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ropensci
Can't retrieve ids from get_wormsid
Hello, I can't seem to get any of the "get_" functions to work when searching with a scientific name (or a vector of scientific names) as the example below with the get_wormsid function:
x <- taxize::get_wormsid('Gadus morhua')
# x <- taxize::get_wormsid('Gadus morhua')
# == 1 queries ===============
#
# Retrieving data for taxon 'Gadus morhua'
#
# x Not Found: Gadus morhua
# == Results =================
#
# * Total: 1
# * Found: 0
# * Not Found: 1
it doesn't matter which species I try to search, it always returns No found values, but it used to work fine before.
Session Info
- Session info ----------------------------------------------------------------------------------------
setting value
version R version 4.1.2 (2021-11-01)
os Windows 10 x64 (build 19044)
system x86_64, mingw32
ui RStudio
language (EN)
collate Spanish_Mexico.1252
ctype Spanish_Mexico.1252
tz America/Mexico_City
date 2022-02-03
rstudio 2021.09.2+382 Ghost Orchid (desktop)
pandoc NA
- Packages --------------------------------------------------------------------------------------------
package * version date (UTC) lib source
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bold 1.2.0 2021-05-11 [1] CRAN (R 4.1.2)
brio 1.1.3 2021-11-30 [1] CRAN (R 4.1.2)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1)
cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.2)
codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.2)
conditionz 0.1.0 2019-04-24 [1] CRAN (R 4.1.2)
crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.2)
crul 1.2.0 2021-11-22 [1] CRAN (R 4.1.1)
curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.1)
data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.1)
desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.2)
devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.2)
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fansi 1.0.2 2022-01-14 [1] CRAN (R 4.1.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.1)
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processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.1)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.1)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.1)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
Rcpp 1.0.8 2022-01-13 [1] CRAN (R 4.1.2)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.2)
reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.2)
rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.2)
rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2)
stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
taxize 0.9.99.947 2022-02-01 [1] Github (ropensci/taxize@a4db9a7)
testthat 3.1.2 2022-01-20 [1] CRAN (R 4.1.2)
tibble 3.1.6 2021-11-07 [1] CRAN (R 4.1.2)
triebeard 0.3.0 2016-08-04 [1] CRAN (R 4.1.2)
urltools 1.7.3 2019-04-14 [1] CRAN (R 4.1.2)
usethis 2.1.5 2021-12-09 [1] CRAN (R 4.1.2)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1)
uuid 1.0-3 2021-11-01 [1] CRAN (R 4.1.2)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.1)
withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2)
worrms 0.4.2 2020-07-08 [1] CRAN (R 4.1.2)
writexl 1.4.0 2021-04-20 [1] CRAN (R 4.1.1)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.2)
zoo 1.8-9 2021-03-09 [1] CRAN (R 4.1.2)
Hello,
It seems to work for me on the same version of taxize. See output below. Can you try again to make sure that it was not a temporary network issue?
x <- taxize::get_wormsid('Gadus morhua')
#> ══ 1 queries ═══════════════
#>
#> Retrieving data for taxon 'Gadus morhua'
#> ✓ Found: Gadus morhua
#> ══ Results ═════════════════
#>
#> • Total: 1
#> • Found: 1
#> • Not Found: 0
x
#> [1] "126436"
#> attr(,"class")
#> [1] "wormsid"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] TRUE
#> attr(,"pattern_match")
#> [1] TRUE
#> attr(,"uri")
#> [1] "http://www.marinespecies.org/aphia.php?p=taxdetails&id=126436"
devtools::session_info()
#> ─ Session info ──────────────────────────────────────────────────────────────
#> hash: baby angel: medium skin tone, raised back of hand: dark skin tone, man farmer: dark skin tone
#>
#> setting value
#> version R version 4.0.4 (2021-02-15)
#> os Pop!_OS 21.04
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2022-02-03
#> pandoc 2.14.0.3 @ /usr/lib/rstudio/bin/pandoc/ (via rmarkdown)
#>
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#> crul 1.2.0 2021-11-22 [1] CRAN (R 4.0.4)
#> curl 4.3.2 2021-06-23 [1] CRAN (R 4.0.3)
#> data.table 1.14.2 2021-09-27 [1] CRAN (R 4.0.3)
#> desc 1.4.0 2021-09-28 [1] CRAN (R 4.0.4)
#> devtools 2.4.2 2021-06-07 [1] CRAN (R 4.0.3)
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#> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.3)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
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#> foreach 1.5.2 2022-02-02 [1] CRAN (R 4.0.4)
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#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
#> styler 1.6.2 2021-09-23 [1] CRAN (R 4.0.4)
#> taxize 0.9.99.947 2022-02-03 [1] Github (ropensci/taxize@a4db9a7)
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#>
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#> [4] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
Created on 2022-02-03 by the reprex package (v2.0.1)
Hello! It seems a problem related to windows maybe? I have the same issue in my PC. However, it works on my mac... (below)
library(taxize)
x <- taxize::get_wormsid('Gadus morhua') #> == 1 queries =============== #> #> Retrieving data for taxon 'Gadus morhua' #> x Not Found: Gadus morhua #> == Results ================= #> #> * Total: 1 #> * Found: 0 #> * Not Found: 1
devtools::session_info() #> - Session info -------------------------------------------------------------- #> hash: face without mouth, handshake: dark skin tone, bomb #> #> setting value #> version R version 4.1.2 (2021-11-01) #> os Windows 10 x64 (build 22000) #> system x86_64, mingw32 #> ui RTerm #> language (EN) #> collate English_United States.1252 #> ctype English_United States.1252 #> tz America/Chihuahua #> date 2022-02-03 #> pandoc 2.11.4 @ C:/Program Files/RStudio/bin/pandoc/ (via rmarkdown) #> #> - Packages ------------------------------------------------------------------- #> package * version date (UTC) lib source #> ape 5.5 2021-04-25 [1] CRAN (R 4.1.0) #> bold 1.2.0 2021-05-11 [1] CRAN (R 4.1.2) #> cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1) #> callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.0) #> cli 3.1.0 2021-10-27 [1] CRAN (R 4.1.1) #> codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.2) #> conditionz 0.1.0 2019-04-24 [1] CRAN (R 4.1.2) #> crayon 1.4.2 2021-10-29 [1] CRAN (R 4.1.1) #> crul 1.1.0 2021-02-15 [1] CRAN (R 4.1.0) #> curl 4.3.2 2021-06-23 [1] CRAN (R 4.1.1) #> data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.1) #> desc 1.4.0 2021-09-28 [1] CRAN (R 4.1.1) #> devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.0) #> digest 0.6.28 2021-09-23 [1] CRAN (R 4.1.1) #> ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0) #> evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.0) #> fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.0) #> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.0) #> foreach 1.5.1 2020-10-15 [1] CRAN (R 4.1.0) #> fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.0) #> glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.0) #> highr 0.9 2021-04-16 [1] CRAN (R 4.1.0) #> htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1) #> httpcode 0.3.0 2020-04-10 [1] CRAN (R 4.1.0) #> iterators 1.0.13 2020-10-15 [1] CRAN (R 4.1.0) #> jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.0) #> knitr 1.36 2021-09-29 [1] CRAN (R 4.1.1) #> lattice 0.20-45 2021-09-22 [2] CRAN (R 4.1.2) #> lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.1) #> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.0) #> memoise 2.0.0 2021-01-26 [1] CRAN (R 4.1.0) #> nlme 3.1-153 2021-09-07 [2] CRAN (R 4.1.2) #> pillar 1.6.4 2021-10-18 [1] CRAN (R 4.1.1) #> pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.0) #> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0) #> pkgload 1.2.3 2021-10-13 [1] CRAN (R 4.1.1) #> plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.0) #> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0) #> processx 3.5.2 2021-04-30 [1] CRAN (R 4.1.0) #> ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.0) #> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1) #> Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.0) #> remotes 2.4.1 2021-09-29 [1] CRAN (R 4.1.1) #> reprex 2.0.1 2021-08-05 [1] CRAN (R 4.1.2) #> reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.1) #> rlang 0.4.12 2021-10-18 [1] CRAN (R 4.1.1) #> rmarkdown 2.11 2021-09-14 [1] CRAN (R 4.1.1) #> rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.0) #> rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.0) #> sessioninfo 1.2.1 2021-11-02 [1] CRAN (R 4.1.1) #> stringi 1.7.5 2021-10-04 [1] CRAN (R 4.1.1) #> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0) #> taxize * 0.9.99 2020-10-30 [1] CRAN (R 4.1.2) #> testthat 3.1.0 2021-10-04 [1] CRAN (R 4.1.1) #> tibble 3.1.5 2021-09-30 [1] CRAN (R 4.1.1) #> triebeard 0.3.0 2016-08-04 [1] CRAN (R 4.1.0) #> urltools 1.7.3 2019-04-14 [1] CRAN (R 4.1.0) #> usethis 2.1.3 2021-10-27 [1] CRAN (R 4.1.1) #> utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1) #> uuid 1.0-3 2021-11-01 [1] CRAN (R 4.1.1) #> vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.0) #> withr 2.4.3 2021-11-30 [1] CRAN (R 4.1.2) #> worrms 0.4.2 2020-07-08 [1] CRAN (R 4.1.2) #> xfun 0.28 2021-11-04 [1] CRAN (R 4.1.2) #> xml2 1.3.2 2020-04-23 [1] CRAN (R 4.1.0) #> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0) #> zoo 1.8-9 2021-03-09 [1] CRAN (R 4.1.0) #> #> [1] C:/Users/zephi/Documents/R/win-library/4.1 #> [2] C:/Program Files/R/R-4.1.2/library #> #> ------------------------------------------------------------------------------
library(taxize)
x <- taxize::get_wormsid('Gadus morhua') #> ══ 1 queries ═══════════════ #> #> Retrieving data for taxon 'Gadus morhua' #> ✔ Found: Gadus morhua #> ══ Results ═════════════════ #> #> • Total: 1 #> • Found: 1 #> • Not Found: 0
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Hello - I have been having the same issue, and it's not working on my Mac. I cannot get either get_wormsid or classification(data, db='worms') to recognize any species rank entries, returning them as 'Not Found'. This only seems to be an issue with WoRMS, as I was able to query the same species successfully with GBIF and EOL. I am, however, able to query ranks above species with no problems using worms.
taxize::get_wormsid('Gadus morhua') ══ 1 queries ═══════════════
Retrieving data for taxon 'Gadus morhua'
✖ Not Found: Gadus morhua ══ Results ═════════════════
• Total: 1 • Found: 0 • Not Found: 1 [1] NA attr(,"class") [1] "wormsid" attr(,"match") [1] "not found" attr(,"multiple_matches") [1] FALSE attr(,"pattern_match") [1] FALSE
classification('Gadus morhua', db = 'worms') ══ 1 queries ═══════════════
Retrieving data for taxon 'Gadus morhua'
✖ Not Found: Gadus morhua ══ Results ═════════════════
• Total: 1
• Found: 0
• Not Found: 1
$Gadus morhua
[1] NA
attr(,"class") [1] "classification" attr(,"db") [1] "worms"
classification('Gadus morhua', db='gbif') ══ 1 queries ═══════════════
Retrieving data for taxon 'Gadus morhua'
✔ Found: Gadus morhua ══ Results ═════════════════
• Total: 1
• Found: 1
• Not Found: 0
$Gadus morhua
name rank id
1 Animalia kingdom 1
2 Chordata phylum 44
3 Actinopterygii class 204
4 Gadiformes order 549
5 Gadidae family 3701
6 Gadus genus 2335052
7 Gadus morhua species 8084280
attr(,"class") [1] "classification" attr(,"db") [1] "gbif"
sessionInfo(package='taxize') R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6.2
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: character(0)
other attached packages: [1] taxize_0.9.99
I cant replicate the error on either the CRAN version or the Github development branch:
> taxize::get_wormsid('Gadus morhua')
══ 1 queries ═══════════════
Retrieving data for taxon 'Gadus morhua'
✓ Found: Gadus morhua
══ Results ═════════════════
• Total: 1
• Found: 1
• Not Found: 0
[1] "126436"
attr(,"class")
[1] "wormsid"
attr(,"match")
[1] "found"
attr(,"multiple_matches")
[1] TRUE
attr(,"pattern_match")
[1] TRUE
attr(,"uri")
[1] "http://www.marinespecies.org/aphia.php?p=taxdetails&id=126436"
> sessionInfo(package='taxize')
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Pop!_OS 21.04
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
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:
character(0)
other attached packages:
[1] taxize_0.9.99
I don't have a Mac to test it on. Can you reinstall taxize and try again?
Hi @zachary-foster - thank you for commenting to help! I uninstalled and reinstalled taxize, and unfortunately I'm still having the same problem. I'm not so far behind on my R/OS updates that it should matter here I think - just doesn't make sense to me why other databases like gbif are working but worms is not, and why it's only the species rank queries that are not working...
remove.packages("taxize") Removing package from ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ (as ‘lib’ is unspecified) install.packages("taxize") trying URL 'https://cran.rstudio.com/bin/macosx/contrib/4.1/taxize_0.9.99.tgz' Content type 'application/x-gzip' length 1496913 bytes (1.4 MB) ================================================== downloaded 1.4 MB
The downloaded binary packages are in /var/folders/v5/0x9gwptx3dncgbxq57rr678c0000gn/T//RtmpadXBC9/downloaded_packages
library(taxize) get_wormsid("Gadus morhua") ══ 1 queries ═══════════════
Retrieving data for taxon 'Gadus morhua'
✖ Not Found: Gadus morhua ══ Results ═════════════════
• Total: 1 • Found: 0 • Not Found: 1 [1] NA attr(,"class") [1] "wormsid" attr(,"match") [1] "not found" attr(,"multiple_matches") [1] FALSE attr(,"pattern_match") [1] FALSE
classification("Gadus morhua", db="worms") ══ 1 queries ═══════════════
Retrieving data for taxon 'Gadus morhua'
✖ Not Found: Gadus morhua ══ Results ═════════════════
• Total: 1
• Found: 0
• Not Found: 1
$Gadus morhua
[1] NA
attr(,"class") [1] "classification" attr(,"db") [1] "worms"
sessionInfo(package='taxize') R version 4.1.1 (2021-08-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Big Sur 11.6.2
Matrix products: default LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: character(0)
other attached packages: [1] taxize_0.9.99
Ok, thanks! I have replicated the error on a clean Windows install. I will try to figure out what is going on.
I have tracked down the error to a function in the worrms packages, which is used to communicate with the Worrms API. I have made an issue there describing the problem. Once it is solved there, the problem should be resolved for taxize as well.
In the mean time, you can get around the issue by replacing the spaces with +:
taxize::get_wormsid("Gadus+morhua")
I am still having this issue on an M1 mac. I had a list of ~8000 taxa, higher level taxa came back successfully while species level taxa came back as NULL.
Replacing whitespace with "+" returned all levels of taxonomy successfully.
