CVS commit: pkgsrc/geography/R-terra

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Wed Dec  4 22:48:27 UTC 2024

Modified Files:
        pkgsrc/geography/R-terra: Makefile distinfo

Log Message:
(Geography/R-terra) Updated 1.7.39 to 1.7.83

# version 1.7-83

## bug fixes

- `flip(direction="vertical")` failed in some cases
  [#1518](https://github.com/rspatial/terra/issues/1518) by Ed Carnell

- `zonal(as.raster=TRUE)` failed when the zonal raster was categorical
  [1514](https://github.com/rspatial/terra/issues/1514) by Jessi L
  Brown

- `distance<data.frame,data.frame>` and `<matrix,matrix>` ignored the
  unit
  argument. [#1545](https://github.com/rspatial/terra/issues/1545) by
  Wencheng Lau-Medrano

- NetCDF files with month time-step encode from 0-11 made R crash
  [#1544](https://github.com/rspatial/terra/issues/1544) by Martin
  Holdrege

- `split<SpatVector>` only worked well if the split field was of type
  character. [#1530](https://github.com/rspatial/terra/issues/1530) by
  Igor Graczykowski

- `gridDist` (and probably some other methods) emitted a "cannot
  overwrite existing file" error when processing large datasets
  [#1522](https://github.com/rspatial/terra/issues/1522) by Clare
  Pearson

- `terrain` did not accept multiple variables
  [#1561](https://github.com/rspatial/terra/issues/1561) by Michael
  Mahoney

- `rotate` was vulnerable to an integer overflow
  [#1562](https://github.com/rspatial/terra/issues/1562) by Sacha
  Ruzzante

- `getTileExtents` could return overlapping tiles or tiles with gaps
  due to floating point
  imprecision. [#1564](https://github.com/rspatial/terra/issues/1564)
  by Michael Sumner

## enhancements

- `as.list<SpatRasterDataset>` sets the names of the list
  [#1513](https://github.com/rspatial/terra/issues/1513)

- a SpatVectorCollection can now be subset with its names; and if made
  from a list it takes the names from the list.
  [1515](https://github.com/rspatial/terra/issues/1515) by jedgroev

- argument `fill_range` to plot<SpatRaster> and `plot<SpatVector>` to
  use the color of the extreme values of the specified range
  [#1553](https://github.com/rspatial/terra/issues/1553) by Mike
  Koontz

- plet<SpatRaster> can now handle rasters with a "local" (Cartesian)
  CRS. [#1570](https://github.com/rspatial/terra/issues/1570) by
  Augustin Lobo.

## new

- `map-region` returns the coordinates of the axes position of a map
  created with `plot<Spat*>`
  [https://github.com/rspatial/terra/issues/1517](https://github.com/rspatial/terra/issues/1517)
  by Daniel Schuch

- `polys<leaflet>` method
  [#1543](https://github.com/rspatial/terra/issues/1543) by Márcia
  Barbosa

- `plot<SpatVectorCollection>` method
  [#1532](https://github.com/rspatial/terra/issues/1532) by jedgroev

- `add_mtext` to add text around the margins of a
  map. [#1567](https://github.com/rspatial/terra/issues/1567) by
  Daniel Schuch

# version 1.7-78

Released 2023-05-22

## bug fixes

- `writeVector` and `readVector` better handle empty geopackage layers
  [#1426](https://github.com/rspatial/terra/issues/1426) by Andrew
  Gene Brown.

- `writeCDF` only wrote global variables if there was more than one
  [#1443](https://github.com/rspatial/terra/issues/1443) by Daniel
  Schlaepfer

- `rasterize` with "by" returned odd layernames
  [#1435](https://github.com/rspatial/terra/issues/1435) by Philippe
  Massicotte

- `convHull`, `minCircle` and `minRect` with a zero-row SpatVector
  crashed R [#1445](https://github.com/rspatial/terra/issues/1445) by
  Andrew Gene Brown

- `rangeFill` with argument `circular=TRUE` did not work properly
  [#1460](https://github.com/rspatial/terra/issues/1460) by Alice

- `crs(describe = TRUE)` returned an mis-ordered extent
  [#1485](https://github.com/rspatial/terra/issues/1485) by Dimitri
  Falk

- `tapp` with a custom function and an index like "yearmonths" could
  shift time for not considering the time
  zone. [#1483](https://github.com/rspatial/terra/issues/1483) by Finn
  Roberts

- `plot<SpatRaster>` could fail when there were multiple values with
  very small differences
  [#1491](https://github.com/rspatial/terra/issues/1491) by srfall

- `as.data.frame<SpatRaster>` with "xy=TRUE" and "wide=FALSE" could
  fail if coordinates were very similar
  [#1476](https://github.com/rspatial/terra/issues/1476) by Pascal
  Oettli

- `rasterizeGeom` now returns the correct layer name
  [#1472](https://github.com/rspatial/terra/issues/1472) by
  HRodenhizer

- `cellSize` with "mask=TRUE" failed if the output was to be written
  to a temp file
  [#1496](https://github.com/rspatial/terra/issues/1496) by Pascal
  Sauer

- `ext<SpatVectorProxy>` did not return the full extent
  [#1501](https://github.com/rspatial/terra/issues/1501) by
  erkent-carb

## enhancements

- `extract` has new argument "small=TRUE" to allow for strict use of
  "touches=FALSE"
  [#1419](https://github.com/rspatial/terra/issues/1419) by Floris
  Vanderhaeghe.

- `as.list<SpatRaster>` has new argument "geom=NULL"

- `rast<list>` now recognizes (x, y, z) base R "image" structures
  [stackoverflow]
  (https://stackoverflow.com/questions/77949551/rspatial-convert-a-grid-list-to-a-raster-using-terra)
  by Ignacio Marzan.

- `inset` has new arguments "offset" and "add"
  [#1422](https://github.com/rspatial/terra/issues/1422) by Armand-CT

- `expanse<SpatRaster>` has argument `usenames`
  [#1446](https://github.com/rspatial/terra/issues/1446) by Bappa Das

- the default color palette is now `terra::map.pal("viridis")` instead
  of `terrain.colors`. The default can be changes with
  `options(terra.pal=...)`
  [#1474](https://github.com/rspatial/terra/issues/1474) by Derek
  Friend

- `as.list<SpatRasterDataset>` now returns a named
  list. [#1513](https://github.com/rspatial/terra/issues/1513) by Eric
  R. Scott

## new

- `bestMatch<SpatRaster>` method

- argument "pairs=TRUE" to `cells` [https://github.com/rspatial/terra/issues/1487](https://github.com/rspatial/terra/issues/1487) by Floris Vanderhaeghe

- `add_grid` to add a grid to a map

# version 1.7-71

Released 2023-01-31

## bug fixes

- k_means did not work if there were NAs
  [#1314](https://github.com/rspatial/terra/issues/1314) by Jakub
  Nowosad

- `layerCor` with a custom function did not work anymore
  [#1387](https://github.com/rspatial/terra/issues/1387) by Jakub
  Nowosad

- `plet` broke when using "panel=TRUE"
  [#1384](https://github.com/rspatial/terra/issues/1384) by Elise
  Hellwig

- using /vis3/ to open a SpatRaster did not work
  [#1382](https://github.com/rspatial/terra/issues/1382) by Mike
  Koontz

- `plot<SpatRaster>(add=TRUE)` sampled the raster data without
  considering the extent of the
  map. [#1394](https://github.com/rspatial/terra/issues/1394) by
  Márcia Barbosa

- `plot<SpatRaster>(add=TRUE)` now only considers the first layer of a
  multi-layer SpatRaster
  [1395](https://github.com/rspatial/terra/issues/1395) by Márcia
  Barbosa

- `set.cats` failed with a tibble was used instead of a data.frame
  [#1406](https://github.com/rspatial/terra/issues/1406) by Mike
  Koontz

- `polys` argument "alpha" was ignored if a single color was
  used. [#1413](https://github.com/rspatial/terra/issues/1413) by
  Derek Friend

- `query` ignore the "vars" argument if all rows were
  selected. [#1398](https://github.com/rspatial/terra/issues/1398) by
  erkent-carb.

- `spatSample` ignored "replace=TRUE" with random sampling,
  na.rm=TRUE, and a sample size larger than the non NA
  cells. [#1411](https://github.com/rspatial/terra/issues/1411) by
  Babak Naimi

- `spatSample` sometimes returned fewer values than requested and
  available for lonlat
  rasters. [#1396](https://github.com/rspatial/terra/issues/1396) by
  Márcia Barbosa.

## enhancements

- `vect<character>` now has argument "opts" for GDAL open options,
  e.g. to declare a file
  encoding. [#1389](https://github.com/rspatial/terra/issues/1389) by
  Mats Blomqvist

- `plot(plg=list(tic=""))` now allows choosing alternative continuous
  legend tic-mark styles ("in", "out", "through" or "none")

- `makeTiles` has new argument "buffer"
  [#1408](https://github.com/rspatial/terra/issues/1408) by Joy
  Flowers.

## new

- `prcomp<SpatRaster>` method
  [#1361](https://github.com/rspatial/terra/issues/1361#issuecomment-1860311029)
  by Jakub Nowosad

- `add_box` to add a box around the map. The box is drawn where the
  axes are, not around the plotting region.

- `getTileExtents` provides the extents of tiles. These may be used in
parallelization. See [#1391](https://github.com/rspa
tial/terra/issues/1391) by Alex Ilich.

# version 1.7-65

Released 2023-12-15

## bug fixes

- `flip` with argument `direction="vertical"` filed in some cases with
   large rasters processed in chunks
   [0b714b0](https://github.com/rspatial/terra/commit/0b714b038b101011ce27391133a7a1f9a91821cc)
   by Dulci on [stackoveflow](
   https://stackoverflow.com/questions/77304534/rspatial-terraflip-error-when-flipping-a-multi-layer-spatrast-object)

- SpatRaster now correctly handles `NA & FALSE` and `NA | TRUE`
  [#1316](https://github.com/rspatial/terra/issues/1316) by John Baums

- `set.names` wasn't working properly for SpatRasterDataset or
  SpatRasterCollection
  [#1333](https://github.com/rspatial/terra/pull/1333) by Derek Friend

- `extract` with argument "layer" not NULL shifted the layers
  [#1332](https://github.com/rspatial/terra/issues/1332) by Ewan
  Wakefield

- `terraOptions` did not capture "memmin" on
  -[stackoverflow](https://stackoverflow.com/questions/77552234/controlling-chunk
  -size-in-terra) by dww

- `rasterize` with points and a built-in function could crash if no
  field was used
  [#1369](https://github.com/rspatial/terra/issues/1369) by
  anjelinejeline

## enhancements

- `mosaic` can now use `fun="modal"`

- `rast<matrix> and rast<data.frame>` now have option 'type="xylz"
  [#1318](https://github.com/rspatial/terra/issues/1318) by Agustin
  Lobo

- `extract<SpatRaster,SpatVector>` can now use multiple summarizing
  functions [#1335](https://github.com/rspatial/terra/issues/1335) by
  Derek Friend

- `disagg` and `focal` have more optimistic memory requirement
  estimation [#1334](https://github.com/rspatial/terra/issues/1334) by
  Mikko Kuronen

## new

- `k_means<SpatRaster>` method
  [#1314](https://github.com/rspatial/terra/issues/1314) by Agustin
  Lobo

- `princomp<SpatRaster>` method
  [#1361](https://github.com/rspatial/terra/issues/1361) by Alex Ilich

- `has.time<SpatRaster>` method

- new argument "raw=FALSE" to `rast`, `sds`, and `sprc` to allow
  ignoring scale and offset
  [1354](https://github.com/rspatial/terra/issues/1354) by Insang Song

# version 1.7-55

Released 2023-10-14

## bug fixes

- `mosaic` ignored the filename argument if the SpatRasterCollection
  only had a single SpatRaster
  [#1267](https://github.com/rspatial/terra/issues/1267) by Michael
  Mahoney

- Attempting to use `extract` with a raster file that had been deleted
  crashed R. [#1268](https://github.com/rspatial/terra/issues/1268) by
  Derek Friend

- `split<SpatVector,SpatVector>` did not work well in all
  cases. [#1256](https://github.com/rspatial/terra/issues/1256) by
  Derek Corcoran Barrios

- `intersect` with two SpatVectors crashed R if there was a date/time
variable [#1273]( https://github.com/rspatial/terra/issues/1273) by
Dave Dixon

- "values=FALSE" was ignored by
  `spatSample<SpatRaster>(method="weights")`
  [#1275](https://github.com/rspatial/terra/issues/1275) by François
  Rousseu

- `coltab<-` again works with a list as value
[#1280](https://github.com/rspatial/terra/issues/1280) by Diego
Hernangómez

- `stretch` with histogram equalization was not memory-safe
  [#1305](https://github.com/rspatial/terra/issues/1305) by Evan Hersh

- `plot` now resets the "mar" parameter
  [#1297](https://github.com/rspatial/terra/issues/1297) by Márcia
  Barbosa

- `plotRGB` ignored the "smooth" argument
  [#1307](https://github.com/rspatial/terra/issues/1307) by Timothée
  Giraud

## enhancements

- argument "gdal" in `project` was renamed to "use_gdal"
  [#1269](https://github.com/rspatial/terra/issues/1269) by Stuart
  Brown.

- SpatVector attributes can now be stored as an ordered factor
  [#1277](https://github.com/rspatial/terra/issues/1277) by Ben Notkin

- `plot<SpatVector>` now uses an "interval" legend when breaks are
  supplied [#1303](https://github.com/rspatial/terra/issues/1303) by
  Gonzalo Rizzo

- `crop<SpatRaster>` now keeps more metadata, including variable names
  [#1302](https://github.com/rspatial/terra/issues/1302) by rhgof

- `extract(fun="table")` now returns an easier to use data.frame
[#1294](https://github.com/rspatial/terra/issues/1294) by Fernando
Aramburu.

## new
- `metags<-` and `metags` to set arbitrary SpatRaster/file level
   metadata [#1304](https://github.com/rspatial/terra/issues/ 1304) by
   Francesco Chianucci

# version 1.7-46

Released 2023-09-06

## bug fixes

- `plot<SpatVector>` used the wrong main label in some cases
  [#1210](https://github.com/rspatial/terra/issues/1210) by Márcia
  Barbosa

- `plotRGB` failed with an "ext=" argument
  [#1228](https://github.com/rspatial/terra/issues/1228) by Dave Edge

- `rast<array>` failed badly when the array had less than three
  dimensions. [#1254](https://github.com/rspatial/terra/issues/1254)
  by andreimirt.

- `all.equal` for a SpatRaster with multiple layers
[#1236](https://github.com/rspatial/terra/issues/1236) by Sarah
Endicot t

- `zonal(wide=FALSE)` could give wrong results if the zonal SpatRaster
  had "layer" as
  layername. [#1251](https://github.com/rspatial/terra/issues/1251) by
  Jeff Hanson

- `panel` now support argument "range"
  [#141](https://github.com/rspatial/terra/issues/1241) by Jakub
  Nowosad

- `rasterize` with `by=` returned wrong layernames if the by field was
  not sorted [#1266](https://github.com/rspatial/terra/issues/1266) by
  Sebastian Dunnett

- `mosaic` with multiple layers was not correct
  [#1262](https://github.com/rspatial/terra/issues/1262) by
  Jean-Romain

## enhancements

- `wrap<SpatRaster>` now stores color tables
  [#1215](https://github.com/rspatial/terra/issues/1215) by Patrick
  Brown

- `global` now has a "maxcell" argument
  [#1213](https://github.com/rspatial/terra/issues/1213) by Alex Ilich

- `layerCor` with fun='pearson' now returns output with the layer
  names [#1206](https://github.com/rspatial/terra/issues/1206)

- `vrt` now has argument "set_names"
  [#1244](https://github.com/rspatial/terra/issues/1244) by sam-a-levy

- `vrt` now has argument "return_filename"
  [#1258](https://github.com/rspatial/terra/issues/1258) by Krzysztof
  Dyba

- `project<SpatRaster>` has new argument "by_util" exposing the GDAL
  warp utility [#1222](https://github.com/rspatial/terra/pull/1222) by
  Michael Sumner.

## new
- `compareGeom` for list and SpatRasterCollection
  [#1207](https://github.com/rspatial/terra/issues/1207) by Sarah
  Endicott

- `is.rotated<SpatRaster>` method
  [#1229](https://github.com/rspatial/terra/issues/1229) by Andy Lyons

- `forceCCW<SpatVector>` method to force counter-clockwise orientation
  of polygons [#1249](https://github.com/rspatial/terra/issues/1249)
  by srfall.

- `vrt_tiles` returns the filenames of the tiles in a vrt file
  [#1261](https://github.com/rspatial/terra/issues/1261) by Derek
  Friend

- `extractAlong` to extract raster cell values for a line that are
  ordered along the
  line. [#1257](https://github.com/rspatial/terra/issues/1257) by
  adamkc.


To generate a diff of this commit:
cvs rdiff -u -r1.13 -r1.14 pkgsrc/geography/R-terra/Makefile
cvs rdiff -u -r1.1 -r1.2 pkgsrc/geography/R-terra/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Modified files:

Index: pkgsrc/geography/R-terra/Makefile
diff -u pkgsrc/geography/R-terra/Makefile:1.13 pkgsrc/geography/R-terra/Makefile:1.14
--- pkgsrc/geography/R-terra/Makefile:1.13      Thu Nov 14 22:20:00 2024
+++ pkgsrc/geography/R-terra/Makefile   Wed Dec  4 22:48:27 2024
@@ -1,14 +1,21 @@
-# $NetBSD: Makefile,v 1.13 2024/11/14 22:20:00 wiz Exp $
+# $NetBSD: Makefile,v 1.14 2024/12/04 22:48:27 mef Exp $
 
 R_PKGNAME=     terra
-R_PKGVER=      1.7-39
-PKGREVISION=   12
+R_PKGVER=      1.7-83
 CATEGORIES=    geography
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Spatial Data Analysis
 LICENSE=       gnu-gpl-v3
 
+# Package suggested but not available: 'leaflet'
+TEST_DEPENDS+= R-tinytest-[0-9]*:../../devel/R-tinytest
+TEST_DEPENDS+= R-ncdf4-[0-9]*:../../math/R-ncdf4
+TEST_DEPENDS+= R-sf-[0-9]*:../../geography/R-sf
+TEST_DEPENDS+= R-deldir-[0-9]*:../../geography/R-deldir
+TEST_DEPENDS+= R-XML-[0-9]*:../../math/R-XML
+TEST_DEPENDS+= R-htmlwidgets-[0-9]*:../../www/R-htmlwidgets
+
 USE_LANGUAGES= c c++
 
 .include "../../math/R/Makefile.extension"

Index: pkgsrc/geography/R-terra/distinfo
diff -u pkgsrc/geography/R-terra/distinfo:1.1 pkgsrc/geography/R-terra/distinfo:1.2
--- pkgsrc/geography/R-terra/distinfo:1.1       Fri Aug 11 00:53:59 2023
+++ pkgsrc/geography/R-terra/distinfo   Wed Dec  4 22:48:27 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.1 2023/08/11 00:53:59 mef Exp $
+$NetBSD: distinfo,v 1.2 2024/12/04 22:48:27 mef Exp $
 
-BLAKE2s (R/terra_1.7-39.tar.gz) = f1352a21b76921afc7e82010bd06197860bdc894b29ece0b15f474a748919463
-SHA512 (R/terra_1.7-39.tar.gz) = 862ff1fe4272063eed41573bea19169a40a7b06a22a9c883e928c0c85826f579dc2b72d9adf2497a4dc32e2c7d7b865d0cd4c78b2020f8f3c83d455bf251a3c6
-Size (R/terra_1.7-39.tar.gz) = 815403 bytes
+BLAKE2s (R/terra_1.7-83.tar.gz) = 138d39eb92dbf2cf9f4613ca45482175773c82354822d8e11bfec29791e4740b
+SHA512 (R/terra_1.7-83.tar.gz) = afb0c3fc7b1bbea563ea629d0470d11dca5bc50363f7a7c3aaeb92558eb0775940c9126a3112a49432fcca475bafe788b4e9b83f67fd991ec3228fc6fa6850d9
+Size (R/terra_1.7-83.tar.gz) = 970353 bytes