"download.file" Incomplete and inconsistent downloads - r

Question

Am trying to understand why I am having inconsistent results downloading CSV files from a website archive. Don't know if the problem is at my end, the other side or just failed communications in between. Any suggestions are welcomed.
Using a R script to automate the downloading of CSV files by month and year from the HYCOM archives for analysis. The script generated the following URL trying URL 'http://ncss.hycom.org/thredds/ncss/GLBu0.08/reanalysis/3hrly?var=salinity&var=water_temp&var=water_u&var=water_v&latitude=13.875&longitude=-72.25&time_start=2012-05-01T00:00:00Z&time_end=2012-05-31T21:00:00Z&vertCoord=&accept=csv'
Running download.file successfully obtains the file about half the time, otherwise fails. Any suggestions are welcomed. The images below shows the failed run. Successful run is below.
Successful Log
#download one month of data
MM = '05'
LastDay = ndays(paste(year,MM,'01',sep="-"))
H1 = paste( as shown in image)
H2 = '-01T00:00:00Z&time_end='
#H3 = 'T21:00:00Z&timeStride=1&vertCoord=&accept=csv'
H3 = 'T21:00:00Z&vertCoord=&accept=csv'
HtmlLink <- paste(H1,year,"-",MM,H2,year,"-",MM,"-",LastDay,H3,sep="")
dest = paste("../data/",year,MM,".csv",sep="")
download.file(url =HtmlLink ,destfile=dest,cacheOK=FALSE, method="auto")
trying URL 'as shown in image'
Content type 'text/plain;charset=UTF-8' length unknown
..................................................
................downloaded 666 KB
user system elapsed
28.278 6.605 5201.421
LOG OF FAILED RUN

Answer 1

You can/should turn the following into a function accepting parameters and replace the hardcoded values with said params (I used httr:::parse_query() to make the list):
library(httr)
URL <- "http://ncss.hycom.org/thredds/ncss/GLBu0.08/reanalysis/3hrly"
params <- list(var = "salinity",
var = "water_temp",
var = "water_u",
var = "water_v",
latitude = "13.875",
longitude = "-72.25",
time_start = "2012-05-01T00:00:00Z",
time_end = "2012-05-31T21:00:00Z",
vertCoord = "",
accept = "csv")
dest_file <- "filename"
res <- GET(url=URL,
query=params,
timeout(360),
write_disk(dest_file, overwrite=TRUE),
verbose())
warn_for_status(res)
You can (eventually) remove the verbose() from that GET call, but it's helpful during debugging.
The main issue is that this server is s l o w and times out before the transfer is complete. Even the value of 360 might not be enough (you'll need to experiment).

Answer 2

Many thanks to all for the help. The suggestion by hrbrmstr appears to be an elegant answer and I look forwards to testing it. However, I was unable to install a working copy using the program manager. Installation from a local download also failed since R complained that the OS X version that I downloaded from CRAN was a windows version, not OS X. Yes, I repeated the download several times to make sure I had the right package.
As suggested by Cyrus Mohammadian, I tried the procedures in the curl library.
Running the same URL, download.file transfers failed about 50% of the time. Using curl reduced the transfer times from 2000 seconds to 1000 seconds with no failures in 12 tries.
## calculate number of days in month
ndays <- function(d) {
last_days <- 28:31
rev(last_days[which(!is.na(
as.Date( paste( substr(d, 1, 8),
last_days, sep = ''),
'%Y-%m-%d')))])[1] }
nlat = 13.875
elon = -72.25
#download one month of data
year = 2008
MM = '01'
LastDay = ndays(paste(year,MM,'01',sep="-"))
H1 = paste('http://ncss.hycom.org/thredds/ncss/GLBu0.08/reanalysis/3hrly?
var=salinity&var=water_temp&var=water_u&var=water_v&latitude=',
nlat,'&longitude=', elon,'&time_start=',sep="")
H2 = '-01T00:00:00Z&time_end='
H3 = 'T21:00:00Z&timeStride=1&vertCoord=&accept=csv'
HtmlLink <- paste(H1,year,"-",MM,H2,year,"-",MM,"-",LastDay,H3,sep="")
dest = paste("../data/",year,MM,".csv",sep="")
curl_download(url =HtmlLink ,destfile=dest,quiet=FALSE, mode="wb")