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ropensci / rfishbase

R interface to the fishbase.org database
https://docs.ropensci.org/rfishbase
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issues with validate_names #266

Open danagrieco opened 1 year ago

danagrieco commented 1 year ago

Hi rfishbase,

I'm having an issue with the validate_names, and I can't seem to figure it out. I ran the code about two weeks ago, and was able to use validate_names with my dataset, and it worked perfectly. Now, before even getting to my dataset, I try to run the simple code, below, to make sure validate names is working, and it produces the following error, below:

validate_names("Abramites ternetzi")

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>

Backtrace: x

  1. +-rfishbase::validate_names("Abramites ternetzi")
  2. | +-... %>% dplyr::pull(Species)
  3. | -rfishbase::synonyms(...)
  4. | +-... %>% ...
  5. | -rfishbase::fb_tbl("synonyms", server, version, db)
  6. | -rfishbase::fb_import(server, version, db, tbl)
  7. | +-rfishbase:::parse_prov(read_prov(server), version)
  8. | | +-base::withVisible(eval(mc, parent.frame()))
  9. | | -base::eval(mc, parent.frame())
  10. | | -base::eval(mc, parent.frame())
  11. | -rfishbase (local) <fn>(prov = read_prov(server), version = version)
  12. | -tibble::tibble(...)
  13. | -tibble:::tibble_quos(xs, .rows, .name_repair)
  14. | -rlang::eval_tidy(xs[[j]], mask)
  15. +-dplyr::pull(., Species)
  16. +-dplyr::left_join(x = tmp, y = ., by = "synonym")
  17. +-dplyr:::left_join.data.frame(x = tmp, y = ., by = "synonym")
  18. | -dplyr::auto_copy(x, y, copy = copy)
  19. | +-dplyr::same_src(x, y)
  20. | -dplyr:::same_src.data.frame(x, y)
  21. | -base::is.data.frame(y)
  22. +-dplyr::distinct(.)
  23. +-dplyr::select(., synonym, Species)
  24. +-dplyr::ungroup(.)
  25. +-dplyr::filter(., !is.na(Species))
  26. +-dplyr::group_by(., synonym)
  27. +-dplyr::mutate(...)
  28. +-dplyr::collect(.)
  29. +-dplyr::select(...)
  30. +-dplyr::mutate(., synonym = paste(SynGenus, SynSpecies))
  31. +-purrr::map_chr(meta, "encodingFormat", .default = NA)
  32. | -purrr:::map_("character", .x, .f, ..., .progress = .progress)
  33. | +-purrr:::with_indexed_errors(...)
  34. | | -base::withCallingHandlers(...)
  35. | -purrr:::call_with_cleanup(...)
  36. -base::.handleSimpleError(...)
  37. -purrr (local) h(simpleError(msg, call))
  38. -cli::cli_abort(...)
  39. -rlang::abort(...)>
cboettig commented 1 year ago

Please try updating to the most recent version?

On Thu, Jun 8, 2023 at 6:22 PM Dana I Grieco @.***> wrote:

Hi rfishbase,

I'm having an issue with the validate_names, and I can't seem to figure it out. I ran the code about two weeks ago, and was able to use validate_names with my dataset, and it worked perfectly. Now, before even getting to my dataset, I try to run the simple code, below, to make sure validate names is working, and it produces the following error, below:

validate_names("Abramites ternetzi")

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>

Backtrace: x

  1. +-rfishbase::validate_names("Abramites ternetzi")

  2. | +-... %>% dplyr::pull(Species)

  3. | -rfishbase::synonyms(...)

  4. | +-... %>% ...

  5. | -rfishbase::fb_tbl("synonyms", server, version, db)

  6. | -rfishbase::fb_import(server, version, db, tbl)

  7. | +-rfishbase:::parse_prov(read_prov(server), version)

  8. | | +-base::withVisible(eval(mc, parent.frame()))

  9. | | -base::eval(mc, parent.frame())

  10. | | -base::eval(mc, parent.frame())

  11. | -rfishbase (local) (prov = read_prov(server), version = version)

  12. | -tibble::tibble(...)

  13. | -tibble:::tibble_quos(xs, .rows, .name_repair)

  14. | -rlang::eval_tidy(xs[[j]], mask)

  15. +-dplyr::pull(., Species)

  16. +-dplyr::left_join(x = tmp, y = ., by = "synonym")

  17. +-dplyr:::left_join.data.frame(x = tmp, y = ., by = "synonym")

  18. | -dplyr::auto_copy(x, y, copy = copy)

  19. | +-dplyr::same_src(x, y)

  20. | -dplyr:::same_src.data.frame(x, y)

  21. | -base::is.data.frame(y)

  22. +-dplyr::distinct(.)

  23. +-dplyr::select(., synonym, Species)

  24. +-dplyr::ungroup(.)

  25. +-dplyr::filter(., !is.na(Species))

  26. +-dplyr::group_by(., synonym)

  27. +-dplyr::mutate(...)

  28. +-dplyr::collect(.)

  29. +-dplyr::select(...)

  30. +-dplyr::mutate(., synonym = paste(SynGenus, SynSpecies))

  31. +-purrr::map_chr(meta, "encodingFormat", .default = NA)

  32. | -purrr:::map_("character", .x, .f, ..., .progress = .progress)

  33. | +-purrr:::with_indexed_errors(...)

  34. | | -base::withCallingHandlers(...)

  35. | -purrr:::call_with_cleanup(...)

  36. -base::.handleSimpleError(...)

  37. -purrr (local) h(simpleError(msg, call))

  38. -cli::cli_abort(...)

  39. -rlang::abort(...)>

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sollucas commented 1 year ago

Hi, I'm also having a problem with validate_names as well. I've updated both the package and R today - I'd last run the code in May and it had worked then. Any advice on the following error appreciated:

validate_names("Abramites ternetzi")

Error in (function (cond) : error in evaluating the argument 'conn' in selecting a method for function 'dbListTables': [UNKNOWN] Failed to stat ':memory:': unknown error

cboettig commented 1 year ago

@sollucas sorry but I'm unable to reproduce the behavior you're seeing. Can you try first purging the cache:

 rfishbase::db_dir()  |> unlink()

Can you please provide more information, including sessionInfo() output after loading rfishbase?

please ensure related dependencies are up-to-date -- eg. consider using pak::pkg_install("rfishbase", upgrade=TRUE).

sollucas commented 1 year ago

Thanks for the response - I've tried the suggestions and unfortunately still getting the same error:

rfishbase::db_dir()  |> unlink()

Warning message: R graphics engine version 16 is not supported by this version of RStudio. The Plots tab will be disabled until a newer version of RStudio is installed. 

library(rfishbase) 
sessionInfo()

R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 [4] LC_NUMERIC=C LC_TIME=English_United Kingdom.1252

time zone: Europe/London tzcode source: internal

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

other attached packages: [1] rfishbase_4.1.2

loaded via a namespace (and not attached): [1] crayon_1.5.2 vctrs_0.6.3 cli_3.6.1 rlang_1.1.1 xfun_0.39 stringi_1.7.12 DBI_1.1.3 purrr_1.0.1
[9] generics_0.1.3 glue_1.6.2 prettyunits_1.1.1 dbplyr_2.3.2 tinytex_0.45 hms_1.1.3 fansi_1.0.4 tibble_3.2.1
[17] tzdb_0.4.0 progress_1.2.2 lifecycle_1.0.3 stringr_1.5.0 compiler_4.3.1 dplyr_1.1.2 fs_1.6.2 pkgconfig_2.0.3
[25] rstudioapi_0.14 R6_2.5.1 readr_2.1.4 tidyselect_1.2.0 utf8_1.2.3 pillar_1.9.0 magrittr_2.0.3 tools_4.3.1 

pak::pkg_install("rfishbase", upgrade=TRUE)

✔ Loading metadata database ... done

ℹ No downloads are needed ✔ 1 pkg + 47 deps: kept 48 [27.6s]

library(rfishbase)
validate_names("Abramites ternetzi")

Error in (function (cond) : error in evaluating the argument 'conn' in selecting a method for function 'dbListTables': [UNKNOWN] Failed to stat ':memory:': unknown error

cboettig commented 1 year ago

note taht you will need to restart R after installing/upgrade packages. I'm very confused why certain packages are not being listed in your sessionInfo() : in particular, duckdb is a required package for rfishbase and I don't see it there....

can you try installing and loading duckdb manually first?

cboettig commented 1 year ago

(aside, but is your RStudio version up-to-date as well?)

sollucas commented 1 year ago

Updated R Studio today (version 2023.06.0) R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" Manually installed 2 missing packages: duckdb and contentid. Restarted my laptop after updating/installing the above and have tried restarting R sessions, with the same error appearing:

library(rfishbase) 
library(duckdb)
library(contentid)
sessionInfo()

R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

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

time zone: Europe/London tzcode source: internal

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

other attached packages: [1] contentid_0.0.17 duckdb_0.8.1 DBI_1.1.3 rfishbase_4.1.2

loaded via a namespace (and not attached): [1] jsonlite_1.8.5 dplyr_1.1.2 compiler_4.3.1 crayon_1.5.2
[5] tidyselect_1.2.0 stringr_1.5.0 progress_1.2.2 fastmap_1.1.1
[9] readr_2.1.4 R6_2.5.1 generics_0.1.3 curl_5.0.1
[13] tibble_3.2.1 openssl_2.0.6 pillar_1.9.0 tzdb_0.4.0
[17] rlang_1.1.1 utf8_1.2.3 cachem_1.0.8 stringi_1.7.12
[21] fs_1.6.2 memoise_2.0.1 cli_3.6.1 magrittr_2.0.3
[25] rstudioapi_0.14 dbplyr_2.3.2 hms_1.1.3 askpass_1.1
[29] lifecycle_1.0.3 prettyunits_1.1.1 vctrs_0.6.3 glue_1.6.2
[33] fansi_1.0.4 purrr_1.0.1 httr_1.4.6 tools_4.3.1
[37] pkgconfig_2.0.3 

validate_names("Abramites ternetzi")

Error in (function (cond) : error in evaluating the argument 'conn' in selecting a method for function 'dbListTables': [UNKNOWN] Failed to stat ':memory:': unknown error

sollucas commented 1 year ago

Hi again - I copied my files to a different drive and am no longer getting the error. Apologies, think this was an issue with the original drive I was using. Thanks very much for your help!