taxizedb
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Published
20 hours ago •
ropensci
ropensci
Query works with taxize but doesn't work with taxizedb
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.
