[R] error message from read.csv in loop

[Rui Barradas]

Hello,

1. When there are systematic errors, use ?try or, better yet, ?tryCatch.
Something like the code below will create a list of errors and read in 
the data if none occurred.
The code starts by creating an empty list for tryCatch results. It uses 
?file.path instead of noquote/paste0 to assemble the file name and wraps 
tryCatch around read.csv. Then, after the for loop, it gets the wrong 
reads and displays the error messages.
3. I'm assuming that after processing the data file by file you discard 
the data.frame if it's read without problems and move on to the next 
one. It would also be possible to store them all in a list, together 
with the errors.


ok <- vector("list", nrow(ora))
for (j in 1:nrow(ora))
{
   mycol  <- ora[j,"fname"]
   mycsv  <- paste0(mycol, ".csv'")
   rdcsv  <- file.path("w:/project/_Joe.B/Oracle/data", mycsv)
   rr <- tryCatch(read.csv(rdcsv), error = function(e) e)
   if(inherits(rr, "error"))
     ok[[i]] <- rr
   else ok[[i]] <- TRUE
}

i_err <- sapply(ok, inherits, "error")
for(e in ok[i_err]) message(e$message)


2. I'm assuming that you want to process file by file and  if the data 
are read without problems you discard the data.frame after processing it 
and move on to the next file. It is also possible to store them all in a 
list, together with the errors.


fun <- function(j, data = ora, mypath = "w:/project/_Joe.B/Oracle/data")
{
   mycol  <- data[j, "fname"]
   mycsv  <- paste0(mycol, ".csv")
   rdcsv  <- file.path(mypath, mycsv)
   tryCatch(read.csv(rdcsv), error = function(e) e)
}

df_list <- lapply(seq_len(nrow(ora)), fun)
i_err <- sapply(df_list, inherits, "error")
df_list[!i_err]  # these are ok

# hypothetical processing strategy
processing_results <- lapply(df_list[!i_err], function(rr) {
   # code goes here
   # ...etc...
})


Hope this helps,

Rui Barradas



Às 19:01 de 09/07/2021, Kai Yang via R-help escreveu:
> Hello List,
> I use for loop to read csv difference file into data frame rr.  The data frame rr will be deleted after a comparison and go to the next csv file.  Below is my code:
> for (j in 1:nrow(ora))
> {
>    mycol  <- ora[j,"fname"]
>    mycsv  <- paste0(mycol,".csv'")
>    rdcsv  <- noquote(paste0("'w:/project/_Joe.B/Oracle/data/", mycsv))
>    rr     <- read.csv(rdcsv)
> }
> but when I run this code, I got error message below:
> Error in file(file, "rt") : cannot open the connection
> In addition: Warning message:
> In file(file, "rt") :
>    cannot open file ''w:/project/_Joe.B/Oracle/data/ASSAY_DEFINITIONS.csv'': No such file or directory
>
> so, I checked the rdcsv and print it out, see below:
> [1] 'w:/project/_Joe.B/Oracle/data/ASSAY_DEFINITIONS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/ASSAY_DISCRETE_VALUES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/ASSAY_QUESTIONS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/ASSAY_RUNS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/DATA_ENTRY_PAGES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/DISCRETE_VALUES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/ENTRY_GROUPS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/GEMD_CODELIST_GROUPS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/GEMD_CODELIST_VALUES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/GEMD_LOT_DEFINITIONS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/GEMD_SAMPLES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/MOLECULAR_WAREHOUSE.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/QUESTION_DEFINITIONS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/QUESTION_GROUPS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/RESPONDENTS.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/RESPONSES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/SAMPLE_LIST.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/SAMPLE_LIST_NAMES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/SAMPLE_PLATE_ADDRESSES.csv'
> [1] 'w:/project/_Joe.B/Oracle/data/STORAGE_UNITS.csv'
> it seems correct. I copy and paste it into a code :
>   rr     <- read.csv( 'w:/project/_Joe.B/Oracle/data/RESPONDENTS.csv')
> and it works fine.
> Can someone help me debug where is the problem in my for loop code?
> Thanks,
> Kai
>
>
>
>
>
> 	[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org 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.


-- 
Este e-mail foi verificado em termos de vírus pelo software antivírus Avast.
https://www.avast.com/antivirus