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
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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