could not reproduce myriam's error

analysis/issues_examples.R

@@ -1,99 +1,15 @@
 # issue described by Myriam Terristi (unnumbered, not on github):
 # error when making land mask tidy
 
-settings <- list(
-  fileprefix = "test",  # simulation name defined by the user
-  model = "pmodel",     # in future could also be "biomee", but not yet implemented
-  year_start = 2018,    # xxx not yet handled
-  year_end = 2018,      # xxx not yet handled
-  grid = list(          # a list specifying the grid which must be common to all forcing data
-    lon_start = -179.75,
-    dlon = 0.5,
-    len_ilon = 720,
-    lat_start = -89.75,
-    dlat = 0.5,
-    len_ilat = 360
-  ),
-  file_landmask = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation.nc",
-  dir_landmask_tidy = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation_tidy/",
-  file_elv = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation.nc",
-  dir_elv_tidy = "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation_tidy/",
-  save_drivers = TRUE,   # whether rsofun driver object is to be saved. Uses additional disk space but substantially speeds up grsofun_run().
-  dir_drivers = here::here("input/tidy/"),  # path where rsofun drivers are to be written
-  overwrite = FALSE,    # whether files with tidy forcing data and drivers are to be overwritten. If false, reads files if available instead of re-creating them.
-  spinupyears = 10,     # model spin-up length
-  recycle = 1,          # climate forcing recycling during the spinup
-  dir_out = here::here("output/tidy/"),     # path for tidy model output
-  dir_out_nc = "xxx",  # xxx not yet handled
-  save = list(         # a named list where names correspond to variable names in rsofun output and the value is a string specifying the temporal resolution to which global output is to be aggregated. 
-    gpp = "mon"
-  ),
-  nthreads = 1,   # distribute to multiple nodes for high performance computing - xxx not yet implemented
-  ncores_max = 1  # set to 1 for un-parallel run
-)
-
 error <- map2tidy::map2tidy(
-  nclist = settings$file_landmask,
+  nclist = "~/data/archive_legacy/landmasks/WFDEI-elevation.nc",  # "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation.nc"
   varnam = "elevation",
   lonnam = "lon",
   latnam = "lat",
   timenam= NA,
   timedimnam= NA,
   do_chunks = TRUE,
-  outdir = settings$dir_landmask_tidy,
+  outdir = "~/data/archive_legacy/landmasks/WFDEI-elevation_tidy/",  # "/Net/Groups/BGI/scratch/mterristi/PhD/Pmodel/grsofun/data/elevation/WFDEI-elevation_tidy/"
   fileprefix = "WFDEI-elevation",
-  overwrite = settings$overwrite
+  overwrite = TRUE
 )
-
-> rlang::last_trace()
-<error/purrr_error_indexed>
-Error in `purrr::map()`:
-ℹ In index: 1.
-Caused by error in `purrr::map()`:
-ℹ In index: 1.
-Caused by error in `nc_atts.NetCDF()`:
-! specified variable not found
----
-Backtrace:
-     ▆
-  1. ├─map2tidy::map2tidy(...)
-  2. │ └─purrr::map(...)
-  3. │   └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
-  4. │     ├─purrr:::with_indexed_errors(...)
-  5. │     │ └─base::withCallingHandlers(...)
-  6. │     ├─purrr:::call_with_cleanup(...)
-  7. │     └─map2tidy (local) .f(.x[[i]], ...)
-  8. │       └─map2tidy::nclist_to_df_byilon(...)
-  9. │         └─purrr::map(...)
- 10. │           └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
- 11. │             ├─purrr:::with_indexed_errors(...)
- 12. │             │ └─base::withCallingHandlers(...)
- 13. │             ├─purrr:::call_with_cleanup(...)
- 14. │             └─map2tidy (local) .f(.x[[i]], ...)
- 15. │               └─map2tidy::nclist_to_df_byfil(...)
- 16. │                 ├─... %>% lubridate::ymd()
- 17. │                 ├─ncmeta::nc_atts(filnam, timenam)
- 18. │                 └─ncmeta:::nc_atts.character(filnam, timenam)
- 19. │                   ├─ncmeta::nc_atts(nc, variable = variable)
- 20. │                   └─ncmeta:::nc_atts.NetCDF(nc, variable = variable)
- 21. │                     └─base::stop("specified variable not found")
- 22. ├─lubridate::ymd(.)
- 23. │ └─lubridate:::.parse_xxx(...)
- 24. │   ├─base::unlist(lapply(list(...), .num_to_date), use.names = FALSE)
- 25. │   └─base::lapply(list(...), .num_to_date)
- 26. ├─stringr::str_remove(., " 0:0:0")
- 27. │ └─stringr::str_replace(string, pattern, "")
- 28. │   └─stringr:::check_lengths(string, pattern, replacement)
- 29. │     └─vctrs::vec_size_common(...)
- 30. ├─stringr::str_remove(., " 00:00:00")
- 31. │ └─stringr::str_replace(string, pattern, "")
- 32. │   └─stringr:::check_lengths(string, pattern, replacement)
- 33. │     └─vctrs::vec_size_common(...)
- 34. ├─stringr::str_remove(., "days since ")
- 35. │ └─stringr::str_replace(string, pattern, "")
- 36. │   └─stringr:::check_lengths(string, pattern, replacement)
- 37. │     └─vctrs::vec_size_common(...)
- 38. ├─dplyr::pull(., value)
- 39. ├─dplyr::filter(., name == "units")
- 40. └─tidyr::unnest(., cols = c(value))
->