rienix rienix - 1 year ago 83
R Question

Path assignment to setwd() is delayed in for/foreach loop

The objective is to change within a for loop the current working directory and do some other stuff in it,.e.g. searching for files. The paths are stored in generic variables.
The R code I am running for this is the following:


# The following lines are generated by an external tool and stored in filePath.info
# Loaded via source("filePaths.info")
result1 <- '/home/user/folder1'
result2 <- '/home/user/folder2'
result3 <- '/home/user/folder3'
number_results <- 3

# So I know that I have all in all 3 folders with results by number_results
# and that the variable name that contains the path to the results is generic:
# string "result" plus 1:number_results.

# Now I want to switch to each result path and do some computation within each folder
start_dir <- getwd()
print(paste0("start_dir: ",start_dir))

# For every result folder switch into the directory of the folder
foreach(i=1:number_results) %do% {
# for (i in 1:number_results){ leads to the same output

# Assign path in variable, not the variable name as string: current_variable <- result1 (not string "result1")
current_variable <- eval(parse(text = paste0("result", i)))
print(paste0(current_variable, " in interation_", i))
# Set working directory to string in variable current_variable
current_dir <- setwd(current_variable)
print(paste0("current_dir: ",current_dir))


# Switch back into original directory
current_dir <- setwd(start_dir)
print(paste0("end_dir: ",current_dir))

The output is the following ...

[1] "start_dir: /home/user"
[1] "/home/user/folder1 in interation_1"
[1] "current_dir: /home/user"
[1] "/home/user/folder2 in interation_2"
[1] "current_dir: /home/user/folder1"
[1] "/home/user/folder3 in interation_3"
[1] "current_dir: /home/user/folder2"
[1] "end_dir: /home/user/folder3"

... while I would have expected this:

[1] "start_dir: /home/user"
[1] "/home/user/folder1 in interation_1"
[1] "current_dir: /home/user/folder1"
[1] "/home/user/folder2 in interation_2"
[1] "current_dir: /home/user/folder2"
[1] "/home/user/folder3 in interation_3"
[1] "current_dir: /home/user/folder3"
[1] "end_dir: /home/user/"

So it turns out that the path assigned to current_dir is somewhat "behind" ...

Why is this the case?
As I am far away from being a R expert, I have no idea what is causing this behaviour and most important how to get the desired behaviour.
So any help, hint, code correction/optimization would be highly appreciated!

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Platform: x86_64-pc-linux-gnu (64-bit)

Answer Source

From the ?setwd help page...

setwd returns the current directory before the change, invisibly and with the same conventions as getwd. It will give an error if it does not succeed (including if it is not implemented).

So when you do

current_dir <- setwd(current_variable)
print(paste0("current_dir: ",current_dir))

You are not getting the "current" directory, you are getting the previous one. You should use getwd() to get the current one

current_dir <- getwd()
print(paste0("current_dir: ",current_dir))
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