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:
require("foreach")
# 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))
# DO SOME OTHER STUFF WITH FILES IN THE CURRENT FOLDER
}
# 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)
From the ?setwd
help page...
setwd
returns the current directory before the change, invisibly and with the same conventions asgetwd
. 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
setwd(current_variable)
current_dir <- getwd()
print(paste0("current_dir: ",current_dir))