get_tsn() Error with tibble >= 3.0

[rix133]

On the latest dev version. e.g. the call to ritis gives an error ropensci/ritis#26

get_tsn("Boleophthalmus dussumieri")

══  1 queries  ═══════════════

Retrieving data for taxon 'Boleophthalmus dussumieri'

Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble
  3.0.0.
Backtrace:
 1. taxize::get_tsn("Boleophthalmus dussumieri")
 2. ritis::terms(sci_com[i], what = searchtype, ...)
 3. base::lapply(query, fun, wt = wt, raw = raw, ...)
 4. ritis (local) FUN(X[[i]], ...)
 5. ritis:::parse_raw(out)
 7. tibble:::as_tibble.NULL()
 8. lifecycle::deprecate_stop("3.0.0", "as_tibble(x = 'can\\'t be missing')")
 9. lifecycle:::deprecate_stop0(msg)

Session Info

> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Estonian_Estonia.utf8  LC_CTYPE=Estonian_Estonia.utf8   
[3] LC_MONETARY=Estonian_Estonia.utf8 LC_NUMERIC=C                     
[5] LC_TIME=Estonian_Estonia.utf8    

time zone: Europe/Tallinn
tzcode source: internal

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

other attached packages:
[1] taxize_0.9.100

loaded via a namespace (and not attached):
  [1] gridExtra_2.3        remotes_2.4.2.1      inline_0.3.19        sandwich_3.0-2      
  [5] readxl_1.4.3         rlang_1.1.2          magrittr_2.0.3       multcomp_1.4-25     
  [9] matrixStats_1.1.0    compiler_4.3.2       loo_2.6.0            callr_3.7.3         
 [13] vctrs_0.6.4          reshape2_1.4.4       httpcode_0.3.0       stringr_1.5.1       
 [17] pkgconfig_2.0.3      crayon_1.5.2         fastmap_1.1.1        backports_1.4.1     
 [21] ellipsis_0.3.2       pander_0.6.5         utf8_1.2.4           threejs_0.3.3       
 [25] promises_1.2.1       markdown_1.11        ps_1.7.5             xfun_0.41           
 [29] jsonlite_1.8.7       later_1.3.1          parallel_4.3.2       prettyunits_1.2.0   
 [33] R6_2.5.1             dygraphs_1.1.1.6     stringi_1.8.1        StanHeaders_2.26.28 
 [37] cellranger_1.1.0     estimability_1.4.1   knitr_1.45           iterators_1.0.14    
 [41] Rcpp_1.0.11          rstan_2.32.3         triebeard_0.4.1      zoo_1.8-12          
 [45] base64enc_0.1-3      bayesplot_1.10.0     httpuv_1.6.12        Matrix_1.6-3        
 [49] splines_4.3.2        igraph_1.5.1         tidyselect_1.2.0     rstudioapi_0.15.0   
 [53] abind_1.4-5          codetools_0.2-19     miniUI_0.1.1.1       curl_5.1.0          
 [57] processx_3.8.2       pkgbuild_1.4.2       lattice_0.22-5       tibble_3.2.1        
 [61] plyr_1.8.9           shiny_1.8.0          bridgesampling_1.1-2 posterior_1.5.0     
 [65] coda_0.19-4          survival_3.5-7       RcppParallel_5.1.7   xml2_1.3.5          
 [69] xts_0.13.1           pillar_1.9.0         ritis_1.0.0          tensorA_0.36.2      
 [73] foreach_1.5.2        checkmate_2.3.0      DT_0.30              stats4_4.3.2        
 [77] shinyjs_2.1.0        distributional_0.3.2 generics_0.1.3       ggplot2_3.4.4       
 [81] rstantools_2.3.1.1   munsell_0.5.0        scales_1.2.1         gtools_3.9.4        
 [85] xtable_1.8-4         glue_1.6.2           emmeans_1.8.9        tools_4.3.2         
 [89] shinystan_2.6.0      data.table_1.14.8    colourpicker_1.3.0   mvtnorm_1.2-3       
 [93] grid_4.3.2           bold_1.3.0           ape_5.7-1            urltools_1.7.3      
 [97] QuickJSR_1.0.7       crosstalk_1.2.0      colorspace_2.1-0     nlme_3.1-163        
[101] cli_3.6.1            fansi_1.0.5          solrium_1.2.0        Brobdingnag_1.2-9   
[105] dplyr_1.1.4          V8_4.4.0             gtable_0.3.4         digest_0.6.33       
[109] crul_1.4.0           TH.data_1.1-2        brms_2.20.4          htmlwidgets_1.6.3   
[113] farver_2.1.1         htmltools_0.5.7      lifecycle_1.0.4      mime_0.12           
[117] shinythemes_1.2.0    MASS_7.3-60 

[zachary-foster]

Thanks for the report! I am not able to reproduce this error. Is this the CRAN version or the current Github version?

library(taxize)
get_tsn("Boleophthalmus dussumieri")
#> ══  1 queries  ═══════════════
#> 
#> Retrieving data for taxon 'Boleophthalmus dussumieri'
#> ✔  Found:  Boleophthalmus dussumieri
#> ══  Results  ═════════════════
#> 
#> • Total: 1 
#> • Found: 1 
#> • Not Found: 0
#> [1] "637041"
#> attr(,"class")
#> [1] "tsn"
#> attr(,"match")
#> [1] "found"
#> attr(,"multiple_matches")
#> [1] FALSE
#> attr(,"pattern_match")
#> [1] FALSE
#> attr(,"uri")
#> [1] "https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=637041"
sessionInfo()
#> R version 4.3.2 (2023-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Pop!_OS 22.04 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/Los_Angeles
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] taxize_0.9.100
#> 
#> loaded via a namespace (and not attached):
#>  [1] bold_1.3.0        solrium_1.2.0     jsonlite_1.8.7    dplyr_1.1.4      
#>  [5] compiler_4.3.2    crayon_1.5.2      tidyselect_1.2.0  reprex_2.0.2     
#>  [9] Rcpp_1.0.11       xml2_1.3.5        urltools_1.7.3    parallel_4.3.2   
#> [13] triebeard_0.4.1   yaml_2.3.7        fastmap_1.1.1     lattice_0.22-5   
#> [17] plyr_1.8.9        R6_2.5.1          generics_0.1.3    curl_5.1.0       
#> [21] knitr_1.45        iterators_1.0.14  tibble_3.2.1      ritis_1.0.0      
#> [25] crul_1.4.0        pillar_1.9.0      rlang_1.1.2       utf8_1.2.4       
#> [29] httpcode_0.3.0    stringi_1.8.2     xfun_0.41         fs_1.6.3         
#> [33] cli_3.6.1         magrittr_2.0.3    withr_2.5.2       digest_0.6.33    
#> [37] foreach_1.5.2     grid_4.3.2        rstudioapi_0.15.0 lifecycle_1.0.4  
#> [41] nlme_3.1-163      vctrs_0.6.4       evaluate_0.23     glue_1.6.2       
#> [45] data.table_1.14.8 codetools_0.2-19  zoo_1.8-12        fansi_1.0.5      
#> [49] ape_5.7-1         rmarkdown_2.25    pkgconfig_2.0.3   tools_4.3.2      
#> [53] htmltools_0.5.7

^{Created on 2023-11-30 with reprex v2.0.2}