btupper
commented
5 months ago Hello,
I'm encountering the same issue. It doesn't seem to depend upon the value provided by the user to the species_list (I thought it might, but now I think I was chasing a red herring.)
Thanks! Ben
r = rfishbase::distribution(species_list = NULL, server = "fishbase")
# Error in `db_query_fields.DBIConnection()`:
# ! Can't query fields.
# Caused by error:
# ! rapi_prepare: Failed to prepare query SELECT *
# FROM species AS q01
# WHERE (0 = 1)
# Error: Catalog Error: Table with name species does not exist!
# Did you mean "pg_views"?
# LINE 2: FROM species AS q01
# ^
# Run `rlang::last_trace()` to see where the error occurred.> rlang::last_trace()
# <error/rlang_error>
# Error in `db_query_fields.DBIConnection()`:
# ! Can't query fields.
# Caused by error:
# ! rapi_prepare: Failed to prepare query SELECT *
# FROM species AS q01
# WHERE (0 = 1)
# Error: Catalog Error: Table with name species does not exist!
# Did you mean "pg_views"?
# LINE 2: FROM species AS q01
# ^
# ---
# Backtrace:
# ▆
# 1. ├─rfishbase::distribution(species_list = NULL, server = "fishbase")
# 2. │ └─rfishbase::faoareas(...)
# 3. │ ├─... %>% dplyr::collect()
# 4. │ └─rfishbase:::species_subset(...)
# 5. │ ├─... %>% collect()
# 6. │ ├─dplyr::select(...)
# 7. │ ├─dplyr::tbl(db, "species")
# 8. │ ├─duckdb:::tbl.duckdb_connection(db, "species")
# 9. │ ├─base::NextMethod("tbl")
# 10. │ └─dplyr:::tbl.DBIConnection(db, "species")
# 11. │ ├─dplyr::tbl(...)
# 12. │ └─dbplyr:::tbl.src_dbi(...)
# 13. │ └─dbplyr::tbl_sql(c(subclass, "dbi"), src = src, from = from, ...)
# 14. │ ├─vars %||% dbplyr_query_fields(src$con, from_sql)
# 15. │ └─dbplyr:::dbplyr_query_fields(src$con, from_sql)
# 16. │ └─dbplyr:::dbplyr_fallback(con, "db_query_fields", ...)
# 17. │ ├─rlang::eval_bare(expr((!!fun)(con, ...)))
# 18. │ └─dbplyr:::db_query_fields.DBIConnection(con, ...)
# 19. ├─dplyr::collect(.)
# 20. ├─dplyr::collect(.)
# 21. ├─dplyr::select(., "SpecCode", Species = sci_name)
# 22. └─dplyr::mutate(., sci_name = paste(Genus, Species))
# Run rlang::last_trace(drop = FALSE) to see 6 hidden frames.r = rfishbase::distribution(species_list = "Ablennes hians", server = "fishbase")
# Error in `db_query_fields.DBIConnection()`:
# ! Can't query fields.
# Caused by error:
# ! rapi_prepare: Failed to prepare query SELECT *
# FROM species AS q01
# WHERE (0 = 1)
# Error: Catalog Error: Table with name species does not exist!
# Did you mean "pg_views"?
# LINE 2: FROM species AS q01
# ^
# Run `rlang::last_trace()` to see where the error occurred.sessionInfo()
# R version 4.2.2 (2022-10-31)
# Platform: x86_64-conda-linux-gnu (64-bit)
# Running under: Rocky Linux 8.8 (Green Obsidian)
#
# Matrix products: default
# BLAS/LAPACK: /mnt/modules/bin/dada2/1.26/lib/libopenblasp-r0.3.21.so
#
# 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
#
# attached base packages:
# [1] stats graphics grDevices utils datasets methods base
#
# other attached packages:
# [1] reprex_2.0.2 refdbtools_0.1.0 dplyr_1.1.2
#
# loaded via a namespace (and not attached):
# [1] httr_1.4.4 pkgload_1.3.2 contentid_0.0.18 bit64_4.0.5
# [5] vroom_1.6.3 jsonlite_1.8.4 rfishbase_4.1.2 brio_1.1.3
# [9] shiny_1.7.4 assertthat_0.2.1 askpass_1.1 yaml_2.3.7
# [13] remotes_2.4.2 progress_1.2.2 sessioninfo_1.2.2 charlier_0.1
# [17] pillar_1.9.0 glue_1.6.2 digest_0.6.31 promises_1.2.0.1
# [21] htmltools_0.5.4 httpuv_1.6.8 clipr_0.8.0 XML_3.99-0.16.1
# [25] pkgconfig_2.0.3 devtools_2.4.5 purrr_1.0.1 xtable_1.8-4
# [29] processx_3.8.0 later_1.3.0 tzdb_0.4.0 tibble_3.2.1
# [33] openssl_2.0.5 generics_0.1.3 usethis_2.1.6 ellipsis_0.3.2
# [37] cachem_1.0.6 withr_2.5.0 cli_3.6.1 magrittr_2.0.3
# [41] crayon_1.5.2 mime_0.12 memoise_2.0.1 evaluate_0.20
# [45] ps_1.7.2 fs_1.6.0 fansi_1.0.4 xml2_1.3.3
# [49] pkgbuild_1.4.0 profvis_0.3.7 tools_4.2.2 prettyunits_1.1.1
# [53] hms_1.1.3 lifecycle_1.0.3 stringr_1.5.0 callr_3.7.3
# [57] compiler_4.2.2 duckdb_0.9.2-1 rlang_1.1.3 rstudioapi_0.14
# [61] htmlwidgets_1.6.1 miniUI_0.1.1.1 rmarkdown_2.20 testthat_3.1.6
# [65] rentrez_1.2.3 DBI_1.1.3 roxygen2_7.2.3 curl_5.0.0
# [69] R6_2.5.1 knitr_1.42 bit_4.0.5 fastmap_1.1.0
# [73] utf8_1.2.2 commonmark_1.8.1 rprojroot_2.0.3 readr_2.1.5
# [77] desc_1.4.2 stringi_1.7.12 parallel_4.2.2 Rcpp_1.0.10
# [81] vctrs_0.6.2 dbplyr_2.3.0 tidyselect_1.2.0 xfun_0.36
# [85] urlchecker_1.0.1 
JustinHinLo
Error in
db_query_fields.DBIConnection(): ! Can't query fields. Caused by error: ! rapi_prepare: Failed to prepare query SELECT * FROM species AS q01 WHERE (0 = 1) Error: Catalog Error: Table with name species does not exist! Did you mean "pg_views"? LINE 2: FROM species AS q01 ^ Runrlang::last_trace()to see where the error occurred.