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Kai Yang

2021-Jul-09 18:01 UTC

[R] error message from read.csv in loop

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]]

Eric Berger

2021-Jul-09 18:15 UTC

head link

[R] error message from read.csv in loop

it complained about  ASSAY_DEFINITIONS not about  RESPONDENTS.
Can you try with the ASSAY_DEFINITIONS  file?


On Fri, Jul 9, 2021 at 9:10 PM Kai Yang via R-help <r-help at
r-project.org>
wrote:
> 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 at 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.
>
	[[alternative HTML version deleted]]

Migdonio González

2021-Jul-09 18:39 UTC

head link

[R] error message from read.csv in loop

It seems that your problem is that you are using single quotes inside of
the double quotes. This is not necessary. Here is the corrected for-loop:

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)
}

Also note that the rr variable will only store the last CSV, not all CSV.
You will need to initialize the rr variable as a list to store all CSVs if
that is what you require. Something like this:

# Initialize the rr variable as a list.
rr <- as.list(rep(NA, nrow(ora)))

# Run the for-loop to store all the CSVs in rr.
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[[j]]     <- read.csv(rdcsv)
}

Regards
Migdonio G.

On Fri, Jul 9, 2021 at 1:10 PM Kai Yang via R-help <r-help at
r-project.org>
wrote:
> 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 at 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.
>
	[[alternative HTML version deleted]]

Kai Yang

2021-Jul-09 19:24 UTC

head link

[R] error message from read.csv in loop

Hi Migdonio,
I did try your code:
# Initialize the rr variable as a list.

rr <- as.list(rep(NA, nrow(ora)))


# Run the for-loop to store all the CSVs in rr.

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[[j]] ? ? <- read.csv(rdcsv)

}

this code is working, but rr is not a data frame, R said: Large list ( 20
elements .....). how can I use it as a data frame one by one?
Thank you for your help
Kai
    On Friday, July 9, 2021, 11:39:59 AM PDT, Migdonio Gonz?lez
<migdonio.gonzalez02 at gmail.com> wrote:
 
 It seems that your problem is that you are using single quotes inside of the
double quotes. This is not necessary. Here is the corrected for-loop:
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)
}
Also note that the rr variable will only store the last CSV, not all CSV. You
will need to initialize the rr variable as a list to store all CSVs if that is
what you require. Something like this:
# Initialize the rr variable as a list.
rr <- as.list(rep(NA, nrow(ora)))
# Run the for-loop to store all the CSVs in rr.
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[[j]] ? ? <- read.csv(rdcsv)
} 

RegardsMigdonio G.

On Fri, Jul 9, 2021 at 1:10 PM Kai Yang via R-help <r-help at
r-project.org> wrote:

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 at 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.

  
	[[alternative HTML version deleted]]

Rui Barradas

2021-Jul-10 06:47 UTC

head link

[R] error message from read.csv in loop

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



?s 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 at 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.

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R help - Jul 2021 - error message from read.csv in loop

[R] error message from read.csv in loop

[R] error message from read.csv in loop

[R] error message from read.csv in loop

[R] error message from read.csv in loop

[R] error message from read.csv in loop