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R CMD check with R_SF_ST_READ_USE_STREAM=true #2296

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rsbivand opened this issue Dec 18, 2023 · 4 comments · May be fixed by #2369
Open

R CMD check with R_SF_ST_READ_USE_STREAM=true #2296

rsbivand opened this issue Dec 18, 2023 · 4 comments · May be fixed by #2369

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@rsbivand
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Running CMD check for GDAL 3.8.2RC1, I set R_SF_ST_READ_USE_STREAM=true, and hit a problem in tests/empty.R, lines 91-92:
00check.log

> y = st_read("empty.gpkg", quiet = TRUE)
> all.equal(x, y)
Error in UseMethod("st_geometry") : 
  no applicable method for 'st_geometry' applied to an object of class "c('double', 'numeric')"
> str(x)
Classes 'sf' and 'data.frame':	2 obs. of  2 variables:
 $ a   : int  2 1
 $ geom:sfc_LINESTRING of length 2; first list element:  'XY' num[0 , 1:2] LINESTRING EMPTY
 - attr(*, "sf_column")= chr "geom"
 - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA
  ..- attr(*, "names")= chr "a"
> str(y)
Classes 'sf' and 'data.frame':	2 obs. of  2 variables:
 $ a   : int  2 1
 $ geom:sfc_MULTILINESTRING of length 2; first list element:  list()
  ..- attr(*, "class")= chr [1:3] "XY" "MULTILINESTRING" "sfg"
 - attr(*, "sf_column")= chr "geom"
 - attr(*, "agr")= Factor w/ 3 levels "constant","aggregate",..: NA
  ..- attr(*, "names")= chr "a"

I guess this is not new for GDAL 3.8.2, will check when this train gets to Bergen.
@rsbivand
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Same error with released GDAL 3.8.1:
00check.log

@edzer
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edzer commented Feb 10, 2024

Confirmed; the issue is that empty.gpkg (zipped: empty.zip) is written with LINESTRING geometries but read with MULTILINESTRING geometries when using the stream interface. @paleolimbot can you see whether this is caused by sf code or by GDAL code?

@paleolimbot
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I will dig deeper after the kids are in bed, but I think the culprit might be the promote multi option when converting from wkb to sfc. That's implemented in wk at the moment (because sf's built in wkb parser doesn't do promote to multi if I remember correctly)

@paleolimbot
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It seems like the two interpretations of "promote to multi" are slightly different: wk seems to do this unconditionally, whereas sf seems to do this only when required. I can't find a PR where this changed...I forget how deeply I poked this when writing implementing this in wk::sfc_writer() but the sf version is definitely the desired behaviour.

library(sf)
#> Linking to GEOS 3.12.1, GDAL 3.8.3, PROJ 9.3.1; sf_use_s2() is TRUE

tf <- tempfile(fileext = ".gpkg")
data.frame(
  a = 2:1,
  geom = sf::st_as_sfc(c("LINESTRING EMPTY", "LINESTRING (1 2, 3 4)"))
) |>
  sf::write_sf(tf)
#> writing: substituting ENGCRS["Undefined Cartesian SRS with unknown unit"] for missing CRS

sf::read_sf(tf, use_stream = FALSE, promote_to_multi = TRUE)
#> Simple feature collection with 2 features and 1 field (with 1 geometry empty)
#> Geometry type: LINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: 1 ymin: 2 xmax: 3 ymax: 4
#> Projected CRS: Undefined Cartesian SRS with unknown unit
#> # A tibble: 2 x 2
#>       a         geom
#>   <int> <LINESTRING>
#> 1     2        EMPTY
#> 2     1   (1 2, 3 4)
sf::read_sf(tf, use_stream = FALSE, promote_to_multi = FALSE)
#> Simple feature collection with 2 features and 1 field (with 1 geometry empty)
#> Geometry type: LINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: 1 ymin: 2 xmax: 3 ymax: 4
#> Projected CRS: Undefined Cartesian SRS with unknown unit
#> # A tibble: 2 x 2
#>       a         geom
#>   <int> <LINESTRING>
#> 1     2        EMPTY
#> 2     1   (1 2, 3 4)

sf::read_sf(tf, use_stream = TRUE, promote_to_multi = TRUE)
#> Simple feature collection with 2 features and 1 field (with 1 geometry empty)
#> Geometry type: MULTILINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: 1 ymin: 2 xmax: 3 ymax: 4
#> Projected CRS: Undefined Cartesian SRS with unknown unit
#> # A tibble: 2 x 2
#>       a              geom
#>   <int> <MULTILINESTRING>
#> 1     2             EMPTY
#> 2     1      ((1 2, 3 4))
sf::read_sf(tf, use_stream = TRUE, promote_to_multi = FALSE)
#> Simple feature collection with 2 features and 1 field (with 1 geometry empty)
#> Geometry type: LINESTRING
#> Dimension:     XY
#> Bounding box:  xmin: 1 ymin: 2 xmax: 3 ymax: 4
#> Projected CRS: Undefined Cartesian SRS with unknown unit
#> # A tibble: 2 x 2
#>       a         geom
#>   <int> <LINESTRING>
#> 1     2        EMPTY
#> 2     1   (1 2, 3 4)

Created on 2024-02-12 with reprex v2.1.0

@paleolimbot paleolimbot linked a pull request Mar 31, 2024 that will close this issue
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Implement promote_to_multi when converting WKB to sfc paleolimbot/sf
3 participants
@edzer @rsbivand @paleolimbot