R: Cannot run certain function after cleaning temporary directory

Question

I get the error:

Error in file(fn, "rb") : cannot open the connection
In addition: Warning message:
In file(fn, "rb") :
  cannot open file 'C:\Users\***\AppData\Local\Temp\Rtmpwh6Zih\raster\r_tmp_2020-05-
13_170601_12152_33882.gri': No such file or directory

When I run the following code in RStudio (1.2.5042):

raster.binair <- vector(mode = "list", length = length(aggregated.rasters)) 
for (i in 1:NROW(aggregated.rasters)) { 
+     clamped <- clamp(aggregated.rasters[[i]], upper=12, useValues=FALSE)
+     raster.binair[[i]] <- clamped
+   } 

"aggregated.rasters" is a list of 96 rasters and when I separately run it, I get the correct list. I recently cleaned my temporary directory (accessed by tempdir()) and deleted the files in there. I suppose the part:

cannot open file 'C:\Users\***\AppData\Local\Temp\Rtmpwh6Zih\raster\r_tmp_2020-05-
13_170601_12152_33882.gri': No such file or directory

is referring to this. I don't know what I did wrong here. Can I get these files back or work around this error?

Answer 1

Files in the temp folder are deleted when an R session ends. So you should never count on them. You can run the code again, but if you want to permanently keep the results you need to write them elsewhere. Here are two options

Write many files

raster.binair <- vector(mode = "list", length = length(aggregated.rasters)) 
for (i in 1:NROW(aggregated.rasters)) { 
    f <- paste0("raster_", i)
    clamped <- clamp(aggregated.rasters[[i]], upper=12, useValues=FALSE, filename=f)
    raster.binair[[i]] <- clamped
} 

Write a single file

raster.binair <- vector(mode = "list", length = length(aggregated.rasters)) 
for (i in 1:NROW(aggregated.rasters)) { 
    raster.binair[[i]]  <- clamp(aggregated.rasters[[i]], upper=12, useValues=FALSE)
} 
s <- stack(raster.binair)
s <- writeRaster(s, filename="mydata.tif")