GDAL Access window out of range on read-in of stars_proxy

[galenholt]

I'm trying to read a stars_proxy object in as stars with st_as_stars , and it is failing with

GDAL Error 5: NETCDF:"path/to/file/MYD11A1.061_1km_aid0001.nc":lon: Access window out of range in RasterIO(). Requested (0,0) of size 1671x1567 on raster of 1671x1.

The proxy object shows the correct dimensions, here x = 1671 and y = 1567, but for some reason the conversion loses y.

I originally encountered this cropping very large files, but I seem to be able to replicate it with something smaller that reads in fine with proxy = FALSE but fails with proxy = TRUE in the example below.

This issue does not happen with all netcdfs I've tried, but I have had it happen with several from different sources. So it might be a netcdf issue, but seems to be a fairly common one.

I have tried a few versions of stars because I've read this specific file in successfully before, and it seems to work for 0.5-05 and below but not for 0.5-6 and above.

library(stars)

download.file("https://raw.githubusercontent.com/galenholt/example/main/MYD11A1.061_1km_aid0001.nc",
              destfile = 'MYD11A1.061_1km_aid0001.nc',
              method = 'curl')

# Works without proxy
t_np <- read_stars("MYD11A1.061_1km_aid0001.nc", sub = "LST_Day_1km", proxy = FALSE)

# Fails with proxy first
t_proxy <- read_stars("MYD11A1.061_1km_aid0001.nc", sub = "LST_Day_1km", proxy = TRUE)
t_p <- st_as_stars(t_proxy)

# But the proxy can see the right values in y
t_proxy

# Can read the proxy in for the first value in y
t1 <- st_as_stars(t_proxy[, 1:10, 1,])

# But not others
t2 <- st_as_stars(t_proxy[, 1:10, 2,])

sessionInfo() is

R version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8 LC_MONETARY=English_Australia.utf8 [4] LC_NUMERIC=C LC_TIME=English_Australia.utf8

time zone: Australia/Sydney tzcode source: internal

attached base packages: [1] stats graphics grDevices datasets utils methods base

other attached packages: [1] stars_0.6-5 sf_1.0-16 abind_1.4-5

loaded via a namespace (and not attached): [1] e1071_1.7-14 magrittr_2.0.3 KernSmooth_2.23-22 parallel_4.3.3 classInt_0.4-10 cli_3.6.2
[7] grid_4.3.3 DBI_1.2.2 renv_1.0.3 proxy_0.4-27 class_7.3-22 compiler_4.3.3
[13] rstudioapi_0.16.0 tools_4.3.3 Rcpp_1.0.12 yaml_2.3.8 rlang_1.1.3 units_0.8-5

Thank you

[edzer]

Thanks, great report! Should work now,

[galenholt]

yep, I can confirm that works. Thank you!