NAs in foreign function call trying to open a netcdf file in R

StackOverflow https://stackoverflow.com/questions/22234158

  •  10-06-2023
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Question

I'm using the library ncdf with R version 3.0.2. I'm trying to open and close some netcdfs over and over again (I can explain why but it isn't needed for this question). 

sapply(1:14000, function(whatever) {
    print(whatever)
      sapply(prediction.cdfs, function(cdf) {
        print(file.path(cdf.dir, cdf))
        nc = open.ncdf(file.path(cdf.dir, cdf))
        close.ncdf(nc)
      })
})

After open and closing over and over again it eventually fails with this error:

[1] 3329                                                                                             

[1] "/opt/devel/cdfs/file_one.cdf"

[1] "/opt/devel/cdfs/file_two.cdf"

[1] "/opt/devel/cdfs/file_three.cdf"

[1] "/opt/devel/cdfs/file_four.cdf"

[1] "/opt/devel/cdfs/file_five.cdf"

Error in open.ncdf(file.path(cdf.dir, cdf)) : 
  NAs in foreign function call (arg 1)

Anyone know what's going on? The error seems stochastic in nature. The time till it barks about the foreign function call is variable. I'm looking for an explanation or just a work around?

Thanks

Was it helpful?

Solution

I believe the problem was from un-closed connections to the same files from a previous step in my analysis. I'm running this on a Linux system, so I tracked the open file connections as the loop was running using

watch ls -l /proc/${PID}/fd

The connections opened and closed just fine, but I saw some old connections laying around from my previous analysis. I closed them and everything run just fine!!!

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