Loop to list files in parts

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I'm trying to copy around 10,000 files and paste it into another directory with the following code:

f <- c (MYFILE $ COL1) # PART 1
m <- paste0 ("(", paste (f, collapse = "|"), ") .xml") #PART 2
files <- list.files (pattern = m) #PART 3

file.copy (paste0 (getwd (), "/", files), paste0 (getwd (), "/ FILES_XML /", files), overwrite = TRUE) # PART 4

When I try to run the files <- list.files (pattern = m) part, the following message appears:

assertion 'tree-> num_tags == num_tags' failed in executing regexp: file 'tre-compile.c', line 634

To prevent the message from appearing, I thought about running the code in 500 parts in 500. How would I do it in parts using for?

Maybe something like the following will do it. Note the use of help("file.path") as a replacement for paste.

n <- length(f)
sp <- rep(1:ceiling(n / 5), each = 5, length.out = n)
lapply(split(f, sp), function(x){
  m <- paste0 ("(", paste (x, collapse = "|"), ")\\.xml")
  files <- list.files(pattern = m)
  infiles <- file.path(getwd(), files)
  outfiles <- file.path(getwd(), "FILES_XML", files)
  file.copy(infiles, outfiles, overwrite = TRUE)
})

Loop over list of files, ls *.csv > filelist.txt # define your list of files. for f in `cat filelist.txt`; do echo ${f}; done;. if a line may include spaces better use a while loop: cat filelist.txt | while� Here i show you four ways to loop a List in Java. Iterator loop; For loop; For loop (Adcance) While loop

Well even though I don't understand your reasoning, how this would prevvent the error message from appearing (?) here is how to run the file.copy part in a loop:

lower <- 1
for (upper in seq(500, 10000, by=500)) {
  file.copy(paste0(getwd (), "/", files[lower:upper]), paste0 (getwd (), "/ FILES_XML /", files[lower:upper]), overwrite = TRUE)
  lower <- upper + 1
}

How To Loop Through Files in a Directory, Iterate through the files in a directory and run commands against them using shell scripting loops. Loop Over Given File Names The simplest usage for for loop is over given file names. We will provide the file files by separating them with spaces. In this example, we will provide file names a, b and c and then print them with some string.

This is a regex error that probably comes from the line files <- list.files(pattern = m), which wouldn't be fixed by chunking the copying process. I bet you can fix it by thinking more carefully when constructing the search string m.

How to write a loop in Bash, Automatically perform a set of actions on multiple files with for loops and find Change directory to your new folder, then list the files in it to confirm that in the final article in this three-part series on programming with Bash. Create a list of file names called filenames with three strings 'Gold.csv', 'Silver.csv', & 'Bronze.csv'. This has been done for you. Use a for loop to create another list called dataframes containing the three DataFrames loaded from filenames:

Analyzing Multiple Data Sets – Programming with R, Use a function to get a list of filenames that match a simple pattern. Use a for loop to process multiple files. It's fragile: if we give it a longer vector, it only prints part of the data, and if we give it a shorter input, it returns NA values because� if a line may include spaces better use a while loop: cat filelist.txt | while read LINE; do echo "${LINE}"; done loop over filenames, but remove file extension , see → basename string split

Loops – The Unix Shell, Write a loop that applies one or more commands separately to each file in a set of files. Each time the loop runs (called an iteration), an item in the list is assigned in sequence to the variable, and the Saving to a File in a Loop - Part One. Loop through list variable in Python and print each element one by one. You have to use Python for loop and looping over a list variable and print it in the output. The list variable is the variable whose values are comma separated. All the items are enclosed within the square brackets.

cfloop: looping over an array, list, file, or struct. Use the cfloop tag to loop over a list, file, or a single or multi-dimensional array. ColdFusion CFML Reference. Learn & Support. Get Started. User Guide.

Comments
  • Thanks. Your suggestion worked, but the process is very slow. See how it is, of the 10,000 files I need to copy, I copied only 40 in 20 minutes.
  • @BrunoAvila I cannot explain why it's so slow, an average of 30 secs per file. What are the file sizes? And have you considered using OS commands? R function system2 might be faster but I would need to know the OS.
  • My files are small, maximum 300kb
  • Thanks. Your suggestion is referring to the last part (file.copy), but the problem occurs a moment earlier (files <- list.files (pattern = m)