vector: standard error messages when importing from GRASS GIS in R

[florisvdh]

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      NA

^{Created 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+08

^{Created 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. (rsbivand/rgrass#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