I wanted to have a simple code at the beginning of my scripts to set the working directory to my Dropbox folder, regardless of which machine I run my code on:
setdir <- function(){
wandir <- paste(path.expand("~"), "/Dropbox/_R", sep = "")
curdir <- getwd()
if(curdir!=wandir){
setwd(wandir)
}
}
setdir()
The trick with the path.expand("~") works on Linux machines, but it doesn't on Windows machines, because it leads to C:/Users/username/Documents instead of C:/Users/username/. Is there a function that would work globally?
Here is a hacky workaround, which is far from a global one:
setdir <- function(){
wandir <- paste(path.expand("~"), "/Dropbox/_R", sep = "")
wandir <- sub("/Documents", "", wandir)
curdir <- getwd()
if(curdir!=wandir){
setwd(wandir)
}
}
setdir()
Related
I am trying to create mapbox tiles using mapboxapi::tippecanoe() in R. Unfortunately, my work computer runs Windows 10, which greatly complicates what I am trying to do. Tippecanoe is a Unix executable, so I downloaded and installed Ubuntu and am running it on a Windows subsystem for Linux. To get tippecanoe to launch, I had to edit the source code of mapboxapi::tippecanoe() to pass arguments to WSL. I then ran into an issue where Tippecanoe would give me an error that it could not open database files. Some research on Github led me to believe that this was related the number of open files limit in Ubuntu. After a lot of digging, I was able to increase ulimit -n to 65535 for on my ubuntu terminal. As soon as I launch Ubuntu, if I type in ulimit -n, I get 65535. However, when I call `sytem2("wsl", "ulimit -n"), I get the default value of 1024. I thought this was due to the user that R was calling in Ubuntu, but running system2("wsl", "whoami") returned the username for who I increased both the hard and soft nofile limits for. I am really stumped. Apologies for not pasting a reproducible example, but I am not sure how to make one for this situation. Any help would be much appreciated. Thanks!
Well after a whole lot of tinkering, this ended up being mostly a straightforward R code issue. The ulimit issue may still have been a problem, but actually I need to fix the R code in mapboxapi::tippecanoe(). Because mapboxapi::tippecanoe()uses the system() command to call tippecanoe, not only did I need to change the call to invoke wsl through a login shell using system2("wsl", "- d Ubuntu -lc 'tippecanoe <arguments to tippecanoe>'"), but I also needed to change the paths that R sent to tippecanoe to be linux paths instead of Window paths. If anyone else is having trouble with this, here is the tweaked mapboxapi::tippecanoe() command code that actually worked for me:
tippecanoe2<-function (input, output, layer_name, min_zoom = NULL,
max_zoom = NULL, drop_rate = NULL, overwrite = TRUE, other_options = NULL,
keep_geojson = FALSE)
{
check_install <- system2("wsl", "tippecanoe -v") == 0
linux_dir<-paste(getwd(), layer_name, sep="/")#make a directory in your linux directory for the .mbtiles
parsed<-strsplit(linux_dir, split="/") #parse the windows directory path
n<-length(parsed[[1]])
dir_out<-paste("",parsed[[1]][n-1], parsed[[1]][n], sep="/") #construct the linux directory path
dir.create(linux_dir)
op<-options(useFancyQuotes = FALSE)
if (!check_install) {
rlang::abort(c("tippecanoe is not installed or cannot be found by the application you are using to run mapboxapi.",
"If you haven't installed tippecanoe, please visit https://github.com/mapbox/tippecanoe for installation instructions.",
"If you have installed tippecanoe, run `Sys.getenv('PATH')` and make sure your application can find tippecanoe. If it cannot, adjust your PATH accordingly."))
}
opts <- c()
if (!is.null(min_zoom)) {
opts <- c(opts, sprintf("-Z%s", min_zoom))
}
if (!is.null(max_zoom)) {
opts <- c(opts, sprintf("-z%s", max_zoom))
}
if (is.null(min_zoom) && is.null(max_zoom)) {
opts <- c(opts, "-zg")
}
if (!is.null(drop_rate)) {
opts <- c(opts, sprintf("-r%s", drop_rate))
}
else {
opts <- c(opts, "-as")
}
if (overwrite) {
opts <- c(opts, "-f")
}
collapsed_opts <- paste0(opts, collapse = " ")
if (!is.null(other_options)) {
extra_opts <- paste0(other_options, collapse = " ")
collapsed_opts <- paste(collapsed_opts, extra_opts)
}
dir <- linux_dir
if (any(grepl("^sf", class(input)))) {
input <- sf::st_transform(input, 4326)
if (is.null(layer_name)) {
layer_name <- stringi::stri_rand_strings(1, 6)
}
if (keep_geojson) {
outfile <- paste0(layer_name, ".geojson")
path <- file.path(dir_out, outfile)
sf::st_write(input, path, quiet = TRUE, delete_dsn = TRUE,
delete_layer = TRUE)
}
else {
tmp <- tempdir("//wsl$/Ubuntu/tmp")#Here you would need to tweak to the file path for your linux distribution's temporary directory
tempfile <- paste0(layer_name, ".geojson")
path <- file.path(tmp, tempfile)
sf::st_write(input, path, quiet = TRUE, delete_dsn = TRUE,
delete_layer = TRUE)
}
call <- sprintf("tippecanoe -o %s/%s %s %s", dir_out, output,
collapsed_opts, path)
call2<-paste("-d Ubuntu /bin/bash -lc", sQuote(call, op), sep=" ")
system2("wsl", call2)
}
else if (inherits(input, "character")) {
if (!is.null(layer_name)) {
collapsed_opts <- paste0(collapsed_opts, " -l ",
layer_name)
}
call <- sprintf("tippecanoe -o %s/%s %s %s", dir_out, output,
collapsed_opts, input)
call2<-paste("-d Ubuntu /bin/bash -lc", sQuote(call, op), sep=" ")
system2("wsl", call2)
}
}
I'm new to R and having trouble with optimizing a function.
My function is to:
create a directory specified in the function
download the zip file from the link inside the function and extract it to the directory
move extracted files to the main directory if files are extracted under a new subfolder
delete the subfolder
It works but consumes a lot of memory and takes 30mins to do such an easy job on a 2.7MB zip file.
Thank you in advance!
create_dir <- function(directory) {
path <- file.path(getwd(), directory)
if (!file.exists(path)) {
dir.create(path)
}
link <-
"https://d396qusza40orc.cloudfront.net/rprog%2Fdata%2Fspecdata.zip"
temp <- tempfile()
download.file(link, temp, mode = "wb")
unzip(temp, exdir = path)
unlink(temp)
existing_loc <- list.files(path, recursive = TRUE)
for (loc in existing_loc) {
if (length(grep("/", loc))) {
file.copy(file.path(path, loc), path)
file.remove(file.path(path, loc))
}
}
dirs <- list.dirs(path)
rm_dirs <- dirs[dirs != path]
if (length(rm_dirs)) {
for (dir in rm_dirs) {
unlink(rm_dirs, recursive = TRUE)
}
}
}
create_dir("testDirectory")
Thanks, I found the problem. It's because of setting a working directory on OneDrive that syncs for every extraction, moving, and deletion of 332 files processed by the function. AntiVirus also run along with OneDrive and caused my PC to freeze for 30 mins by using 70% of CPU.
I am using RSelenium to navigate towards a webpage which contains a button to download a file. I use RSelenium to click this button which downloads the file. However, the files are by default downloaded in my folder 'downloads', whereas I want to file to be downloaded in my working directory. I tried specifying a chrome profile as below but this did not seem to do the job:
wd <- getwd()
cprof <- getChromeProfile(wd, "Profile 1")
remDr <- remoteDriver(browserName= "chrome", extraCapabilities = cprof)
The file is still downloaded in the folder 'downloads', rather than my working directory. How can this be solved?
The solution involves setting the appropriate chromeOptions outlined at https://sites.google.com/a/chromium.org/chromedriver/capabilities . Here is an example on a windows 10 box:
library(RSelenium)
eCaps <- list(
chromeOptions =
list(prefs = list(
"profile.default_content_settings.popups" = 0L,
"download.prompt_for_download" = FALSE,
"download.default_directory" = "C:/temp/chromeDL"
)
)
)
rD <- rsDriver(extraCapabilities = eCaps)
remDr <- rD$client
remDr$navigate("http://www.colorado.edu/conflict/peace/download/")
firstzip <- remDr$findElement("xpath", "//a[contains(#href, 'zip')]")
firstzip$clickElement()
> list.files("C:/temp/chromeDL")
[1] "peace.zip"
I've been trying the alternatives, and it seems that #Bharath's first comment about giving up on fiddling with the prefs (it doesn't seem possible to do that) and instead moving the file from the default download folder to the desired folder is the way to go. The trick to making this a portable solution is finding where the default download directory is—of course it varies by os (which you can get like so)—and you need to find the user's username too:
desired_dir <- "~/Desktop/cool_downloads"
file_name <- "whatever_I_downloaded.zip"
# build path to chrome's default download directory
if (Sys.info()[["sysname"]]=="Linux") {
default_dir <- file.path("home", Sys.info()[["user"]], "Downloads")
} else {
default_dir <- file.path("", "Users", Sys.info()[["user"]], "Downloads")
}
# move the file to the desired directory
file.rename(file.path(default_dir, file_name), file.path(desired_dir, file_name))
Look this alternative way.
Your download folder should be empty.
# List the files inside the folder
down.list <- list.files(path = "E:/Downloads/",all.files = T,recursive = F)
# Move all files to specific folder
file.rename(from = paste0("E:/Downloads/",down.list),to = paste0("E:/1/scrape/",down.list))
My current directory is c:/users/akshay/Documents
But all my data is in the directory "specdata" whose path address is c:/users/akshay/Documents/specdata
when i type these commands separately in console it works successfully.
path <- "C:/Users/akshay/Documents"
directory <- "specdata"
setwd(paste(path, directory, sep="/", collapse=NULL))
But when i use it in function like this it wont change my working directory.
pollutantmean <- function(directory){
directory <- character(1)
path <- character(1)
path <- "C:/Users/akshay/Documents"
setwd(paste(path, directory, sep="/", collapse=NULL))
}
But when i pass
>pollutantmean("specdata")
It wont change my working directory why is it so?
what is the problem?
Maybe try returning the paste. Also, you don't need the character() functions.
pollutantmean <- function(directory){
path <- "C:/Users/akshay/Documents"
return(paste(path, directory, sep="/", collapse=NULL))
}
pollutantmean("specdata")
Output:
> pollutantmean("test")
[1] "C:/Users/akshay/Documents/test"
Change directory:
pollutantmean<-function(directory){ + path<-"C:/Users/akshay/Documents" + setwd(paste(path,directory,sep="/",collapse=NULL)) + }
I'm attempting to use R to open a .Rproj file used in RStudio. I have succeeded with the code below (stolen from Ananda here). However, the connection to open RStudio called from R is not closed after the file is opened. How can I sever this "connection" after the .Rproj file is opened? (PS this has not been tested on Linux or Mac yet).
## Create dummy .Rproj
x <- c("Version: 1.0", "", "RestoreWorkspace: Default", "SaveWorkspace: Default",
"AlwaysSaveHistory: Default", "", "EnableCodeIndexing: Yes",
"UseSpacesForTab: No", "NumSpacesForTab: 4", "Encoding: UTF-8",
"", "RnwWeave: knitr", "LaTeX: pdfLaTeX")
loc <- file.path(getwd(), "Bar.rproj")
cat(paste(x, collapse = "\n"), file = loc)
## wheresRStudio function to find RStudio location
wheresRstudio <-
function() {
myPaths <- c("rstudio", "~/.cabal/bin/rstudio",
"~/Library/Haskell/bin/rstudio", "C:\\PROGRA~1\\RStudio\\bin\\rstudio.exe",
"C:\\RStudio\\bin\\rstudio.exe")
panloc <- Sys.which(myPaths)
temp <- panloc[panloc != ""]
if (identical(names(temp), character(0))) {
ans <- readline("RStudio not installed in one of the typical locations.\n
Do you know where RStudio is installed? (y/n) ")
if (ans == "y") {
temp <- readline("Enter the (unquoted) path to RStudio: ")
} else {
if (ans == "n") {
stop("RStudio not installed or not found.")
}
}
}
temp
}
## function to open .Rproj files
open_project <- function(Rproj.loc) {
action <- paste(wheresRstudio(), Rproj.loc)
message("Preparing to open project!")
system(action)
}
## Test it (it works but does no close)
open_project(loc)
It's not clear what you're trying to do exactly. What you've described doesn't really sound to me like a "connection" -- it's a system call.
I think what you're getting at is that after you run open_project(loc) in your above example, you don't get your R prompt back until you close the instance of RStudio that was opened by your function. If that is the case, you should add wait = FALSE to your system call.
You might also need to add an ignore.stderr = TRUE in there to get directly back to the prompt. I got some error about "QSslSocket: cannot resolve SSLv2_server_method" on my Ubuntu system, and after I hit "enter" it took me back to the prompt. ignore.stderr can bypass that (but might also mean that the user doesn't get meaningful errors in the case of serious errors).
In other words, I would change your open_project() function to the following and see if it does what you expect:
open_project <- function(Rproj.loc) {
action <- paste(wheresRstudio(), Rproj.loc)
message("Preparing to open project!")
system(action, wait = FALSE, ignore.stderr = TRUE)
}