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ropensci / spocc

Species occurrence data toolkit for R
https://docs.ropensci.org/spocc
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occ() not able to find GBIF records #233

Closed mannfred closed 3 years ago

mannfred commented 3 years ago

Hi @sckott,

Thanks for the great package!

I recently started having trouble with occ(). Running the examples from ?occ() e.g.

(res <- occ(query = 'Accipiter striatus', from = 'gbif', limit = 5))

gives me:

Searched: gbif
Occurrences - Found: 0, Returned: 0
Search type: Scientific
Warning messages:
1: gbif: No records returned in GBIF for Accipiter striatus 
2: gbif: Column 47 of item 1 is length 3 inconsistent with column 1 which is length 5. Only length-1 columns are recycled.

If I remove limit=5 the error changes to:

(res <- occ(query = 'Accipiter striatus', from = 'gbif'))
Searched: gbif
Occurrences - Found: 0, Returned: 0
Search type: Scientific
Warning messages:
1: gbif: No records returned in GBIF for Accipiter striatus 
2: gbif: Column 47 of item 1 is length 4 inconsistent with column 1 which is length 300. Only length-1 columns are recycled.

I'm using the dev version from GitHub (remotes::install_github("ropensci/spocc"))

Session Info ``` - Session info ------------------------------------------------------------------------ setting value version R version 4.0.2 (2020-06-22) os Windows 10 x64 system x86_64, mingw32 ui RStudio language (EN) collate English_Canada.1252 ctype English_Canada.1252 tz America/Los_Angeles date 2020-09-06 - Packages ---------------------------------------------------------------------------- package * version date lib source assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2) backports 1.1.9 2020-08-24 [1] CRAN (R 4.0.2) callr 3.4.3 2020-03-28 [1] CRAN (R 4.0.2) cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2) colorspace 1.4-1 2019-03-18 [1] CRAN (R 4.0.2) conditionz 0.1.0 2019-04-24 [1] CRAN (R 4.0.2) crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) crul 1.0.0 2020-07-30 [1] CRAN (R 4.0.2) curl 4.3 2019-12-02 [1] CRAN (R 4.0.2) data.table 1.13.0 2020-07-24 [1] CRAN (R 4.0.2) desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) devtools 2.3.1 2020-07-21 [1] CRAN (R 4.0.2) digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.2) ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2) fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2) fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2) geoaxe 0.1.0 2016-02-19 [1] CRAN (R 4.0.2) ggplot2 3.3.2 2020-06-19 [1] CRAN (R 4.0.2) glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) gtable 0.3.0 2019-03-25 [1] CRAN (R 4.0.2) htmltab * 0.7.1.1 2020-03-22 [1] CRAN (R 4.0.2) htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2) httpcode 0.3.0 2020-04-10 [1] CRAN (R 4.0.2) httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) installr * 0.22.0 2019-08-02 [1] CRAN (R 4.0.2) jsonlite 1.7.0 2020-06-25 [1] CRAN (R 4.0.2) knitr 1.29 2020-06-23 [1] CRAN (R 4.0.2) lattice 0.20-41 2020-04-02 [2] CRAN (R 4.0.2) lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.0.2) lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) lubridate 1.7.9 2020-06-08 [1] CRAN (R 4.0.2) magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) mapproj 1.2.7 2020-02-03 [1] CRAN (R 4.0.2) maps 3.3.0 2018-04-03 [1] CRAN (R 4.0.2) memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2) munsell 0.5.0 2018-06-12 [1] CRAN (R 4.0.2) oai 0.3.0 2019-09-07 [1] CRAN (R 4.0.2) pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2) pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) plyr 1.8.6 2020-03-03 [1] CRAN (R 4.0.2) prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2) ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) rbison 1.0.0 2020-06-08 [1] CRAN (R 4.0.2) Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2) rebird 1.1.0 2019-10-24 [1] CRAN (R 4.0.2) remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) rgbif 3.2.0 2020-07-23 [1] CRAN (R 4.0.2) rgeos 0.5-3 2020-05-08 [1] CRAN (R 4.0.2) ridigbio 0.3.5 2017-02-16 [1] CRAN (R 4.0.2) rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2) rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2) rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) rvertnet 0.8.0 2020-01-29 [1] CRAN (R 4.0.2) scales 1.1.1 2020-05-11 [1] CRAN (R 4.0.2) sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) sp 1.4-2 2020-05-20 [1] CRAN (R 4.0.2) spocc * 1.1.0 2020-09-07 [1] Github (ropensci/spocc@2217923) stringi 1.4.6 2020-02-17 [1] CRAN (R 4.0.0) stringr * 1.4.0 2019-02-10 [1] CRAN (R 4.0.2) testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) triebeard 0.3.0 2016-08-04 [1] CRAN (R 4.0.2) urltools 1.7.3 2019-04-14 [1] CRAN (R 4.0.2) usethis 1.6.1 2020-04-29 [1] CRAN (R 4.0.2) uuid 0.1-4 2020-02-26 [1] CRAN (R 4.0.0) vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2) whisker 0.4 2019-08-28 [1] CRAN (R 4.0.2) withr 2.2.0 2020-04-20 [1] CRAN (R 4.0.2) xfun 0.16 2020-07-24 [1] CRAN (R 4.0.2) XML 3.99-0.5 2020-07-23 [1] CRAN (R 4.0.2) xml2 1.3.2 2020-04-23 [1] CRAN (R 4.0.2) yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2) ```
carolinagrando commented 3 years ago

I am also having this trouble when I try to run!

Dm <- "Dipteryx micrantha" occ_spocc_Dm <- spocc::occ(query = 'Dm', from = "gbif", has_coords = TRUE, limit = 1e6)

Warning messages: 1: gbif: No records returned in GBIF for Dipteryx micrantha 2: gbif: Column 46 of item 1 is length 4 inconsistent with column 1 which is length 129. Only length-1 columns are recycled.

sckott commented 3 years ago

that's a problem in rgbif. it's alreday fixed in rgbif. update rgbif like:

remotes::install_github("ropensci/rgbif")
or
install.packages("rgbif", repos="https://dev.ropensci.org")
mannfred commented 3 years ago

Much appreciated!

As you suggested,

install.packages("rgbif", repos="https://dev.ropensci.org")

updated rgbif and solved this problem.

carolinagrando commented 3 years ago

Thank you so much!