What you are seeing is not a popup it is a download dialog. The download dialog is native in all browsers and cannot be controlled with JavaScript. You can configure Firefox to automatically download for certain file types. You havent given us alot of information.
It can be done by setting an appropriate profile. Here is an example that downloads some financial data. We set four options in a bespoke profile. We have to jump through some hoops selecting options before we get a file to download:
require(RSelenium)
fprof <- makeFirefoxProfile(list(browser.download.dir = "C:\\temp"
, browser.download.folderList = 2L
, browser.download.manager.showWhenStarting = FALSE
, browser.helperApps.neverAsk.saveToDisk = "application/zip"))
RSelenium::startServer()
remDr <- remoteDriver(extraCapabilities = fprof)
remDr$open(silent = TRUE)
remDr$navigate("https://www.chicagofed.org/applications/bhc_data/bhcdata_index.cfm")
# click year 2012
webElem <- remDr$findElement("name", "SelectedYear")
webElems <- webElem$findChildElements("css selector", "option")
webElems[[which(sapply(webElems, function(x){x$getElementText()}) == "2012" )]]$clickElement()
# click required quarter
webElem <- remDr$findElement("name", "SelectedQuarter")
Sys.sleep(1)
webElems <- webElem$findChildElements("css selector", "option")
webElems[[which(sapply(webElems, function(x){x$getElementText()}) == "4th Quarter" )]]$clickElement()
# click button
webElem <- remDr$findElement("id", "downloadDataFile")
webElem$clickElement()