Error with mdim test: Error: cannot open driver

[barracuda156]

Any idea why this may be failing?

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: powerpc-apple-darwin10.0.0d2 (32-bit)

> Sys.setenv(TZ="")
> suppressPackageStartupMessages(library(stars))
> matrix(1:4,2)
     [,1] [,2]
[1,]    1    3
[2,]    2    4
> m = matrix(1:4,2)
> s = st_as_stars(m)
> 
> s = st_set_dimensions(s, st_dimensions(s), xy = NULL) 
> sfc = st_sfc(st_point(0:1), st_point(3:2))
> s = st_set_dimensions(s, 1, sfc) |> st_set_crs(4326)
> tm = as.POSIXct("2023-03-04 12:35") + c(0, 3600)
> s = st_set_dimensions(s, 2, tm)
> f = tempfile(fileext = ".nc")
> write_mdim(s, f, as_float = FALSE)
Error: cannot open driver
Execution halted

[barracuda156]

The same failure occurs with examples:

The error most likely occurred in:

> ### Name: mdim
> ### Title: Read or write data using GDAL's multidimensional array API
> ### Aliases: mdim read_mdim write_mdim
> 
> ### ** Examples
> 
> set.seed(135)
> m = matrix(runif(10), 2, 5)
> names(dim(m)) = c("stations", "time")
> times = as.Date("2022-05-01") + 1:5
> pts = st_as_sfc(c("POINT(0 1)", "POINT(3 5)"))
> s = st_as_stars(list(Precipitation = m)) |>
+  st_set_dimensions(1, values = pts) |>
+  st_set_dimensions(2, values = times)
> nc = tempfile(fileext=".nc")
> if (compareVersion(sf_extSoftVersion()["GDAL"], "3.4.0") > -1) {
+   write_mdim(s, nc)
+   # try ncdump on the generated file
+   print(read_mdim(nc))
+ }
Error: cannot open driver

[edzer]

I'm seeing

Sys.setenv(TZ="")
library(stars)
# Loading required package: abind
# Loading required package: sf
# Linking to GEOS 3.12.1, GDAL 3.8.4, PROJ 9.3.1; sf_use_s2() is TRUE
m = matrix(1:4,2)
s = st_as_stars(m)
s = st_set_dimensions(s, st_dimensions(s), xy = NULL)
sfc = st_sfc(st_point(0:1), st_point(3:2))
s = st_set_dimensions(s, 1, sfc) |> st_set_crs(4326)
tm = as.POSIXct("2023-03-04 12:35") + c(0, 3600)
s = st_set_dimensions(s, 2, tm)
f = tempfile(fileext = ".nc")
write_mdim(s, f, as_float = FALSE)
# Warning messages:
# 1: In CPL_write_mdim(file, driver, dimx, cdl, wkt, xy, root_group_options,  :
#   GDAL Error 6: SetIndexingVariable() not implemented
# 2: In CPL_write_mdim(file, driver, dimx, cdl, wkt, xy, root_group_options,  :
#   GDAL Error 6: SetIndexingVariable() not implemented
read_mdim(f)
# stars object with 2 dimensions and 1 attribute
# attribute(s):
#     Min. 1st Qu. Median Mean 3rd Qu. Max.
# A1     1    1.75    2.5  2.5    3.25    4
# dimension(s):
#    from to                  offset   delta  refsys point
# X1    1  2                      NA      NA  WGS 84  TRUE
# X2    1  2 2023-03-04 12:35:00 UTC 1 hours POSIXct    NA
#                      values
# X1 POINT (0 1), POINT (3 2)
# X2                     NULL

Is this a GDAL version issue?

[barracuda156]

@edzer Perhaps 3.9.0 is not too old? https://ports.macports.org/port/gdal

[edzer]

It's not about the age, but about how GDAL was built: linked against libnetcdf, or not. If not, the netcdf driver is missing and you get errors of this type.

[barracuda156]

@edzer I am building GDAL now with netcdf support enabled. Once confirmed tests pass then, I will close both issues as resolved.

P. S. Perhaps it is worth adding a note about this requirement though. Currently nothing is said about GDAL being linked to netcdf: https://cran.r-project.org/web/packages/stars/index.html
sf is also silent: https://cran.r-project.org/web/packages/sf/index.html
So how one is supposed to know it is necessary?

[edzer]

I could add a message at startup time of stars when the netcdf driver is missing.

[barracuda156]

I could add a message at startup time of stars when the netcdf driver is missing.

That will be helpful, I think.

[barracuda156]

@edzer Files are now found, but specifically mdim example and test still fail for me, though differently:

* checking examples ...sh: line 1: 70105 Segmentation fault      LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/opt/local/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R'
 ERROR
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> ### Name: mdim
> ### Title: Read or write data using GDAL's multidimensional array API
> ### Aliases: mdim read_mdim write_mdim
> 
> ### ** Examples
> 
> set.seed(135)
> m = matrix(runif(10), 2, 5)
> names(dim(m)) = c("stations", "time")
> times = as.Date("2022-05-01") + 1:5
> pts = st_as_sfc(c("POINT(0 1)", "POINT(3 5)"))
> s = st_as_stars(list(Precipitation = m)) |>
+  st_set_dimensions(1, values = pts) |>
+  st_set_dimensions(2, values = times)
> nc = tempfile(fileext=".nc")
> if (compareVersion(sf_extSoftVersion()["GDAL"], "3.4.0") > -1) {
+   write_mdim(s, nc)
+   # try ncdump on the generated file
+   print(read_mdim(nc))
+ }
Warning in CPL_write_mdim(file, driver, dimx, cdl, wkt, xy, root_group_options,  :
  GDAL Error 6: SetIndexingVariable() not implemented
Warning in CPL_write_mdim(file, driver, dimx, cdl, wkt, xy, root_group_options,  :
  GDAL Error 6: SetIndexingVariable() not implemented

 *** caught segfault ***
address 0xc0000000, cause 'memory not mapped'

Traceback:
 1: CPL_write_mdim(file, driver, dimx, cdl, wkt, xy, root_group_options,     options, as_float)
 2: gdal_write_mdim(filename, driver, c(dim(x), attr(cdl, "dims")),     cdl, wkt, xy, root_group_options = root_group_options, options = options,     as_float = as_float)
 3: write_mdim(s, nc)
An irrecoverable exception occurred. R is aborting now ...

  Running ‘mdim.R’/opt/local/Library/Frameworks/R.framework/Resources/bin/BATCH: line 60: 70383 Segmentation fault      ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/mdim.R’ failed.
Last 13 lines of output:
  > sfc = st_sfc(st_point(0:1), st_point(3:2))
  > s = st_set_dimensions(s, 1, sfc) |> st_set_crs(4326)
  > tm = as.POSIXct("2023-03-04 12:35") + c(0, 3600)
  > s = st_set_dimensions(s, 2, tm)
  > f = tempfile(fileext = ".nc")
  > write_mdim(s, f, as_float = FALSE)
  
   *** caught segfault ***
  address 0xc0000000, cause 'memory not mapped'
  
  Traceback:
   1: CPL_write_mdim(file, driver, dimx, cdl, wkt, xy, root_group_options,     options, as_float)
   2: gdal_write_mdim(filename, driver, c(dim(x), attr(cdl, "dims")),     cdl, wkt, xy, root_group_options = root_group_options, options = options,     as_float = as_float)
   3: write_mdim(s, f, as_float = FALSE)
  An irrecoverable exception occurred. R is aborting now ...
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/opt/local/var/macports/build/_opt_PPCSnowLeopardPorts_R_R-stars/R-stars/work/stars/stars.Rcheck/00check.log’
for details.

But it looks like it is using R BATCH, which is known to be broken for w/e reason: https://trac.macports.org/ticket/67059

All other tests now pass (with GDAL +netcdf).