Error when trying to download species models with ebirdst_download()

[KWB4484]

Hello. When I run ebirdst_download(species="Sharp-tailed Grouse") I get and error

"Error in ebirdst_download(species = "Sharp-tailed Grouse") :
Cannot access Status and Trends data URL. Ensure that you have a working internet connection and a valid API key for the Status and Trends data."

If I run this code below, which I took from the source code, I can download a species models. Am I messing something up or is this a bug? I suspect the former, but thought I'd ask. Thanks!

path = rappdirs::user_data_dir("ebirdst")
species <- get_species(species)
which_run <- which(ebirdst::ebirdst_runs$species_code == species)
run <- ebirdst::ebirdst_runs$run_name[which_run]
key<-Sys.getenv("EBIRDST_KEY")
api_url <- "https://st-download.ebird.org/v1/"
list_obj_url <- stringr::str_glue("{api_url}list-obj/{species}?key={key}")
files <-jsonlite::read_json(list_obj_url, simplifyVector = TRUE)
files <- data.frame(file = files)
files <- files[!stringr::str_detect(files$file, "\\.db$"), , drop = FALSE]
files$src_path <- stringr::str_glue("{api_url}fetch?objKey={files$file}",
                                    "&key={key}")
files$dest_path <- file.path(path, files$file)
files$exists <- file.exists(files$dest_path)
dirs <- unique(dirname(files$dest_path))
for (d in dirs) {
  dir.create(d, showWarnings = FALSE, recursive = TRUE)
}

old_timeout <- getOption("timeout")
options(timeout = max(3000, old_timeout))

for (i in seq_len(nrow(files))) {
  dl_response <- utils::download.file(files$src_path[i],
                                      files$dest_path[i],
                                      mode = "wb")
  if (dl_response != 0) {
    stop("Error downloading file: ", files$file[i])
  }
}

[mstrimas]

Hi,

I just tested ebirdst_download(species="Sharp-tailed Grouse") and it's working fine for me. I'd suggest:

1. Make sure you have a valid API key by visiting https://ebird.org/st/request. Update the key if needed, add it to your Renviron file with set_ebirdst_access_key("XXXXXXX", overwrite = TRUE), and restart R.
2. Ensure you have the latest version of the package by installing from GitHub with: remotes::install_github("CornellLabofOrnithology/ebirdst")

If it's still not working, let me know and I'll try to get to the bottom of it.

[KWB4484]

Thanks for the quick and helpful reply. I confirmed I have a valid key and Sys.getenv("EBIRDST_KEY") returns the correct key. I couldn't update the package though -- I got an error (see below). I appreciate the help but don't feel like you need to spend time on it. Like I said previously, I can at least download the models by running lines from the download function...so at least I'm not stuck anymore. I mostly just wanted to make sure it wasn't a bug. Seems like it's something that just doesn't work for me for whatever reason.

remotes::install_github("CornellLabofOrnithology/ebirdst")
Downloading GitHub repo CornellLabofOrnithology/ebirdst@HEAD
v  checking for file 'C:\Users\kbarnes\AppData\Local\Temp\1\RtmpG2AuLf\remotes1facac4c2\CornellLabofOrnithology-ebirdst-0a5d459/DESCRIPTION' ...
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
    ERROR
   copying to build directory failed
Error: Failed to install 'ebirdst' from GitHub:
  System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long path
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long path
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long path
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long path
E>  ERROR
E> copying to build directory failed

[mstrimas]

There has been some weirdness going on the past couple days with the eBird servers and it's possible this is related. It's worth waiting a couple days and checking again to see if it works.

Regarding the problem installing from GitHub, this sometimes happens on Windows because CornellLabofOrnithology/ebirdst is so long, you could try this instead:

remotes::install_github("ebird/ebirdst")

[KWB4484]

Ok will do.

And thanks for the suggestion. Just as an FYI -- less warnings than last time, but looks like the sapsucker got rejected.

remotes::install_github("ebird/ebirdst")
Downloading GitHub repo ebird/ebirdst@HEAD
v  checking for file 'C:\Users\kbarnes\AppData\Local\Temp\1\RtmpG2AuLf\remotes1fac576f7735\ebird-ebirdst-0a5d459/DESCRIPTION' (439ms)
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     problem copying .\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_hr_2019_abundance-seasonal_breeding.tif to C:\Users\kbarnes\AppData\Local\Temp\1\Rtmpq4iuwx\Rbuild21204cc957f9\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_hr_2019_abundance-seasonal_breeding.tif: No such file or directory
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     problem copying .\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_lr_2019_abundance-seasonal_breeding.tif to C:\Users\kbarnes\AppData\Local\Temp\1\Rtmpq4iuwx\Rbuild21204cc957f9\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_lr_2019_abundance-seasonal_breeding.tif: No such file or directory
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     problem copying .\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_mr_2019_abundance-seasonal_breeding.tif to C:\Users\kbarnes\AppData\Local\Temp\1\Rtmpq4iuwx\Rbuild21204cc957f9\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_mr_2019_abundance-seasonal_breeding.tif: No such file or directory
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
   Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
     over-long path
    ERROR
   copying to build directory failed
Error: Failed to install 'ebirdst' from GitHub:
  System command 'Rcmd.exe' failed, exit status: 1, stdout + stderr (last 10 lines):
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   problem copying .\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_mr_2019_abundance-seasonal_breeding.tif to C:\Users\kbarnes\AppData\Local\Temp\1\Rtmpq4iuwx\Rbuild21204cc957f9\ebird-ebirdst-0a5d459\example-data\yebsap-ERD2019-STATUS-20200930-8d36d265-example\abundance_seasonal\yebsap-ERD2019-STATUS-20200930-8d36d265-example_mr_2019_abundance-seasonal_breeding.tif: No such file or directory
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long path
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long path
E> Warning in file.copy(pkgname, Tdir, recursive = TRUE, copy.date = TRUE) :
E>   over-long pat

[mstrimas]

That's a pain, it's related to this issue r-lib/remotes#84

In the short term, they suggest using remotes::install_github("ebird/ebirdst", build = FALSE) may resolve the problem . For a proper solution, I clearly need to shorten the path names in the package, which I'll do in the next version. I guess for now you'll have to stick with the CRAN version of ebirdst. Sorry!

[mstrimas]

We've shortened the path names of the downloaded files and I've permanently moved the package to https://github.com/ebird/ebirdst, which should resolve this issue.