parse_raw() errors on empty input when tibble >= 3.0.0

[rix133]

The call to ritis::terms gives an error

ritis::terms("Boleophthalmus dussumieri", what = "scientific")



Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble
  3.0.0.

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 

[carolinetang77]

The same error occurs in ritis::full_record() and ritis::hierarchy_full():

ritis::full_record("175299")
Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble 3.0.0.

ritis::hierarchy_full("175299")
Error:
! The `x` argument of `as_tibble()` can't be missing as of tibble 3.0.0.

[rix133]

ok anyhow seems that the whole ITIS service is down right now and it does not handle this well

[rix133]

so the input that the parse raw gets from ITIS json request is "" (empty string) and the tibble wants some input in here

ritis/R/zzz.R

Line 62 in 95f190c

return(tibble::as_tibble())

[jcblum]

Thanks for noting the ITIS outage, @rix133, and for tracing this issue to the root cause. By the time I could investigate, I could no longer reproduce the error (since ITIS was responding again), so your follow-up was a big help!

tibble::tibble() returns an empty tibble, so I think that's the immediate fix here. However, I also think it would be nice if there was more user feedback that the ITIS request came back empty. I'm opening a separate feature issue for that.