vector: standard error messages when importing from GRASS GIS in R #47
Description
This usecase is for R where we are using package {terra}. It uses GDAL for reading & writing any supported data source format. With the GDAL-GRASS standalone driver installed this works fine for raster, but throws standard error messages when reading a vector layer.
The examples below use vector data sources in the GRASS GIS 'North Carolina basic dataset', downloaded from https://grass.osgeo.org/download/data/.
Example 1: point data
library(terra)
#> terra 1.7.78
result_1 <- vect(
x = "/home/floris/grassdata/nc_basic_spm_grass7/PERMANENT/vector/schools/head",
layer = "schools"
)
#> Warning: Cannot reset cursor. (GDAL error 1)
#> Warning: Attributes not found. (GDAL error 1)
result_1
#> class : SpatVector
#> geometry : points
#> dimensions : 167, 29 (geometries, attributes)
#> extent : 619215.1, 671714.6, 203559, 248159.8 (xmin, xmax, ymin, ymax)
#> source : head (schools)
#> coord. ref. : +proj=lcc +lat_0=33.75 +lon_0=-79 +lat_1=36.1666666666667 +lat_2=34.3333333333333 +x_0=609601.22 +y_0=0 +datum=NAD83 +units=m +no_defs
#> names : cat TAG NAMESHORT NAMELONG CORECAPACI
#> type : <int> <chr> <chr> <chr> <num>
#> values : 1 568 SWIFT CREEK SWIFT CREEK EL~ 448
#> 2 340 BRIARCLIFF BRIARCLIFF ELE~ 540
#> 3 414 FARMINGTON WOODS FARMINGTON WOO~ 523
#> MOBILEUNIT MOBILECAPA GLEVEL LOGRADE HIGRADE (and 19 more)
#> <num> <num> <chr> <chr> <chr>
#> 2 NaN E NA NA
#> 0 NaN E NA NA
#> 7 NaN E NA NACreated on 2024-06-15 with reprex v2.1.0
Collected standard output and standard error
DBMI-SQLite driver error:
DB_PREVIOUS is not supported
DBMI-SQLite driver error:
DB_PREVIOUS is not supported
DB_PREVIOUS is defined in GRASS GIS in include/grass/dbmi.h.
Example 2: polygon data
library(terra)
#> terra 1.7.78
result_2 <- vect(
x = "/home/floris/grassdata/nc_basic_spm_grass7/PERMANENT/vector/zipcodes/head",
layer = "zipcodes"
)
#> Warning: Cannot reset cursor. (GDAL error 1)
#> Warning: Attributes not found. (GDAL error 1)
result_2
#> class : SpatVector
#> geometry : polygons
#> dimensions : 48, 12 (geometries, attributes)
#> extent : 610047.9, 677060.7, 196327.5, 258102.6 (xmin, xmax, ymin, ymax)
#> source : head (zipcodes)
#> coord. ref. : +proj=lcc +lat_0=33.75 +lon_0=-79 +lat_1=36.1666666666667 +lat_2=34.3333333333333 +x_0=609601.22 +y_0=0 +datum=NAD83 +units=m +no_defs
#> names : cat OBJECTID WAKE_ZIPCO PERIMETER ZIPCODE_ ZIPCODE_ID
#> type : <int> <int> <num> <num> <num> <num>
#> values : 1 1 2.625e+08 8.075e+04 2 27
#> 2 2 3.163e+07 3.106e+04 7 25
#> 3 3 5.44e+08 1.153e+05 8 20
#> ZIPNAME ZIPNUM ZIPCODE NAME SHAPE_Leng SHAPE_Area
#> <chr> <num> <chr> <chr> <num> <num>
#> CREEDMOOR 2.752e+04 CREEDMOOR 27522 CREEDMOOR 8.078e+04 2.624e+08
#> YOUNGSVILLE 2.76e+04 YOUNGSVILLE 27596 YOUNGSVILLE 3.106e+04 3.163e+07
#> RALEIGH 2.762e+04 RALEIGH 27615 RALEIGH 1.153e+05 5.44e+08Created on 2024-06-15 with reprex v2.1.0
Collected standard output and standard error
DBMI-SQLite driver error:
DB_PREVIOUS is not supported
DBMI-SQLite driver error:
DB_PREVIOUS is not supported
DB_PREVIOUS is defined in GRASS GIS in include/grass/dbmi.h.
R session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.4.0 (2024-04-24)
#> os Linux Mint 21.3
#> system x86_64, linux-gnu
#> ui X11
#> language nl_BE:nl
#> collate nl_BE.UTF-8
#> ctype nl_BE.UTF-8
#> tz Europe/Brussels
#> date 2024-06-15
#> pandoc 3.1.11 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.6.2 2023-12-11 [3] RSPM (R 4.3.0)
#> codetools 0.2-20 2024-03-31 [3] RSPM (R 4.3.0)
#> digest 0.6.35 2024-03-11 [3] RSPM (R 4.3.0)
#> evaluate 0.24.0 2024-06-10 [3] RSPM (R 4.4.0)
#> fastmap 1.2.0 2024-05-15 [3] RSPM (R 4.4.0)
#> fs 1.6.4 2024-04-25 [3] RSPM (R 4.3.0)
#> glue 1.7.0 2024-01-09 [3] RSPM (R 4.3.0)
#> htmltools 0.5.8.1 2024-04-04 [3] RSPM (R 4.3.0)
#> knitr 1.47.2 2024-06-04 [1] Github (yihui/knitr@f50b75b)
#> lifecycle 1.0.4 2023-11-07 [3] RSPM (R 4.3.0)
#> magrittr 2.0.3 2022-03-30 [3] RSPM (R 4.2.0)
#> purrr 1.0.2 2023-08-10 [3] RSPM (R 4.2.0)
#> R.cache 0.16.0 2022-07-21 [3] RSPM (R 4.2.0)
#> R.methodsS3 1.8.2 2022-06-13 [3] RSPM (R 4.2.0)
#> R.oo 1.26.0 2024-01-24 [3] RSPM (R 4.3.0)
#> R.utils 2.12.3 2023-11-18 [3] RSPM (R 4.3.0)
#> Rcpp 1.0.12 2024-01-09 [3] RSPM (R 4.3.0)
#> reprex 2.1.0 2024-01-11 [3] RSPM (R 4.3.0)
#> rlang 1.1.4 2024-06-04 [3] RSPM (R 4.4.0)
#> rmarkdown 2.27 2024-05-17 [3] RSPM (R 4.4.0)
#> rstudioapi 0.16.0 2024-03-24 [3] RSPM (R 4.3.0)
#> sessioninfo 1.2.2 2021-12-06 [3] RSPM (R 4.2.0)
#> styler 1.10.3 2024-04-07 [3] RSPM (R 4.3.0)
#> terra * 1.7-78 2024-05-22 [1] RSPM (R 4.4.0)
#> vctrs 0.6.5 2023-12-01 [3] RSPM (R 4.3.0)
#> withr 3.0.0 2024-01-16 [3] RSPM (R 4.3.2)
#> xfun 0.44 2024-05-15 [3] RSPM (R 4.4.0)
#> yaml 2.3.8 2023-12-11 [3] RSPM (R 4.3.0)
#>
#> [1] /home/floris/lib/R/library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────Motivation:
In R the GRASS GIS interface is provided by package {rgrass} (@rsbivand), which in turn uses the {terra} package (@rhijmans) for reading & writing with GDAL. In the {rgrass} package we intend to (re-)implement the GDAL-GRASS driver to access layers in order to avoid the extra r.out.gdal or v.out.ogr steps that cause extra writing & reading overhead. (https://github.com/rsbivand/rgrass/issues/75)
System specs:
$ ogrinfo --version
GDAL 3.8.4, released 2024/02/08
$
$ apt policy libgdal-grass
libgdal-grass:
Installed: 1:1.0.2-7+jammy3
Candidate: 1:1.0.2-7+jammy3
Version table:
*** 1:1.0.2-7+jammy3 500
500 http://ppa.launchpad.net/ubuntugis/ubuntugis-unstable/ubuntu jammy/main amd64 Packages
100 /var/lib/dpkg/status
3.4.1-3 500
500 http://ftp.belnet.be/ubuntu jammy/universe amd64 Packages
$
$ inxi -Sxxx
System:
Host: xxx Kernel: 5.15.0-112-generic x86_64 bits: 64 compiler: gcc
v: 11.4.0 Desktop: Cinnamon 6.0.4 tk: GTK 3.24.33 wm: muffin vt: 7
dm: LightDM 1.30.0 Distro: Linux Mint 21.3 Virginia
base: Ubuntu 22.04 jammy