Error while combined with ggplot: Error: node stack overflow
GuiSPinto opened this issue · comments
Hi!
I keep getting this error since quite recently. I tried to reinstall all the packages but the error persists. However, the spatvectors do work with base plot.
The error also shows up either when downloading a spatvector or creating a new one:
library(terra)
library(tidyterra)
library(ggplot2)
GER <- geodata::gadm(country=c("Germany"),level=0,path=tempdir())
ggplot(GER) + geom_spatvector()
or:
library(terra)
library(tidyterra)
library(ggplot2)
points <- data.frame(GridID = c(1,2,3,4,5,6), Lat = c(53.8900,53.8900,53.8900,53.8900,53.8900,53.9125), Long = c(14.2425,14.2875,14.3325,14.3775,14.4225,11.2275))
grids <- terra::vect(x = points, geom = c("Long","Lat"), crs = "+proj=longlat +datum=WGS84 +no_defs +type=crs")
ggplot(grids) + geom_spatvector()
Error: node stack overflow In addition: There were 50 or more warnings (use warnings() to see the first 50) Error during wrapup: node stack overflow Error: no more error handlers available (recursive errors?); invoking 'abort' restart
If I try to store the ggplot in a variable, I get an additional warning:
g1 <- ggplot(grids) + geom_spatvector()
In CPL_crs_from_input(x) : GDAL Error 1: PROJ: proj_create_from_database: C:\Program Files\PostgreSQL\13\share\contrib\postgis-3.1\proj\proj.db lacks DATABASE.LAYOUT.VERSION.MAJOR / DATABASE.LAYOUT.VERSION.MINOR metadata. It comes from another PROJ installation.
It is working in my local machine (Windows R 4.3.3) and in all the test I put together., that tests this in several platforms with different R versions.
It seems to me that this is realted with GDAL rather than tidyterra. Could you please uninstall sf and terra, re-install them and re-check?
In my machine_
library(terra)
#> terra 1.7.71
library(tidyterra)
#>
#> Attaching package: 'tidyterra'
#> The following object is masked from 'package:stats':
#>
#> filter
library(ggplot2)
GER <- geodata::gadm(country = c("Germany"), level = 0, path = tempdir())
ggplot(GER) +
geom_spatvector()
points <- data.frame(
GridID = c(1, 2, 3, 4, 5, 6),
Lat = c(53.8900, 53.8900, 53.8900, 53.8900, 53.8900, 53.9125),
Long = c(14.2425, 14.2875, 14.3325, 14.3775, 14.4225, 11.2275)
)
grids <- terra::vect(
x = points,
geom = c("Long", "Lat"),
crs = "+proj=longlat +datum=WGS84 +no_defs +type=crs"
)
ggplot(grids) +
geom_spatvector()
Created on 2024-03-12 with reprex v2.1.0
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.3 (2024-02-29 ucrt)
#> os Windows 11 x64 (build 22631)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate Spanish_Spain.utf8
#> ctype Spanish_Spain.utf8
#> tz Europe/Madrid
#> date 2024-03-12
#> pandoc 3.1.1 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> class 7.3-22 2023-05-03 [1] CRAN (R 4.3.1)
#> classInt 0.4-10 2023-09-05 [1] CRAN (R 4.3.1)
#> cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.2)
#> codetools 0.2-19 2023-02-01 [2] CRAN (R 4.3.3)
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#> dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.3.2)
#> e1071 1.7-14 2023-12-06 [1] CRAN (R 4.3.2)
#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.3.2)
#> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.3.2)
#> farver 2.1.1 2022-07-06 [1] CRAN (R 4.3.0)
#> fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.0)
#> fs 1.6.3 2023-07-20 [1] CRAN (R 4.3.1)
#> generics 0.1.3 2022-07-05 [1] CRAN (R 4.3.0)
#> geodata 0.5-9 2023-10-13 [1] CRAN (R 4.3.1)
#> ggplot2 * 3.5.0 2024-02-23 [1] CRAN (R 4.3.2)
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#> highr 0.10 2022-12-22 [1] CRAN (R 4.3.0)
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#> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.2)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.0)
#> munsell 0.5.0 2018-06-12 [1] CRAN (R 4.3.0)
#> pillar 1.9.0 2023-03-22 [1] CRAN (R 4.3.0)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.3.0)
#> proxy 0.4-27 2022-06-09 [1] CRAN (R 4.3.0)
#> purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.1)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.3.0)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.3.0)
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#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.0)
#> sf 1.0-15 2023-12-18 [1] CRAN (R 4.3.3)
#> styler 1.10.2 2023-08-29 [1] CRAN (R 4.3.1)
#> terra * 1.7-71 2024-01-31 [1] CRAN (R 4.3.2)
#> tibble 3.2.1 2023-03-20 [1] CRAN (R 4.3.0)
#> tidyr 1.3.1 2024-01-24 [1] CRAN (R 4.3.2)
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#> yaml 2.3.8 2023-12-11 [1] CRAN (R 4.3.2)
#>
#> [1] C:/Users/diego/AppData/Local/R/win-library/4.3
#> [2] C:/Program Files/R/R-4.3.3/library
#>
#> ──────────────────────────────────────────────────────────────────────────────Hey there!
Thanks for the answer. It still doesn't work (see below). It probably is something related to GDAL, since I keep getting this error/warning when projecting:
GER <- project(GER, "EPSG:3006")
Error: [project] output crs is not valid
In addition: Warning message:
PROJ: proj_create_from_database: C:\Program Files\PostgreSQL\13\share\contrib\postgis-3.1\proj\proj.db lacks DATABASE.LAYOUT.VERSION.MAJOR / DATABASE.LAYOUT.VERSION.MINOR metadata. It comes from another PROJ installation. (GDAL error 1)
Any ideas on how I could completely remove GDAL and re-install it on Windows?
Here the same errors:
> R.version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
crt ucrt
system x86_64, mingw32
status
major 4
minor 3.1
year 2023
month 06
day 16
svn rev 84548
language R
version.string R version 4.3.1 (2023-06-16 ucrt)
nickname Beagle Scouts
> install.packages(c("sf", "terra"))
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/sf_1.0-15.zip'
Content type 'application/zip' length 39200041 bytes (37.4 MB)
downloaded 37.4 MB
trying URL 'https://cran.rstudio.com/bin/windows/contrib/4.3/terra_1.7-71.zip'
Content type 'application/zip' length 39567537 bytes (37.7 MB)
downloaded 37.7 MB
package ‘sf’ successfully unpacked and MD5 sums checked
package ‘terra’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\ly60anep\AppData\Local\Temp\RtmpOcZ7ej\downloaded_packages
> library(terra)
terra 1.7.71
Warning message:
package ‘terra’ was built under R version 4.3.3
> library(tidyterra)
Attaching package: ‘tidyterra’
The following object is masked from ‘package:stats’:
filter
Warning message:
package ‘tidyterra’ was built under R version 4.3.3
> library(ggplot2)
Warning message:
package ‘ggplot2’ was built under R version 4.3.3
> GER <- geodata::gadm(country = c("Germany"), level = 0, path = tempdir())
trying URL 'https://geodata.ucdavis.edu/gadm/gadm4.1/pck/gadm41_DEU_0_pk.rds'
Content type 'unknown' length 2255014 bytes (2.2 MB)
downloaded 2.2 MB
> ggplot(GER) +
+ geom_spatvector()
Error: node stack overflow
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Error during wrapup: node stack overflow
Error: no more error handlers available (recursive errors?); invoking 'abort' restart
Hey there!
So, it took a while and some digging, but I solved the problem. Actually, the whole thing happened because of different GDAL installations and where the packages were looking for it.
What I did was just re-set the environmental variable from PROJ_LIB:
Sys.setenv(PROJ_LIB="C:\\Users\\ly60anep\\AppData\\Local\\R\\win-library\\4.3\\terra\\proj")
It was, however, not permanent, what I fixed using:
usethis::edit_r_profile()
It also solved other problems I had related to re-projections, such as:
Error: [project] output crs is not valid
In addition: Warning message:
PROJ: proj_create_from_database: C:\Program Files\PostgreSQL\13\share\contrib\postgis-3.1\proj\proj.db lacks DATABASE.LAYOUT.VERSION.MAJOR / DATABASE.LAYOUT.VERSION.MINOR metadata. It comes from another PROJ installation. (GDAL error 1)