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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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cannot execute estimate function #265

Open charles-patrick-lavin opened 1 year ago

charles-patrick-lavin commented 1 year ago

Hello all - I have utilised the estimate function for over a year now.

As of today, I am unable to perform the estimate function, receiving the following error:

code

SAU_FB <- rfishbase::estimate(species_list = SAU_final_spp$scientific_name)

Error in purrr::map_chr(): ℹ In index: 1. Caused by error: ! Result must be length 1, not 2. Run rlang::last_trace() to see where the error occurred.

rlang::last_trace() <error/purrr_error_indexed> Error in purrr::map_chr(): ℹ In index: 1. Caused by error: ! Result must be length 1, not 2.

Backtrace: ▆

  1. ├─rfishbase::estimate(species_list = SAU_final_spp$scientific_name)
  2. │ ├─fb_tbl(endpt, server, version, db) %>% fix_ids()
  3. │ └─rfishbase::fb_tbl(endpt, server, version, db)
  4. │ └─rfishbase::fb_import(server, version, db, tbl)
  5. │ ├─rfishbase:::parse_prov(read_prov(server), version)
  6. │ │ ├─base::withVisible(eval(mc, parent.frame()))
  7. │ │ └─base::eval(mc, parent.frame())
  8. │ │ └─base::eval(mc, parent.frame())
  9. │ └─rfishbase (local) <fn>(prov = read_prov(server), version = version)
  10. │ └─tibble::tibble(...)
  11. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
  12. │ └─rlang::eval_tidy(xs[[j]], mask)
  13. ├─rfishbase:::fix_ids(.)
  14. │ ├─"Speccode" %in% colnames(full_data)
  15. │ └─base::colnames(full_data)
  16. │ └─base::is.data.frame(x)
  17. └─purrr::map_chr(meta, "encodingFormat", .default = NA)
  18. └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
  19. ├─purrr:::with_indexed_errors(...)
  20. │ └─base::withCallingHandlers(...)
  21. └─purrr:::call_with_cleanup(...) Run rlang::last_trace(drop = FALSE) to see 4 hidden frames.

here is the sessionInfo

sessionInfo() R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19045)

Matrix products: default

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

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

other attached packages: [1] factoextra_1.0.7 FactoMineR_2.4 segmented_1.6-0 nlme_3.1-160 MASS_7.3-58.1 ggpmisc_0.5.0
[7] ggpp_0.4.5 ggpubr_0.4.0 corrplot_0.92 worrms_0.4.2 rfishbase_4.1.1 caTools_1.18.2
[13] car_3.1-0 carData_3.0-5 data.table_1.14.2 plyr_1.8.8 forcats_0.5.1 stringr_1.4.0
[19] dplyr_1.0.9 readr_2.1.2 tidyr_1.2.0 tibble_3.1.7 ggplot2_3.4.1 tidyverse_1.3.1
[25] purrr_1.0.1

loaded via a namespace (and not attached): [1] bitops_1.0-7 fs_1.5.2 lubridate_1.9.2 progress_1.2.2 httr_1.4.5
[6] tools_4.2.2 backports_1.4.1 utf8_1.2.2 R6_2.5.1 DT_0.23
[11] DBI_1.1.3 colorspace_2.0-3 withr_2.5.0 tidyselect_1.2.0 prettyunits_1.1.1
[16] compiler_4.2.2 cli_3.6.1 rvest_1.0.2 quantreg_5.93 flashClust_1.01-2
[21] SparseM_1.81 xml2_1.3.3 scales_1.2.1 digest_0.6.29 pkgconfig_2.0.3
[26] htmltools_0.5.4 dbplyr_2.2.1 fastmap_1.1.0 htmlwidgets_1.5.4 rlang_1.1.0
[31] readxl_1.4.0 rstudioapi_0.14 generics_0.1.3 jsonlite_1.8.2 magrittr_2.0.3
[36] leaps_3.1 Matrix_1.5-1 Rcpp_1.0.10 munsell_0.5.0 fansi_1.0.3
[41] abind_1.4-5 lifecycle_1.0.3 scatterplot3d_0.3-41 stringi_1.7.6 grid_4.2.2
[46] ggrepel_0.9.1 crayon_1.5.1 lattice_0.20-45 haven_2.5.0 splines_4.2.2
[51] hms_1.1.1 pillar_1.8.1 ggsignif_0.6.3 reprex_2.0.1 glue_1.6.2
[56] modelr_0.1.8 vctrs_0.5.0 tzdb_0.3.0 MatrixModels_0.5-0 cellranger_1.1.0
[61] gtable_0.3.2 assertthat_0.2.1 cachem_1.0.6 broom_0.8.0 rstatix_0.7.0
[66] survival_3.4-0 memoise_2.0.1 cluster_2.1.4 timechange_0.2.0 ellipsis_0.3.2

Does anyone know how I can address this? Many thanks for your time.

cboettig commented 1 year ago

apologies, we're in the middle of the new deploy and waiting for the next version to hit CRAN. can you try:

remotes::install_github("ropensci/rfishbase")

restart R and try again?

Thanks for the bug report!

Nicolescm commented 1 year ago

apologies, we're in the middle of the new deploy and waiting for the next version to hit CRAN. can you try:

remotes::install_github("ropensci/rfishbase")

restart R and try again?

Thanks for the bug report!

I had the same issue, but the reinstallation worked! Thanks

charles-patrick-lavin commented 1 year ago

Thank you all for your rapid response. Everything is working after reinstallation. Also many thanks for wonderful rfishbase!