Running classification() in R markdown doesn't show options when multiple UIDs are found

[JacobyBaker]

Hello,

I ran across an issue using classification() in R markdown when multiple UIDs are found or a taxon. In my example, three UIDs are found for the taxon 'Ctenophora' and I am asked to enter the row number of the taxon I wish to choose. However, in R markdown the list of options do not show in the Console, so I unable to assess which is most appropriate. If I run the exact same code in a regular R script file the options do show up. Has this happened with others?

Code run:

classification(spnames, db = "ncbi", verbose = FALSE)

##########
Console output when run in R markdown:

Retrieving data for taxon 'Ctenophora'





More than one UID found for taxon 'Ctenophora'!

            Enter rownumber of taxon (other inputs will return 'NA'):

1: 

##########
Console output when run in a plain R script:

Retrieving data for taxon 'Ctenophora'





More than one UID found for taxon 'Ctenophora'!

            Enter rownumber of taxon (other inputs will return 'NA'):

  status   rank     division scientificname  commonname     uid genus species subsp modificationdate
1 active  genus      diatoms     Ctenophora             1003038                     2015/09/16 00:00
2 active  genus        flies     Ctenophora              516519                     2016/03/23 00:00
3 active phylum comb jellies     Ctenophora ctenophores   10197                     2017/06/14 00:00
1: 

Session Info

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
 [1] wesanderson_0.3.7  ggbump_0.1.0       osmdata_0.2.5      geosphere_1.5-18   sf_1.0-14          taxize_0.9.100     ggstar_1.0.4       tidytree_0.4.4    
 [9] treeio_1.24.3      ggnewscale_0.4.9   cowplot_1.1.1      gridExtra_2.3      mvnormalTest_1.0.0 rstatix_0.7.2      MASS_7.3-60        ggtreeExtra_1.10.0
[17] ggtree_3.8.2       ape_5.7-1          reshape2_1.4.4     mapview_2.11.0     ggmap_3.0.2        mapdata_2.3.1      maps_3.4.1         metacoder_0.3.6   
[25] taxa_0.4.2         vctrs_0.6.3        phyloseq_1.44.0    forcats_1.0.0      stringr_1.5.0      purrr_1.0.1        tidyr_1.3.0        tibble_3.2.1      
[33] tidyverse_2.0.0    RColorBrewer_1.1-3 viridis_0.6.4      viridisLite_0.4.2  magrittr_2.0.3     ggthemes_4.2.4     dplyr_1.1.2        ggalt_0.4.0       
[41] ggpubr_0.6.0       ggplot2_3.4.2      vegan_2.6-4        lattice_0.21-8     permute_0.9-7      lubridate_1.9.2    readr_2.1.4        qiime2R_0.99.6    

loaded via a namespace (and not attached):
  [1] bitops_1.0-7            bold_1.3.0              httr_1.4.6              webshot_0.5.5           ash_1.0-15              numDeriv_2016.8-1.1    
  [7] tools_4.3.0             backports_1.4.1         utf8_1.2.3              R6_2.5.1                DT_0.28                 lazyeval_0.2.2         
 [13] mgcv_1.9-0              nortest_1.0-4           rhdf5filters_1.12.1     withr_2.5.0             sp_2.0-0                leaflet_2.1.2          
 [19] leafem_0.2.0            cli_3.6.1               Biobase_2.60.0          textshaping_0.3.6       pspline_1.0-19          pacman_0.5.1           
 [25] labeling_0.4.2          mvtnorm_1.2-4           proxy_0.4-27            systemfonts_1.0.4       yulab.utils_0.0.6       foreign_0.8-84         
 [31] svglite_2.1.1           rstudioapi_0.15.0       httpcode_0.3.0          generics_0.1.3          gridGraphics_0.5-1      crosstalk_1.2.0        
 [37] vroom_1.6.3             car_3.1-2               Matrix_1.6-0            biomformat_1.28.0       fansi_1.0.4             S4Vectors_0.38.1       
 [43] abind_1.4-5             terra_1.7-39            lifecycle_1.0.3         yaml_2.3.7              carData_3.0-5           rhdf5_2.44.0           
 [49] grid_4.3.0              crayon_1.5.2            conditionz_0.1.0        pillar_1.9.0            knitr_1.43              codetools_0.2-19       
 [55] fastmatch_1.1-3         glue_1.6.2              ggfun_0.1.1             data.table_1.14.8       urltools_1.7.3          png_0.1-8              
 [61] gtable_0.3.3            rerddap_1.0.4           xfun_0.39               pcaPP_2.0-4             survival_3.5-5          ncdf4_1.21             
 [67] iterators_1.0.14        units_0.8-2             ellipsis_0.3.2          brew_1.0-8              nlme_3.1-162            satellite_1.0.4        
 [73] bit64_4.0.5             GenomeInfoDb_1.36.1     KernSmooth_2.23-22      rpart_4.1.19            colorspace_2.1-0        BiocGenerics_0.46.0    
 [79] DBI_1.1.3               Hmisc_5.1-0             raster_3.6-23           nnet_7.3-19             ade4_1.7-22             NADA_1.6-1.1           
 [85] phangorn_2.11.1         processx_3.8.2          tidyselect_1.2.0        moments_0.14.1          bit_4.0.5               compiler_4.3.0         
 [91] extrafontdb_1.0         curl_5.0.1              httr2_0.2.3             htmlTable_2.4.1         xml2_1.3.5              plotly_4.10.2          
 [97] triebeard_0.4.1         checkmate_2.2.0         scales_1.2.1            proj4_1.0-12            classInt_0.4-9          quadprog_1.5-8         
[103] callr_3.7.3             rappdirs_0.3.3          digest_0.6.33           rmarkdown_2.23          XVector_0.40.0          htmltools_0.5.5        
[109] pkgconfig_2.0.3         jpeg_0.1-10             base64enc_0.1-3         extrafont_0.19          stabledist_0.7-1        fastmap_1.1.1          
[115] ADGofTest_0.3           rlang_1.1.1             htmlwidgets_1.6.2       zCompositions_1.4.0-1   farver_2.1.1            zoo_1.8-12             
[121] jsonlite_1.8.7          RCurl_1.98-1.12         Formula_1.2-5           GenomeInfoDbData_1.2.10 ggplotify_0.1.1         patchwork_1.1.2        
[127] Rhdf5lib_1.22.0         munsell_0.5.0           Rcpp_1.0.11             stringi_1.7.12          zlibbioc_1.46.0         plyr_1.8.8             
[133] parallel_4.3.0          Biostrings_2.68.1       splines_4.3.0           multtest_2.56.0         hms_1.1.3               leafpop_0.1.0          
[139] ps_1.7.5                uuid_1.1-0              igraph_1.5.0.1          ggsignif_0.6.4          stats4_4.3.0            crul_1.4.0             
[145] evaluate_0.21           leaflet.providers_1.9.0 hoardr_0.5.3            tzdb_0.4.0              foreach_1.5.2           RgoogleMaps_1.4.5.3    
[151] Rttf2pt1_1.3.12         broom_1.0.5             e1071_1.7-13            class_7.3-22            ragg_1.2.5              gsl_2.1-8              
[157] copula_1.1-3            truncnorm_1.0-9         aplot_0.1.10            IRanges_2.34.1          cluster_2.1.4           timechange_0.2.0