridDataFrame} and \code{SpatialPixelsDataFrame} objects, see \url{https://www.r-spatial.org/r/2016/03/08/plotting-spatial-grids.html} for examples
+    \item improve base plot methods for \code{SpatialGridDataFrame} and \code{SpatialPixelsDataFrame} objects, see \url{https://r-spatial.org/r/2016/03/08/plotting-spatial-grids.html} for examples
 	\item improve the graticule \code{labels} methods, see \code{?gridlines}
 	\item fix hole assignment for triangles, reported in \url{https://stat.ethz.ch/pipermail/r-sig-geo/2016-March/024214.html}
     \item \code{as.SpatialPolygons.GridTopology} drops rownames of coordinates generated, but keeps coordinate (column) names from the \code{cellcentre.offset} slot of the grid

inst/include/sp.h

@@ -8,7 +8,7 @@
 #endif
 /* remember to touch local_stubs.c */
 
-#define SP_VERSION "1.4-5"
+#define SP_VERSION "1.4-6"
 
 #include <R.h>
 /* RSB 091203 */

man/CRS-class.Rd

@@ -26,7 +26,7 @@ Objects can be created by calls of the form \code{CRS("projargs")}, where "proja
 
 \section{Methods}{
   \describe{
-    \item{show}{\code{signature(object = "CRS")}: print projection arguments in object }
+    \item{show}{\code{signature(object = "CRS")}: print deprecated Proj.4 projection arguments and WKT2 2019 representation if available }
     \item{wkt}{\code{signature(object = "CRS")}: return WKT comment on object}
     \item{rebuild_CRS}{rebuild a CRS object, usually used to add a WKT comment with PROJ >= 6 and GDAL >= 3}
   }
@@ -88,6 +88,12 @@ if (run) {
 if (run) {
   print(CRSargs(CRS("+init=epsg:28992")))
 }
+if (run) {
+  print(CRSargs(CRS("EPSG:28992")))
+}
+if (run) {
+  print(CRSargs(CRS(SRS_string="EPSG:28992")))
+}
 if (run) {
   o <- try(CRS(SRS_string="ESRI:102760"))
   if (!inherits(o, "try-error")) print(CRSargs(o))

man/SpatialGridDataFrame-class.Rd

@@ -90,7 +90,7 @@ value such as \code{1/6} to specify relative size; default \code{lcm(2.8)}}
   and \code{\link{SpatialPixelsDataFrame-class} which holds possibly incomplete
   grids }
 
-  Plotting gridded data with sp: \url{https://www.r-spatial.org/r/2016/03/08/plotting-spatial-grids.html}
+  Plotting gridded data with sp: \url{https://r-spatial.org/r/2016/03/08/plotting-spatial-grids.html}
 }
 \examples{
 data(meuse.grid) # only the non-missing valued cells

src/sp.h

@@ -8,7 +8,7 @@
 #endif
 /* remember to touch local_stubs.c */
 
-#define SP_VERSION "1.4-5"
+#define SP_VERSION "1.4-6"
 
 #include <R.h>
 /* RSB 091203 */

tests/fail1.Rout.save

@@ -1,6 +1,6 @@
 
-R version 4.0.2 (2020-06-22) -- "Taking Off Again"
-Copyright (C) 2020 The R Foundation for Statistical Computing
+R version 4.0.4 (2021-02-15) -- "Lost Library Book"
+Copyright (C) 2021 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
 R is free software and comes with ABSOLUTELY NO WARRANTY.
@@ -213,11 +213,30 @@ y         50.955770 0.0003318105       112
 Error in CRS("+proj=latlon +ellps=WGS84") : 
   northings must follow eastings: +proj=latlon +ellps=WGS84
 > try(CRS("+proj=lonlat +ellps=WGS84"))
-CRS arguments: +proj=longlat +ellps=WGS84 +no_defs 
+Coordinate Reference System:
+Deprecated Proj.4 representation: +proj=longlat +ellps=WGS84 +no_defs 
+WKT2 2019 representation:
+GEOGCRS["unknown",
+    DATUM["Unknown based on WGS84 ellipsoid",
+        ELLIPSOID["WGS 84",6378137,298.257223563,
+            LENGTHUNIT["metre",1],
+            ID["EPSG",7030]]],
+    PRIMEM["Greenwich",0,
+        ANGLEUNIT["degree",0.0174532925199433],
+        ID["EPSG",8901]],
+    CS[ellipsoidal,2],
+        AXIS["longitude",east,
+            ORDER[1],
+            ANGLEUNIT["degree",0.0174532925199433,
+                ID["EPSG",9122]]],
+        AXIS["latitude",north,
+            ORDER[2],
+            ANGLEUNIT["degree",0.0174532925199433,
+                ID["EPSG",9122]]]] 
 Warning message:
 In CRS("+proj=lonlat +ellps=WGS84") :
   'lonlat' changed to 'longlat': +proj=longlat +ellps=WGS84
 > 
 > proc.time()
    user  system elapsed 
-  0.585   0.045   0.630 
+  0.500   0.042   0.536 

vignettes/CRS_warnings.Rmd

@@ -0,0 +1,64 @@
+---
+title: "Testing packages using CRS objects"
+author: "Roger Bivand"
+output:
+  html_document:
+    toc: true
+    toc_float:
+      collapsed: false
+      smooth_scroll: false
+    toc_depth: 2
+vignette: >
+  %\VignetteIndexEntry{Testing packages using CRS objects}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+## Introduction
+
+As has been explained in https://CRAN.R-project.org/package=rgdal/vignettes/CRS_projections_transformations.html, coordinate reference systems are represented differently when PROJ < 6 and PROJ >= 6.
+
+To alert interactive users to the possibility that their workflows might be degraded unless they take the representational changes into account, the **sp** `proj4string()` method issues warnings if a `"CRS"` object does not have an accompanying `WKT2 2019` representation (stored in a `comment` attached to the `"CRS"` object). This is because `proj4string()` only returns the PROJ 4 representation, not the accompanying `WKT2 2019` representation if any, so may constitute a loss of information. See also https://stat.ethz.ch/pipermail/r-sig-geo/2020-May/028125.html for further discussion.
+
+In general, it is good practice to replace all use in packages of `proj4string()` with `slot(, "proj4string")` and its assignment form by the assignment form of `slot()`; when `sp::proj4string()` is not called, many of the warnings are suppressed anyway.  
+
+On attaching **rgdal**:
+
+
+```{r, echo=FALSE}
+run <- FALSE
+if (requireNamespace("rgdal", quietly=TRUE)) run <- TRUE
+```
+
+
+```{r, eval=run}
+library(rgdal)
+```
+a package startup message is displayed if PROJ >= 6 and GDAL >= 3, including the important information that: 
+
+> To mute warnings of possible GDAL/OSR exportToProj4() degradation, use  options("rgdal_show_exportToProj4_warnings"="none") before loading rgdal.
+
+In **sp** 1.4 and **rgdal** 1.5, the default option value is `"all"`, in **sp** >= 1.5 and **rgdal** >= 1.6, the default will be flipped to `"none"`.
+
+## Testing
+
+Both CRAN checks and use of checks by end users may trigger spurious errors, if the versions of PROJ and GDAL differ from those on the development platform. Since the `WKT2 2019` representation is only generated on systems with PROJ >= 6 (and GDAL >= 3), warnings should not be expected when the same code is run on platforms with older versions of PROJ and GDAL. There are many such platforms, including RHEL and CentOS systems, as well as Ubuntu 18 and others. Think of a large lab with a cluster runnning such a system version, and that those installing software may wish to run `R CMD check` or just your test suite to confirm that things are as they should be. They will be dismayed to find that tests fail, but will not be able to find out whether this matters for them. 
+
+Consequently, it is best either not to check warnings that perform differently when run under different versions of upstream external software (PROJ and GDAL), or to condition on the software versions with different expectations depending on the version. 
+
+To mute warnings in all settings, add the option above early in any relevant test file. 
+
+Fine-grained control may be obtained using `rgdal::rgdal_extSoftVersion()`:
+
+```{r, eval=run}
+rgdal::rgdal_extSoftVersion()
+```
+and its shorter version, testing only PROJ >= 6 (and GDAL >= 3):
+
+```{r, eval=run}
+rgdal::new_proj_and_gdal()
+```
+Using this test, a warning might be expected if recent PROJ and GDAL are used, and before the warning default is flipped in **sp** > 1.4 and **rgdal** > 1.5.
+
+In **sf**, use `sf::sf_extSoftVersion()` to determine versions if necessary.
+