Query works with taxize but doesn't work with taxizedb

[stitam]

Hi,

This function from the taxize package works:

taxize::classification("podoviridae", "ncbi")
#> No ENTREZ API key provided
#>  Get one via taxize::use_entrez()
#> See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
#> ══  1 queries  ═══════════════
#> 
#> Retrieving data for taxon 'podoviridae'
#> ✓  Found:  podoviridae
#> ══  Results  ═════════════════
#> 
#> • Total: 1 
#> • Found: 1 
#> • Not Found: 0
#> No ENTREZ API key provided
#>  Get one via taxize::use_entrez()
#> See https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/
#> $podoviridae
#>             name         rank      id
#> 1        Viruses superkingdom   10239
#> 2  Duplodnaviria        clade 2731341
#> 3 Heunggongvirae      kingdom 2731360
#> 4    Uroviricota       phylum 2731618
#> 5 Caudoviricetes        class 2731619
#> 6   Caudovirales        order   28883
#> 7    Podoviridae       family   10744
#> 
#> attr(,"class")
#> [1] "classification"
#> attr(,"db")
#> [1] "ncbi"

The equivalent from taxizedb does not:

taxizedb::classification("podoviridae")
#> Error: Problem with `summarise()` column `taxids`.
#> ℹ `taxids = paste(.data$tax_id, collapse = "|")`.
#> x Column `tax_id` not found in `.data`
#> ℹ The error occurred in group 1: name = "podoviridae".

session_info:

devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                         
#>  version  R version 4.1.2 (2021-11-01)  
#>  os       Debian GNU/Linux 11 (bullseye)
#>  system   x86_64, linux-gnu             
#>  ui       X11                           
#>  language en_GB:en                      
#>  collate  en_GB.UTF-8                   
#>  ctype    en_GB.UTF-8                   
#>  tz       Europe/Budapest               
#>  date     2021-11-10                    
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date       lib source        
#>  assertthat    0.2.1   2019-03-21 [3] CRAN (R 4.0.0)
#>  cachem        1.0.3   2021-02-04 [3] CRAN (R 4.0.3)
#>  callr         3.7.0   2021-04-20 [1] CRAN (R 4.1.2)
#>  cli           3.0.1   2021-07-17 [1] CRAN (R 4.1.1)
#>  crayon        1.4.1   2021-02-08 [1] CRAN (R 4.1.1)
#>  desc          1.2.0   2018-05-01 [3] CRAN (R 4.0.0)
#>  devtools      2.3.2   2020-09-18 [3] CRAN (R 4.0.2)
#>  digest        0.6.27  2020-10-24 [3] CRAN (R 4.0.3)
#>  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.1)
#>  evaluate      0.14    2019-05-28 [3] CRAN (R 4.0.0)
#>  fastmap       1.1.0   2021-01-25 [3] CRAN (R 4.0.3)
#>  fs            1.5.0   2020-07-31 [3] CRAN (R 4.0.2)
#>  glue          1.4.2   2020-08-27 [1] CRAN (R 4.1.1)
#>  highr         0.8     2019-03-20 [3] CRAN (R 4.0.0)
#>  htmltools     0.5.1.1 2021-01-22 [3] CRAN (R 4.0.3)
#>  knitr         1.31    2021-01-27 [3] CRAN (R 4.0.3)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.1)
#>  magrittr      2.0.1   2020-11-17 [1] CRAN (R 4.1.1)
#>  memoise       2.0.0   2021-01-26 [3] CRAN (R 4.0.3)
#>  pkgbuild      1.2.0   2020-12-15 [3] CRAN (R 4.0.3)
#>  pkgload       1.1.0   2020-05-29 [3] CRAN (R 4.0.1)
#>  prettyunits   1.1.1   2020-01-24 [3] CRAN (R 4.0.0)
#>  processx      3.5.2   2021-04-30 [1] CRAN (R 4.1.2)
#>  ps            1.5.0   2020-12-05 [3] CRAN (R 4.0.3)
#>  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)
#>  remotes       2.2.0   2020-07-21 [3] CRAN (R 4.0.2)
#>  reprex        2.0.1   2021-08-05 [1] CRAN (R 4.1.2)
#>  rlang         0.4.11  2021-04-30 [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 [3] CRAN (R 4.0.3)
#>  rstudioapi    0.13    2020-11-12 [3] CRAN (R 4.0.3)
#>  sessioninfo   1.1.1   2018-11-05 [3] CRAN (R 4.0.0)
#>  stringi       1.5.3   2020-09-09 [3] CRAN (R 4.0.2)
#>  stringr       1.4.0   2019-02-10 [3] CRAN (R 4.0.0)
#>  testthat      3.0.1   2020-12-17 [3] CRAN (R 4.0.3)
#>  usethis       2.0.0   2020-12-10 [3] CRAN (R 4.0.3)
#>  withr         2.4.1   2021-01-26 [3] CRAN (R 4.0.3)
#>  xfun          0.26    2021-09-14 [1] CRAN (R 4.1.1)
#>  yaml          2.2.1   2020-02-01 [3] CRAN (R 4.0.0)
#> 
#> [1] /home/tamas/R/x86_64-pc-linux-gnu-library/4.1
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library

packageVersion("taxize")
#> [1] '0.9.99'

packageVersion("taxizedb")
#> [1] '0.3.0'

Other taxa seem to be working. Any ideas what may be causing this strange behavior? Many thanks.

[sckott]

unfortunately, taxizedb::classificaiton expects a taxon id, not a taxon name

taxizedb::classification(10744)

[stitam]

Thanks @sckott! I think I got confused because on the other hand, taxizedb::classification("autographiviridae") works.

[sckott]

weird, didn't realize names sometimes work.

on a related note, if you want to take over maintainer role, please do

[maelle]

This repository is about to be archived.

[maelle]

unarchiving it thanks to @stitam 😸