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sp_2.0-0 draft changing to status 2L #135

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merged 6 commits into from
Jun 20, 2023
Merged

sp_2.0-0 draft changing to status 2L #135

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66cc5c2
switch to 2L
rsbivand May 26, 2023
bd980df
add options for message
rsbivand Jun 2, 2023
2035697
stronger rgeos warnings
rsbivand Jun 6, 2023
c123464
permit workaround when sf not present for is.projected
rsbivand Jun 7, 2023
0ec24a3
tidy up _R_CHECK_SUGGESTS_ONLY_=true for sp
rsbivand Jun 8, 2023
5ec376f
warn on missing sf if _SP_STARTUP_MESSAGE_="none"
rsbivand Jun 8, 2023
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8 changes: 6 additions & 2 deletions DESCRIPTION
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@@ -1,5 +1,5 @@
Package: sp
Version: 1.6-1
Version: 2.0-0
Title: Classes and Methods for Spatial Data
Authors@R: c(person("Edzer", "Pebesma", role = c("aut", "cre"),
email = "[email protected]"),
Expand All @@ -21,7 +21,11 @@ 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
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
retrieving coordinates, for subsetting, print, summary, etc. From this
version, evolution status is set to '2L' using 'sf' in place of 'rgdal',
see <https://r-spatial.org/r/2023/05/15/evolution4.html> for details.
Retiring packages 'maptools', 'rgdal' and 'rgeos' will be dropped by
October 2023.
License: GPL (>= 2)
URL: https://github.com/edzer/sp/ https://edzer.github.io/sp/
BugReports: https://github.com/edzer/sp/issues
Expand Down
32 changes: 30 additions & 2 deletions R/AAA.R
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Expand Up @@ -10,16 +10,25 @@ assign("PolypathRule", "winding", envir = .spOptions)
assign("col.regions", bpy.colors(), envir = .spOptions)
assign("thin_PROJ6_warnings", FALSE, envir=.spOptions)
assign("PROJ6_warnings_count", 0L, envir=.spOptions)
assign("evolution_status", 0L, envir=.spOptions)
assign("evolution_status", 2L, envir=.spOptions) # default changed 2.0-0
assign("startup_message", "load", 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()
if (get("startup_message", envir=.spOptions) == "load")
smess_func()
}

.onAttach <- function(lib, pkg) {
if (get("startup_message", envir=.spOptions) == "attach")
smess_func()
}


load_stuff <- function() {
rgdal_show_exportToProj4_warnings <- options("rgdal_show_exportToProj4_warnings")
if (!is.null(rgdal_show_exportToProj4_warnings)) {
Expand Down Expand Up @@ -54,7 +63,26 @@ load_stuff <- function() {
assign("evolution_status", unname(evolution_status), envir=.spOptions)
}
}
Smess <- paste("The legacy packages maptools, rgdal, and rgeos, underpinning this package\nwill retire shortly. Please refer to R-spatial evolution reports on\nhttps://r-spatial.org/r/2023/05/15/evolution4.html for details.\nThis package is now running under evolution status", get_evolution_status(), "\n")
startup_message <- unlist(options("sp_startup_message"))
if (!is.null(startup_message)) {
startup_message <- as.character(startup_message)
stopifnot(is.character(startup_message))
stopifnot(isTRUE(startup_message %in% c("attach", "load", "none")))
assign("startup_message", unname(startup_message), envir=.spOptions)
} else {
startup_message <- Sys.getenv("_SP_STARTUP_MESSAGE_")
if (nchar(startup_message) > 0L) {
startup_message <- as.character(startup_message)
stopifnot(is.character(startup_message))
stopifnot(isTRUE(startup_message %in% c("attach", "load", "none")))
assign("startup_message", unname(startup_message), envir=.spOptions)
}
}
}

smess_func <- function() {
where <- get("startup_message", envir=.spOptions)
Smess <- paste("The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,\nwhich was just ", where, "ed, will retire in October 2023.\nPlease refer to R-spatial evolution reports for details, especially\nhttps://r-spatial.org/r/2023/05/15/evolution4.html.\nThe sp package is now running under evolution status ", get_evolution_status(), "\n", ifelse(get_evolution_status() == 2L, " (status 2 uses the sf package in place of rgdal)\n", ""), sep="")
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Thanks, this is an important change in wording. As from sp 1.6-1, loading any package that imports sp outputs a verbose and confusing message about "this package" where sp is meant, e.g.:

R> library(rmapshaper)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 2

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@rsbivand rsbivand Jun 14, 2023 •
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The current status in this PR is:

> loadNamespace("sp")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
     (status 2 uses the sf package in place of rgdal)

See also Trackage/trip#52 (comment) for @mdsumner 's helpful nudge. There are now also an environment variable and an option to change the default setting ("load" default, "attach" or "none"). From reactions on twitter, some ecologists see the end of the world coming from retiring packages breaking legacy workflows, hence the noisy start-up message, telling them where to go for information.

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The verbose start-up message is certainly useful for when sp is being attached. I am less sure about loading as I guess many sp-importing packages have already adapted to evolution status 2 in which case the message is mostly redundant and rather disturbing (but I guess you want to spread the word).

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Current rev-deps show about 220 packages failing when retiring packages are not on the library path and _R_CHECK_SUGGESTS_ONLY_=true _R_CHECK_FORCE_SUGGESTS_=FALSE. Many of these have stale declarations from when raster needed rgdal and rgeos in Suggests:, most of these were alerted in December 2022, but haven't responded. Hence the nneed for noise at this point.

The evidential background includes the GDAL barn-raising process, when the representation of coordinate reference systems was changed upstream of us - I see plenty of package code turning off messages, and staying with explicitly defunct representations. So lots of hheads buried securely in sand, I'm afraid.

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Thanks, I see. The obvious downside of the "load" default for "sp_startup_message" is that the loading of all sp-importing packages that have already been updated or are otherwise unaffected by the evolution becomes unnecessarily noisy. So I think in the near future, sp should really only speak out when attached.

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@rsbivand rsbivand Jun 14, 2023 •
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Exactly. The aim is to track the updating/mitigation rate, and relax the message to default "attach" as soon as there is realistic (for some definition) movement. I think few users update.packages at all frequently, so may well still be on sp 1.6-0 at best. I'm thinking of starting a cron job to pull nightly and CMD check new versions of the 200+ packages on my watch list as they update - any ideas? This does miss new packages, so I'd have to look for new reverse dependencies too.

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Watchlist check running, reporting thrice weekly at: https://github.com/r-spatial/evolution/tree/main/watchlist_output. The input were packages with CMD check errors or warnings with _SP_EVOLUTION_STATUS_=2 R_LIBS=/home/rsb/lib/r_libs _R_CHECK_SUGGESTS_ONLY_=true _R_CHECK_FORCE_SUGGESTS_=FALSE (no retiring packages on library path), initially 223 of 696 packages package_dependencies(packages = c("sp", "maptools", "rgdal", "rgeos"), pdb, which = "most", recursive = FALSE, reverse = TRUE) reduced to 222 by dropping rgeos, the released version of which has had an extra parenthesis in a WKT string since forever and which is now caught by GEOS 3.12.0beta. I included sp because some packages using sp silently assume that rgdal oe rgeos are available.

packageStartupMessage(Smess, appendLF = FALSE)
}

Expand Down
6 changes: 5 additions & 1 deletion README.md
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Expand Up @@ -6,7 +6,11 @@

R Classes and Methods for Spatial Data.

*Before* **sp** is loaded, `options("sp_evolution_status")` may be set to `0L` for legacy behaviour, `1L` for setting `CRS(, doCheckCRSArgs=FALSE, )` and other minor steps to block calls out to **rgdal** etc., and `2L` to use **sf** internally (not completed yet). If this option is not set, the environment variable `_SP_EVOLUTION_STATUS_` can be used, again *before* **sp** is loaded, set to `"0"`, `"1"` or `"2"`; this is used for running revdep checks under different evolution scenarios, anticipating [retirement of maptools, rgdal and rgeos](https://r-spatial.org/r/2022/04/12/evolution.html).
From version 2.0.0, `sp` evolution status is changed to `2L` to use **sf** internally in place of `rgdal`, from default `0L` until now. See [this report](https://r-spatial.org/r/2023/05/15/evolution4.html) for adaptation details, and [this report](https://r-spatial.org/r/2023/04/10/evolution3.html) for progress on retiring `maptools`, `rgdal` and `rgeos`.

*Before* **sp** is loaded, `options("sp_evolution_status")` may be set to `0L` for legacy behaviour, `1L` for setting `CRS(, doCheckCRSArgs=FALSE, )` and other minor steps to block calls out to **rgdal** etc., and `2L` to use **sf** internally. If this option is not set, the environment variable `_SP_EVOLUTION_STATUS_` can be used, again *before* **sp** is loaded, set to `"0"`, `"1"` or `"2"`; this is used for running revdep checks under different evolution scenarios, anticipating [retirement of maptools, rgdal and rgeos](https://r-spatial.org/r/2022/04/12/evolution.html).

From `sp 1.6.0` published on CRAN 2023-01-19, these status settings may also be changed when `sp` is loaded, using `sp::get_evolution_status()` returning the current value, and `sp::set_evolution_status(value)`, where value can take the integer values `0L`, `1L` and `2L`. `sp 1.6.1` published on CRAN 2023-05-25 added start-up messages to alert users to imminent changes.

See:

Expand Down
2 changes: 1 addition & 1 deletion inst/include/sp.h
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Expand Up @@ -8,7 +8,7 @@
#endif
/* remember to touch local_stubs.c */

#define SP_VERSION "1.6-1"
#define SP_VERSION "2.0-0"

#include <R.h>
/* RSB 091203 */
Expand Down
2 changes: 1 addition & 1 deletion src/sp.h
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Expand Up @@ -8,7 +8,7 @@
#endif
/* remember to touch local_stubs.c */

#define SP_VERSION "1.6-1"
#define SP_VERSION "2.0-0"

#include <R.h>
/* RSB 091203 */
Expand Down
16 changes: 9 additions & 7 deletions tests/agg.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> if (require(rgeos, quietly = TRUE)) {
+ g = SpatialGrid(GridTopology(c(5,5), c(10,10), c(3,3)))
+ p = as(g, "SpatialPolygons")
Expand Down Expand Up @@ -55,15 +57,15 @@ This package is now running under evolution status 0
+ # aggregate(p, sq, mean, areaWeighted=TRUE)[[1]]))
+ }
rgeos version: 0.6-3, (SVN revision 696)
GEOS runtime version: 3.11.1-CAPI-1.17.1
GEOS runtime version: 3.11.3dev-CAPI-1.17.3
Please note that rgeos will be retired during October 2023,
plan transition to sf or terra functions using GEOS at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html for details.
GEOS using OverlayNG
Linking to sp version: 1.6-0
Linking to sp version: 2.0-0
Polygon checking: TRUE

>
> proc.time()
user system elapsed
0.652 0.055 0.701
0.321 0.054 0.367
12 changes: 7 additions & 5 deletions tests/base.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> data(meuse)
> x = meuse[1:10, ] # limit the output
> coordinates(x) = c("x", "y") # names
Expand Down Expand Up @@ -464,4 +466,4 @@ Data attributes:
>
> proc.time()
user system elapsed
0.386 0.062 0.439
0.391 0.057 0.439
39 changes: 28 additions & 11 deletions tests/fail1.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> data(meuse)
> x = meuse
>
Expand Down Expand Up @@ -214,14 +216,32 @@ x 5.721109 0.0005312853 84
y 50.955770 0.0003318105 112
>
> try(CRS("+proj=latlon +ellps=WGS84"))
Error in CRS("+proj=latlon +ellps=WGS84") :
northings must follow eastings: +proj=latlon +ellps=WGS84
Coordinate Reference System:
Deprecated Proj.4 representation: +proj=longlat +ellps=WGS84 +no_defs
WKT2 2019 representation:
GEOGCRS["unknown",
DATUM["Unknown based on WGS 84 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]]]]
> try(CRS("+proj=lonlat +ellps=WGS84"))
Coordinate Reference System:
Deprecated Proj.4 representation: +proj=longlat +ellps=WGS84 +no_defs
WKT2 2019 representation:
GEOGCRS["unknown",
DATUM["Unknown based on WGS84 ellipsoid",
DATUM["Unknown based on WGS 84 ellipsoid",
ELLIPSOID["WGS 84",6378137,298.257223563,
LENGTHUNIT["metre",1],
ID["EPSG",7030]]],
Expand All @@ -237,10 +257,7 @@ GEOGCRS["unknown",
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
0.547 0.073 0.612
0.721 0.065 0.778
12 changes: 7 additions & 5 deletions tests/grid.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> data(meuse.grid)
> x = meuse.grid
> coordinates(x) = c("x", "y")
Expand Down Expand Up @@ -280,4 +282,4 @@ Coordinate Reference System (CRS) arguments: NA
>
> proc.time()
user system elapsed
0.432 0.067 0.490
0.427 0.060 0.478
16 changes: 9 additions & 7 deletions tests/over2.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
>
> if (require(rgeos, quietly = TRUE)) {
+ g = SpatialGrid(GridTopology(c(0,0), c(1,1), c(3,3)))
Expand Down Expand Up @@ -63,17 +65,17 @@ This package is now running under evolution status 0
+ rgeos::overGeomGeom(pt,pt,minDimension=0)
+ }
rgeos version: 0.6-3, (SVN revision 696)
GEOS runtime version: 3.11.1-CAPI-1.17.1
GEOS runtime version: 3.11.3dev-CAPI-1.17.3
Please note that rgeos will be retired during October 2023,
plan transition to sf or terra functions using GEOS at your earliest convenience.
See https://r-spatial.org/r/2023/05/15/evolution4.html for details.
GEOS using OverlayNG
Linking to sp version: 1.6-0
Linking to sp version: 2.0-0
Polygon checking: TRUE

pt1
1
>
> proc.time()
user system elapsed
0.705 0.047 0.745
0.379 0.051 0.421
15 changes: 10 additions & 5 deletions tests/pass1.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> data(meuse)
> x = meuse
> coordinates(x) = cbind(rnorm(155), rnorm(155))
Expand Down Expand Up @@ -289,6 +291,9 @@ Data attributes:
>
> # test behaviour on zero-length objects:
> demo(meuse, ask = FALSE, echo = FALSE)
Warning message:
In CPL_crs_from_input(x) :
GDAL Message 1: +init=epsg:XXXX syntax is deprecated. It might return a CRS with a non-EPSG compliant axis order.
> p = as(meuse, "SpatialPoints")
>
> p[0]
Expand Down Expand Up @@ -602,4 +607,4 @@ Error in SpatialPointsDataFrame(pts, df, match.ID = TRUE) :
>
> proc.time()
user system elapsed
0.595 0.087 0.673
0.816 0.081 0.890
12 changes: 7 additions & 5 deletions tests/point.in.polygon.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
>
> # open polygon:
> print(point.in.polygon(1:10,1:10,c(3,5,5,3),c(3,3,5,5)))
Expand All @@ -31,4 +33,4 @@ This package is now running under evolution status 0
>
> proc.time()
user system elapsed
0.191 0.042 0.223
0.196 0.037 0.223
12 changes: 7 additions & 5 deletions tests/sel.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> x = c(0.5, 1.5, 0.5, 1.5, 1.6)
> y = c(1.5, 1.5, 0.5, 0.5, 0.5)
> xy = cbind(x,y)
Expand Down Expand Up @@ -205,4 +207,4 @@ e 2 c
>
> proc.time()
user system elapsed
0.399 0.046 0.436
0.389 0.054 0.434
12 changes: 7 additions & 5 deletions tests/sp1.Rout.save
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Expand Up @@ -17,10 +17,12 @@ Type 'q()' to quit R.

> options("rgdal_show_exportToProj4_warnings"="none")
> library(sp)
The legacy packages maptools, rgdal, and rgeos, underpinning this package
will retire shortly. Please refer to R-spatial evolution reports on
https://r-spatial.org/r/2023/05/15/evolution4.html for details.
This package is now running under evolution status 0
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
> data(meuse)
> x = meuse
> nm <- names(meuse)
Expand Down Expand Up @@ -335,4 +337,4 @@ Data attributes:
>
> proc.time()
user system elapsed
0.300 0.038 0.329
0.284 0.054 0.329
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