Grid_metrics fails to create grid_metrics.vrt

Question

I need to obtain the metrics for a denoised normalized dataset. This is part of the code that I am using:

ctg_denoised <- readLAScatalog("G:/NoBackUp/denoised/")
opt_chunk_buffer(ctg_denoised) <- 10
opt_output_files(ctg_denoised) <- "G:/NoBackUp/metrics/*_metrics"

#METRICS CALCULATION
metrics <- grid_metrics(ctg_denoised, .stdmetrics_z , sqrt(250))

When I apply grid_metrics to the catalog of normalized als data it completes the processing but does not manage to merge all the rasters created into a single .vrt file. The catalog consists in 1773 files and the result of grid_metrics is a list of 1773. The error after running grid metrics says the following and the warnings are repetitive, the repeat the following warnings (1-13):

CreateProcess' failed to run 'C:\PROGRA~3\ANACON~1\Library\bin\gdalbuildvrt.exe "G:/NoBackUp/grid_metrics.vrt" "G:/NoBackUp/33-1-456-133-76_gf_norm_p95_p95.tif" "G:/NoBackUp/33-1-456-133-77_gf_norm_p95_p95.tif" "G:/NoBackUp/33-1-456-133-79_gf_norm_p95_p95.tif"There were 50 or more warnings (use warnings() to see the first 50)
>Warnings()
1: In min(x, na.rm = TRUE) : no non-missing arguments to min; returning Inf
2: In max(x, na.rm = TRUE) : no non-missing arguments to max; returning -Inf
3: In min(x, na.rm = TRUE) : no non-missing arguments to min; returning Inf
4: In max(x, na.rm = TRUE) : no non-missing arguments to max; returning -Inf
5: In min(x) : no non-missing arguments to min; returning Inf
6: In max(x) : no non-missing arguments to max; returning -Inf
7: In min(x, na.rm = TRUE) : no non-missing arguments to min; returning Inf
8: In max(x, na.rm = TRUE) : no non-missing arguments to max; returning -Inf
9: In min(x, na.rm = TRUE) : no non-missing arguments to min; returning Inf
10: In max(x, na.rm = TRUE) : no non-missing arguments to max; returning -Inf
11: In min(x) : no non-missing arguments to min; returning Inf
12: In max(x) : no non-missing arguments to max; returning -Inf
13: In points2grid(points, tolerance, round) :
  grid has empty column/rows in dimension 1

When I run the code with a small dataset the .vrt file is created so I don´t know if when treating big dataset is there a specific way of doing it. So far I have tried to apply info from this question but it didn´t work:

library(raster)
r <- stack(metrics[[1]])
for(i in 2:length(metrics)) r <- addLayer(r, metrics[[i]])
class(r)

also I have tried from this question but an error occurred:

metrics_merge <- do.call(raster::merge, metrics)
Error in as.data.frame(x) : argument "x" is missing, with no default

Answer 1

I did not manage to solve why grid_metrics fails to create the .vrt file when applied to a big catalog but I managed to be able to create the same output. I solved my problem by usig the gdalUtils tools from QGIS instead of Anaconda as the error said "CreateProcess' failed to run 'C:\PROGRA~3\ANACON~1\Library\bin\gdalbuildvrt.exe" and also the gdalbuildvrtcommand failed every time I tried to run it for the denoised normalized catalog, which led me to believed that this Anaconda´s gdalUtils was the reason. I changed the directory of gdalUtilsby following this question:

library(usethis)
edit_r_profile()
gdalUtils::gdal_setInstallation("C:\\Program Files\\QGIS 3.4\\bin")

Although it did not make grid_metrics generate the .vrtfile, I was able to run gdalbuildvrtfor the catalog:

library(gdalUtils)
vrt <- gdalUtils::gdalbuildvrt(gdalfile = "G:/NoBackUp/metrics/*.tif", 
                               output.vrt = "G:/NoBackUp/metrics/grid_metrics.vrt"
                               , overwrite = TRUE)

vrt.file <- stack("G:/NoBackUp/metrics/grid_metrics.vrt")

It takes considerably longer to create this .vrt file by this method and to read it as a stack or brick also takes really long but it manages to create the same output.