Hey Bhaskar,
Dave Pierce here, the author and maintainer of the ncdf4 package. What
platform are you working on? If you work on Linux, I'd be happy to send you
a new source tar version of the ncdf4 package I've made that handles this
case. It now has a settable parameter in nc_open called "return_on_error",
and if you set that to TRUE, then nc_open always returns. If no error was
encountered, then the return list element $error is FALSE, and if an error
was encountered, $error is set to TRUE. So you could do this:
for( ifile in 1:nfiles ) {
nc = nc_open( filename[ifile], return_on_error=TRUE )
if( nc$error == FALSE ) {
... do your processing here ...
}
else
print(paste("Error encountered, skipping file", filename[ifile]))
Regards,
--Dave
On Tue, Mar 24, 2020 at 5:13 AM Bhaskar Mitra <[email protected]>
wrote:
> Hello Everyone,
>
> I have written a loop which reads hundreds of .nc files
> and extract information from each .nc file and
> exports that corresponding information as a csv file.
>
> The loop works fine until it encounters a .nc file which it cannot read
> and the loop stops.
>
> I would appreciate if anyone can suggest how can I modify
> the loop, whereby the loop will continue to run by bypassing those
> particular
> files which it cannot read or if any particular file has an error.
>
> In the end, I was also hoping to modify the loop such that it
> will generate a report which will inform me which
> files were not read by the loop. The codes are given below
>
> Thanks for your help,
>
> Regards,
> Bhaskar Mitra
>
>
> #_------------------------------------------------------------------
>
>
> library(ncdf4)
> library(reshape2)
> library(dplyr)
> library(stringr)
>
>
> setwd("directory path")
>
> Output <- "directory path"
>
> flist <- list.files(path ="NCFiles/", pattern = "^.*\\.(nc|NC|Nc|Nc)$")
>
> for (i in 1: length(flist))
> {
>
> nc <- nc_open(paste0("NCFiles/",flist[i]))
> mean1 <- ncvar_get(nc,attributes(nc$dim)$names[3])
> nc_close(nc)
>
> mean_chl_df <- melt(mean1)
> trial.table.df <-as.data.frame(mean_chl_df)
>
>
> write.csv(trial.table.df,paste0(Output,"/",tools::file_path_sans_ext(flist[i]),".csv"))
>
> }
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [email protected] mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
-------------------------------------------------------------------
David W. Pierce
Division of Climate, Atmospheric Science, and Physical Oceanography
Scripps Institution of Oceanography
(858) 534-8276 (voice) / (858) 534-8561 (fax) [email protected]
-------------------------------------------------------------------
[[alternative HTML version deleted]]
______________________________________________
[email protected] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
