Error messages in C5

[Robinlovelace]

I'm seeing the following errors in Chapter 5:

> elev = rast(system.file("raster/elev.tif", package = "spData"))
> elev_2 = extend(elev, c(1, 2))
> 
> # Chunk 52: extend-example
> source("https://github.com/Robinlovelace/geocompr/raw/main/code/05-extend-example.R", print.eval = TRUE)
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x)  : attempt to apply non-function
> 
> # Chunk 53: 05-geometry-operations-37
> elev_3 = elev + elev_2
Error: [+] extents do not match
> 
> # Chunk 54: 05-geometry-operations-38
> elev_4 = extend(elev, elev_2)
> 
> # Chunk 55: 05-geometry-operations-39
> origin(elev_4)
[1] 0 0
> 
> # Chunk 56
> # change the origin
> origin(elev_4) = c(0.25, 0.25)
> elev_poly = st_as_sf(as.polygons(elev, dissolve = FALSE))
> elev4_poly = st_as_sf(as.polygons(elev_4, dissolve = FALSE))
> tm_shape(elev4_poly) +
+   tm_grid() +
+   tm_polygons(col = "elev") + 
+   tm_shape(elev_poly) +
+   tm_polygons(col = "elev") +
+   tm_layout(frame = FALSE, legend.show = FALSE,
+             inner.margins = c(0.1, 0.12, 0, 0))
Error: The shape elev4_poly only contains empty units.
> elev4_poly$geometry

With up-to-date versions of packages, session info below.

``` devtools::session_info() ─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.1.2 (2021-11-01) os Ubuntu 20.04.3 LTS system x86_64, linux-gnu ui RStudio language en_GB:en collate en_GB.UTF-8 ctype en_GB.UTF-8 tz Europe/London date 2021-12-17 rstudio 2022.01.0-daily+300.pro1 Prairie Trillium (server) pandoc 2.16.2 @ /usr/lib/rstudio-server/bin/quarto/bin/ (via rmarkdown)

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callr 3.7.0 2021-04-20 [3] CRAN (R 4.0.5)
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fastmap 1.1.0 2021-01-25 [2] CRAN (R 4.1.1)
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glue 1.6.0 2021-12-17 [1] CRAN (R 4.1.2)
highr 0.9 2021-04-16 [3] CRAN (R 4.0.5)
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jqr 1.2.2 2021-11-08 [2] CRAN (R 4.1.2)
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knitr 1.37 2021-12-16 [1] CRAN (R 4.1.2)
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magrittr 2.0.1 2020-11-17 [2] CRAN (R 4.1.1)
maptools 1.1-2 2021-09-07 [2] CRAN (R 4.1.1)
memoise 2.0.1 2021-11-26 [3] CRAN (R 4.1.2)
munsell 0.5.0 2018-06-12 [2] CRAN (R 4.0.2)
pillar 1.6.4 2021-10-18 [2] CRAN (R 4.1.1)
pkgbuild 1.3.0 2021-12-09 [3] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.1.1)
pkgload 1.2.4 2021-11-30 [3] CRAN (R 4.1.2)
png 0.1-7 2013-12-03 [2] CRAN (R 4.0.2)
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proxy 0.4-26 2021-06-07 [2] CRAN (R 4.0.4)
ps 1.6.0 2021-02-28 [2] CRAN (R 4.1.1)
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R6 2.5.1 2021-08-19 [2] CRAN (R 4.1.1)
ragg 1.2.1 2021-12-06 [2] CRAN (R 4.1.2)
raster 3.5-9 2021-12-10 [2] CRAN (R 4.1.2)
RColorBrewer 1.1-2 2014-12-07 [2] CRAN (R 4.1.1)
Rcpp 1.0.7 2021-07-07 [2] CRAN (R 4.1.1)
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rgdal 1.5-28 2021-12-15 [1] CRAN (R 4.1.2)
rgeos 0.5-9 2021-12-15 [1] CRAN (R 4.1.2)
rlang 0.4.12 2021-10-18 [2] CRAN (R 4.1.1)
rmapshaper 0.4.5 2021-05-26 [2] CRAN (R 4.0.4)
rmarkdown 2.11 2021-09-14 [2] CRAN (R 4.1.1)
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rvest 1.0.2 2021-10-16 [3] CRAN (R 4.1.1)
s2 1.0.7 2021-09-28 [2] CRAN (R 4.1.1)
scales 1.1.1 2020-05-11 [2] CRAN (R 4.1.1)
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sf * 1.0-5 2021-12-17 [1] CRAN (R 4.1.2)
sp 1.4-6 2021-11-14 [2] CRAN (R 4.1.2)
spData * 2.0.1 2021-09-21 [2] Github (Nowosad/spData@9c942ba)
spDataLarge * 2.0.3 2021-12-17 [1] Github (Nowosad/spDataLarge@d1ef6d4)
stars 0.5-5 2021-12-17 [1] Github (r-spatial/stars@4292774)
stringi 1.7.6 2021-11-29 [2] CRAN (R 4.1.2)
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tmaptools 3.1-1 2021-01-19 [2] CRAN (R 4.0.3)
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xml2 1.3.3 2021-11-30 [3] CRAN (R 4.1.2)
yaml 2.2.1 2020-02-01 [2] CRAN (R 4.1.1)

[1] /home/robin/R/x86_64-pc-linux-gnu-library/4.1
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library

[Robinlovelace]

After working around issues described in #696 I can confirm this error also appears on GitHub actions: https://github.com/Robinlovelace/geocompr/runs/4566258946?check_suite_focus=true#step:4:3459

[Robinlovelace]

This is the figure that the failing code produces.

[Robinlovelace]

Currently code generating the figure above is failing with the following message:

Quitting from lines 681-688 (05-geometry-operations.Rmd) 
Error: $ operator is invalid for atomic vectors

Source: https://github.com/Robinlovelace/geocompr/runs/4566328620?check_suite_focus=true#step:4:3484

[Robinlovelace]

Same issue for this figure:

Error:

 Quitting from lines 705-706 (05-geometry-operations.Rmd) 
Error: $ operator is invalid for atomic vectors
In addition: There were 11 warnings (use warnings() to see them)

Source: https://github.com/Robinlovelace/geocompr/runs/4566374987?check_suite_focus=true

[Robinlovelace]

Also affects code in line 752 in the chunk:

{r resampl, echo=FALSE, fig.cap="Visual comparison of the original raster and five different resampling methods."}

[Robinlovelace]

And these lines beginning on line 786:

library(tmap)
library(rcartocolor)
terrain_colors = carto_pal(7, "Geyser")
pz1 = tm_shape(srtm) +
  tm_raster(palette = terrain_colors, legend.show = FALSE, style = "cont") +
  tm_shape(zion) +
  tm_borders(lwd = 2) +
  tm_layout(main.title = "A. Original", inner.margins = 0)
pz2 = tm_shape(srtm_cropped) +
  tm_raster(palette = terrain_colors, legend.show = FALSE, style = "cont") +
  tm_shape(zion) +
  tm_borders(lwd = 2) +
  tm_layout(main.title = "B. Crop", inner.margins = 0)
pz3 = tm_shape(srtm_masked) +
  tm_raster(palette = terrain_colors, legend.show = FALSE, style = "cont") +
  tm_shape(zion) +
  tm_borders(lwd = 2) +
  tm_layout(main.title = "C. Mask", inner.margins = 0)
pz4 = tm_shape(srtm_inv_masked) +
  tm_raster(palette = terrain_colors, legend.show = FALSE, style = "cont") +
  tm_shape(zion) +
  tm_borders(lwd = 2) +
  tm_layout(main.title = "D. Inverse mask", inner.margins = 0)
tmap_arrange(pz1, pz2, pz3, pz4, ncol = 4, asp = NA)

[Robinlovelace]

Update: on dev versions of stars and terra I think the above issues go away. However, this one remains, quick fix @Nowosad ?

Quitting from lines 1198-1199 (05-geometry-operations.Rmd) 
Error: Invalid color specification. The available raster variables are: "values".

Source: https://github.com/Robinlovelace/geocompr/runs/4566539012?check_suite_focus=true#step:4:4012

[Nowosad]

I will fix that soon - this is a minor issue of the new (and more robust) conversions between terra and stars.

[Nowosad]

Hi @Robinlovelace I am quite sure that most of the errors are due to the older versions of stars/terra/tmap. I do not get them with the most recent dev versions of these packages (except one, probably a terra bug -- see rspatial/terra#450).