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issues with validate_names #266

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danagrieco opened this issue Jun 8, 2023 · 8 comments
Open

issues with validate_names #266

danagrieco opened this issue Jun 8, 2023 · 8 comments

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@danagrieco
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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
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cboettig commented Jun 8, 2023 via email

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

@sollucas
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sollucas commented Jul 4, 2023

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
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sollucas commented Jul 6, 2023

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!

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@cboettig @danagrieco @sollucas