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First invoking raster::raster() and _then_ write GPKG with terra::writeVector() triggers a GDAL ENCODING warning (on Ubuntu / Linux Mint) #1377

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florisvdh opened this issue Dec 19, 2023 · 1 comment
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First invoking raster::raster() and _then_ write GPKG with terra::writeVector() triggers a GDAL ENCODING warning (on Ubuntu / Linux Mint) #1377

florisvdh opened this issue Dec 19, 2023 · 1 comment

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@florisvdh
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In Ubuntu / Linux Mint, but not on Windows and macOS systems, there's an odd effect of having called raster::raster() in an R session before writing a GeoPackage with terra::writeVector(). GDAL raises an ENCODING warning in that specific scenario. See reprexes below.

I don't know whether the solution is here or in the raster package; posting it in terra is a wild guess...

> terra::gdal()
[1] "3.6.4"
# Normally no warning appears when writing a GeoPackage
tmp1 <- tempfile(fileext = ".gpkg")
obj <- terra::vect(
  x = c("POINT (7e5 7e5)", "POINT (6e5 6.5e5)"),
  crs = "EPSG:3812"
)
terra::writeVector(obj, tmp1)
unlink(tmp1)

Created on 2023-12-19 with reprex v2.0.2

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.2 (2023-10-31)
#>  os       Linux Mint 21.2
#>  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     2023-12-19
#>  pandoc   3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  cli           3.6.2   2023-12-11 [3] RSPM (R 4.3.0)
#>  codetools     0.2-19  2023-02-01 [3] RSPM (R 4.2.0)
#>  digest        0.6.33  2023-07-07 [3] RSPM (R 4.2.0)
#>  evaluate      0.23    2023-11-01 [3] RSPM (R 4.3.0)
#>  fastmap       1.1.1   2023-02-24 [3] RSPM (R 4.2.0)
#>  fs            1.6.3   2023-07-20 [3] RSPM (R 4.2.0)
#>  glue          1.6.2   2022-02-24 [3] RSPM (R 4.2.0)
#>  htmltools     0.5.7   2023-11-03 [3] RSPM (R 4.3.0)
#>  knitr         1.45    2023-10-30 [3] RSPM (R 4.3.0)
#>  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          1.25.0  2022-06-12 [3] RSPM (R 4.2.0)
#>  R.utils       2.12.3  2023-11-18 [3] RSPM (R 4.3.0)
#>  Rcpp          1.0.11  2023-07-06 [3] RSPM (R 4.2.0)
#>  reprex        2.0.2   2022-08-17 [3] RSPM (R 4.2.0)
#>  rlang         1.1.2   2023-11-04 [3] RSPM (R 4.3.0)
#>  rmarkdown     2.25    2023-09-18 [3] RSPM (R 4.3.0)
#>  rstudioapi    0.15.0  2023-07-07 [3] RSPM (R 4.2.0)
#>  sessioninfo   1.2.2   2021-12-06 [3] RSPM (R 4.2.0)
#>  styler        1.10.2  2023-08-29 [3] RSPM (R 4.2.0)
#>  terra         1.7-65  2023-12-15 [1] RSPM (R 4.3.2)
#>  vctrs         0.6.5   2023-12-01 [3] RSPM (R 4.3.0)
#>  withr         2.5.2   2023-10-30 [3] RSPM (R 4.3.0)
#>  xfun          0.41    2023-11-01 [3] RSPM (R 4.3.0)
#>  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
#> 
#> ──────────────────────────────────────────────────────────────────────────────
# If raster::raster() was called before, a GDAL ENCODING warning appears
tmp2 <- tempfile(fileext = ".gpkg")
obj <- terra::vect(
  x = c("POINT (7e5 7e5)", "POINT (6e5 6.5e5)"),
  crs = "EPSG:3812"
)
raster::raster()
#> class      : RasterLayer 
#> dimensions : 180, 360, 64800  (nrow, ncol, ncell)
#> resolution : 1, 1  (x, y)
#> extent     : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
#> crs        : +proj=longlat +datum=WGS84 +no_defs
terra::writeVector(obj, tmp2)
#> Warning in x@cpp$write(filename, layer, filetype, insert[1], overwrite[1], :
#> GDAL Message 6: dataset /tmp/RtmpLA62Py/file649273f54794.gpkg does not support
#> layer creation option ENCODING
unlink(tmp2)

Created on 2023-12-19 with reprex v2.0.2

# If raster::raster() was called before, NO warning appears if we don't write GPKG
tmp2 <- tempfile()
obj <- terra::vect(
  x = c("POINT (7e5 7e5)", "POINT (6e5 6.5e5)"),
  crs = "EPSG:3812"
)
raster::raster()
#> class      : RasterLayer 
#> dimensions : 180, 360, 64800  (nrow, ncol, ncell)
#> resolution : 1, 1  (x, y)
#> extent     : -180, 180, -90, 90  (xmin, xmax, ymin, ymax)
#> crs        : +proj=longlat +datum=WGS84 +no_defs
terra::writeVector(obj, tmp2)
unlink(tmp2)

Created on 2023-12-19 with reprex v2.0.2

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.3.2 (2023-10-31)
#>  os       Linux Mint 21.2
#>  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     2023-12-19
#>  pandoc   3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  class         7.3-22  2023-05-03 [3] RSPM (R 4.2.0)
#>  classInt      0.4-10  2023-09-05 [3] RSPM (R 4.3.0)
#>  cli           3.6.2   2023-12-11 [3] RSPM (R 4.3.0)
#>  codetools     0.2-19  2023-02-01 [3] RSPM (R 4.2.0)
#>  DBI           1.1.3   2022-06-18 [3] RSPM (R 4.2.0)
#>  digest        0.6.33  2023-07-07 [3] RSPM (R 4.2.0)
#>  dplyr         1.1.4   2023-11-17 [3] RSPM (R 4.3.0)
#>  e1071         1.7-14  2023-12-06 [3] RSPM (R 4.3.0)
#>  evaluate      0.23    2023-11-01 [3] RSPM (R 4.3.0)
#>  fansi         1.0.6   2023-12-08 [3] RSPM (R 4.3.0)
#>  fastmap       1.1.1   2023-02-24 [3] RSPM (R 4.2.0)
#>  fs            1.6.3   2023-07-20 [3] RSPM (R 4.2.0)
#>  generics      0.1.3   2022-07-05 [3] RSPM (R 4.2.0)
#>  glue          1.6.2   2022-02-24 [3] RSPM (R 4.2.0)
#>  htmltools     0.5.7   2023-11-03 [3] RSPM (R 4.3.0)
#>  KernSmooth    2.23-22 2023-07-10 [3] RSPM (R 4.2.0)
#>  knitr         1.45    2023-10-30 [3] RSPM (R 4.3.0)
#>  lattice       0.22-5  2023-10-24 [3] RSPM (R 4.3.0)
#>  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)
#>  pillar        1.9.0   2023-03-22 [3] RSPM (R 4.2.0)
#>  pkgconfig     2.0.3   2019-09-22 [3] CRAN (R 4.0.1)
#>  proxy         0.4-27  2022-06-09 [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          1.25.0  2022-06-12 [3] RSPM (R 4.2.0)
#>  R.utils       2.12.3  2023-11-18 [3] RSPM (R 4.3.0)
#>  R6            2.5.1   2021-08-19 [3] RSPM (R 4.2.0)
#>  raster        3.6-26  2023-10-14 [3] RSPM (R 4.3.0)
#>  Rcpp          1.0.11  2023-07-06 [3] RSPM (R 4.2.0)
#>  reprex        2.0.2   2022-08-17 [3] RSPM (R 4.2.0)
#>  rlang         1.1.2   2023-11-04 [3] RSPM (R 4.3.0)
#>  rmarkdown     2.25    2023-09-18 [3] RSPM (R 4.3.0)
#>  rstudioapi    0.15.0  2023-07-07 [3] RSPM (R 4.2.0)
#>  sessioninfo   1.2.2   2021-12-06 [3] RSPM (R 4.2.0)
#>  sf            1.0-15  2023-12-18 [1] CRAN (R 4.3.2)
#>  sp            2.1-2   2023-11-26 [3] RSPM (R 4.3.0)
#>  styler        1.10.2  2023-08-29 [3] RSPM (R 4.2.0)
#>  terra         1.7-65  2023-12-15 [1] RSPM (R 4.3.2)
#>  tibble        3.2.1   2023-03-20 [3] RSPM (R 4.3.0)
#>  tidyselect    1.2.0   2022-10-10 [3] RSPM (R 4.2.0)
#>  units         0.8-5   2023-11-28 [3] RSPM (R 4.3.0)
#>  utf8          1.2.4   2023-10-22 [3] RSPM (R 4.3.0)
#>  vctrs         0.6.5   2023-12-01 [3] RSPM (R 4.3.0)
#>  withr         2.5.2   2023-10-30 [3] RSPM (R 4.3.0)
#>  xfun          0.41    2023-11-01 [3] RSPM (R 4.3.0)
#>  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
#> 
#> ──────────────────────────────────────────────────────────────────────────────
@florisvdh
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florisvdh commented Dec 19, 2023 •
edited
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Adding some context. This was discovered in a GitHub Actions R-CMD-check workflow of {qgisprocess} after having added unit tests with terra::SpatVector() to the test file that tests the handling of {terra} objects. Only the Ubuntu jobs were affected. It was observed locally that the many warnings disappear after the test file for handling {raster} objects is removed. That file is run before the {terra} test file because of alphabetical order.

@florisvdh florisvdh mentioned this issue Dec 19, 2023
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