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trashbirdecology / bbsAssistant

An R package for downloading and handling data and information from the North American Breeding Bird Survey.
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get_regions() raises an error #51

Closed mbjoseph closed 4 years ago

mbjoseph commented 4 years ago

Hey @TrashBirdEcology! Awesome package. Maybe this is a bug? :man_shrugging:

Describe the bug

The get_regions() function raises an error that seems to be caused by attempting to read a README.txt file from the FTP server that no longer exists.

To Reproduce

library(bbsAssistant)
regions <- get_regions()
#> Parsed with column specification:
#> cols(
#>   X1 = col_character(),
#>   X2 = col_character()
#> )
#> Parsed with column specification:
#> cols(
#>   X1 = col_character(),
#>   X2 = col_character(),
#>   X3 = col_character()
#> )
#> Warning in dir.create(codesDir): '/tmp/RtmpHiEJfU/reprex156458487ca2/
#> bbsData/codes' already exists
#> Warning in download.file(url = File, destfile = paste0(codesDir, "/
#> README.txt")): cannot open URL 'ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/
#> DataFiles/README.txt': FTP status was '550 Requested action not taken; file
#> unavailable'
#> Error in download.file(url = File, destfile = paste0(codesDir, "/README.txt")): cannot open URL 'ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/README.txt'

Created on 2019-08-14 by the reprex package (v0.3.0)

Expected behavior

I was expecting to get the region data, like in the README.

Session info

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 18.04 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bbsAssistant_1.0.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2      rstudioapi_0.10 whisker_0.3-2   knitr_1.24      magrittr_1.5    hms_0.5.0       here_0.1        R6_2.4.0        rlang_0.4.0    
[10] tools_3.6.1     packrat_0.5.0   xfun_0.8        withr_2.1.2     clipr_0.7.0     htmltools_0.3.6 rprojroot_1.3-2 digest_0.6.20   tibble_2.1.3   
[19] crayon_1.3.4    processx_3.4.1  callr_3.3.1     readr_1.3.1     ps_1.3.0        vctrs_0.2.0     fs_1.3.1        curl_4.0        zeallot_0.1.0  
[28] evaluate_0.14   rmarkdown_1.14  reprex_0.3.0    compiler_3.6.1  pillar_1.4.2    backports_1.1.4 pkgconfig_2.0.2

Additional context

The error seems to stem from this file not existing: ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/README.txt

Maybe it was removed in the most recent BBS data update?

trashbirdecology commented 4 years ago

Max, Thanks for reaching out. Unfortunately the BBS recently overhauled their website, rendering some functions defunct. We are actively working on the updates now. Feel free to clone the branch add_data. Otherwise, we will release a new update in a few days, hopefully, which should solve all existing bugs.

Thanks for reaching out!

Jessica L. Burnett School of Natural Resources University of Nebraska-Lincoln +1.352.792.5425

GitHub http://github.com/trashbirdecology CV/Resume https://github.com/TrashBirdEcology/cv/blob/master/burnett_extendedCV.pdf Nebraska Cooperative Fish & Wildlife Research Unit http://snr.unl.edu/necoopunit/ ORC ID: 0000-0002-0896-5099 https://orcid.org/0000-0002-0896-5099

http://snr.unl.edu/necoopunit/

On Wed, Aug 14, 2019 at 10:28 AM Max Joseph notifications@github.com wrote:

Hey @TrashBirdEcology https://github.com/TrashBirdEcology! Awesome package. Maybe this is a bug? 🤷‍♂

Describe the bug

The get_regions() function raises an error that seems to be caused by attempting to read a README.txt file from the FTP server that no longer exists.

To Reproduce

library(bbsAssistant) regions <- get_regions()

> Parsed with column specification:

> cols(

> X1 = col_character(),

> X2 = col_character()

> )

> Parsed with column specification:

> cols(

> X1 = col_character(),

> X2 = col_character(),

> X3 = col_character()

> )

> Warning in dir.create(codesDir): '/tmp/RtmpHiEJfU/reprex156458487ca2/

> bbsData/codes' already exists

> Warning in download.file(url = File, destfile = paste0(codesDir, "/

> README.txt")): cannot open URL 'ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/

> DataFiles/README.txt': FTP status was '550 Requested action not taken; file

> unavailable'

> Error in download.file(url = File, destfile = paste0(codesDir, "/README.txt")): cannot open URL 'ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/README.txt'

Created on 2019-08-14 by the reprex package https://reprex.tidyverse.org (v0.3.0)

Expected behavior

I was expecting to get the region data, like in the README.

Session info

R version 3.6.1 (2019-07-05)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Pop!_OS 18.04 LTS

Matrix products: default

BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1

LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:

[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8

[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:

[1] stats graphics grDevices utils datasets methods base

other attached packages:

[1] bbsAssistant_1.0.0

loaded via a namespace (and not attached):

[1] Rcpp_1.0.2 rstudioapi_0.10 whisker_0.3-2 knitr_1.24 magrittr_1.5 hms_0.5.0 here_0.1 R6_2.4.0 rlang_0.4.0

[10] tools_3.6.1 packrat_0.5.0 xfun_0.8 withr_2.1.2 clipr_0.7.0 htmltools_0.3.6 rprojroot_1.3-2 digest_0.6.20 tibble_2.1.3

[19] crayon_1.3.4 processx_3.4.1 callr_3.3.1 readr_1.3.1 ps_1.3.0 vctrs_0.2.0 fs_1.3.1 curl_4.0 zeallot_0.1.0

[28] evaluate_0.14 rmarkdown_1.14 reprex_0.3.0 compiler_3.6.1 pillar_1.4.2 backports_1.1.4 pkgconfig_2.0.2

Additional context

The error seems to stem from this file not existing: ftp://ftpext.usgs.gov/pub/er/md/laurel/BBS/DataFiles/README.txt

Maybe it was removed in the most recent BBS data update?

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mbjoseph commented 4 years ago

Awesome! Thanks @TrashBirdEcology :+1:

trashbirdecology commented 4 years ago

@mbjoseph , I have updated the vignette and package to reflect these changes. Please let me know if you run into any other issues, or have additional recommendations! Thanks again