zachary-foster
commented
7 months ago Thanks! I am unable to reproduce this error. Can you add a sessionInfo() output?
library(taxize)
synonyms(sci_id = 'Ameiva atrigularis', db = 'itis')
#> ══ 1 queries ═══════════════
#>
#> Retrieving data for taxon 'Ameiva atrigularis'
#> ✔ Found: Ameiva atrigularis
#> ══ Results ═════════════════
#>
#> • Total: 1
#> • Found: 1
#> • Not Found: 0
#> $`Ameiva atrigularis`
#> data frame with 0 columns and 0 rows
#>
#> attr(,"class")
#> [1] "synonyms"
#> attr(,"db")
#> [1] "itis"
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_0.5.7Created on 2023-11-30 with reprex v2.0.2
gledits2
labmizrahi
andrewdeines
Session Info
```r R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045) Matrix products: default locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C [5] LC_TIME=English_United States.utf8 time zone: America/New_York tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] taxize_0.9.100 caribmacro_1.1.0 here_1.0.1 loaded via a namespace (and not attached): [1] gtable_0.3.4 ggplot2_3.4.3 lattice_0.21-8 vctrs_0.6.3 tools_4.3.1 generics_0.1.3 curl_5.0.2 parallel_4.3.1 [9] tibble_3.2.1 proxy_0.4-27 fansi_1.0.4 pkgconfig_2.0.3 KernSmooth_2.23-21 data.table_1.14.8 uuid_1.1-1 lifecycle_1.0.3 [17] conditionz_0.1.0 compiler_4.3.1 stringr_1.5.0 munsell_0.5.0 ritis_1.0.0 codetools_0.2-19 class_7.3-22 lazyeval_0.2.2 [25] pillar_1.9.0 crayon_1.5.2 whisker_0.4.1 classInt_0.4-9 solrium_1.2.0 iterators_1.0.14 foreach_1.5.2 nlme_3.1-162 [33] tidyselect_1.2.0 digest_0.6.33 stringi_1.7.12 sf_1.0-14 dplyr_1.1.3 rprojroot_2.0.3 grid_4.3.1 colorspace_2.1-0 [41] cli_3.6.1 magrittr_2.0.3 bold_1.3.0 triebeard_0.4.1 crul_1.4.0 utf8_1.2.3 e1071_1.7-13 ape_5.7-1 [49] scales_1.2.1 oai_0.4.0 httr_1.4.7 rgbif_3.7.7 zoo_1.8-12 rlang_1.1.1 urltools_1.7.3 Rcpp_1.0.11 [57] glue_1.6.2 DBI_1.1.3 httpcode_0.3.0 xml2_1.3.5 rstudioapi_0.15.0 jsonlite_1.8.7 R6_2.5.1 plyr_1.8.8 [65] units_0.8-3 ```Hi,
I am trying to look up the known synonyms for a list of species. In the past, I have used taxize::synonyms with great success. However, now when I run the following code, I get an error about a tibble not being able to be made because a parameter is needed as of tibble 3.0.0.
Here is the code I am trying to run:
And this is the output I get with the traceback
══ 1 queries ═══════════════
Retrieving data for taxon 'Ameiva atrigularis'
Error: ! The
xargument ofas_tibble()can't be missing as of tibble 3.0.0. Runrlang::last_trace()to see where the error occurred.I tried to run it again after reinstalling taxize through remotes::install_github("ropensci/taxize") and it still returned the same error. The interesting this is that I ran this code in September without issue.