Unable to get ecosystems using sealifebase server

[matteoloschi]

Hi,

I am writing to signal a problem using sealifebase as server in ecosystem() and species_by_ecosystem() functions. For example:

library(rfishbase)

ecosystem(server="sealifebase")
Error in `dplyr::collect()`:
! Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! String contains null byte
Run `rlang::last_trace()` to see where the error occurred.

However, there is no error message using fishbase:

ecosystem(server="fishbase")
Joining with `by = join_by(Subfamily, GenCode, FamCode)`
Joining with `by = join_by(FamCode)`
Joining with `by = join_by(Order, Ordnum, Class, ClassNum)`
Joining with `by = join_by(Class, ClassNum)`
Joining with `by = join_by(SpecCode)`
# A tibble: 0 × 101
# ℹ 101 variables: autoctr <int>, E_CODE <int>, EcosystemRefno <int>, SpecCode <int>, Stockcode <int>, Status <chr>,
#   CurrentPresence <chr>, Abundance <chr>, LifeStage <chr>, Remarks.x <chr>, Entered.x <int>, DateEntered.x <dttm>,
#   Modified.x <int>, DateModified.x <dttm>, Expert.x <int>, DateChecked.x <dttm>, WebURL <chr>, TS.x <dttm>,
#   Species <chr>, EcosystemName <chr>, EcosystemType <chr>, MEOW <int>, LME <int>, MPA <int>, E_CODE_Large <int>,
#   E_CODE_Larger <int>, E_CODE_Largest <int>, E_CODE_Ecoregion <int>, MEOWCode <int>, MEOWLevel <chr>, Ready <int>,
#   OtherNames <chr>, Location <chr>, LocationMap <chr>, MapRef <int>, Salinity <chr>, RiverLength <int>, Area <int>,
#   SizeRef <int>, DrainageArea <int>, NorthernLat <int>, NrangeNS <chr>, SouthernLat <int>, SrangeNS <chr>, …
# ℹ Use `colnames()` to see all variable names

Similarly, following the example in the reference manual https://cran.r-project.org/web/packages/rfishbase/rfishbase.pdf#page=38 an error message is returned:

species_by_ecosystem(ecosystem = "Arctic", server = "sealifebase")
Error in `dplyr::collect()`:
! Failed to collect lazy table.
Caused by error in `duckdb_result()`:
! String contains null byte
Run `rlang::last_trace()` to see where the error occurred.

How can this be solved?

Thank you in advance

Session info

R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Italian_Italy.utf8  LC_CTYPE=Italian_Italy.utf8    LC_MONETARY=Italian_Italy.utf8
[4] LC_NUMERIC=C                   LC_TIME=Italian_Italy.utf8    

time zone: Europe/Rome
tzcode source: internal

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

other attached packages:
[1] dplyr_1.1.4     rfishbase_5.0.1

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5      httr_1.4.7       cli_3.6.3        rlang_1.1.4      stringi_1.8.4    DBI_1.2.3       
 [7] purrr_1.0.2      generics_0.1.3   duckdbfs_0.0.9   jsonlite_1.8.9   glue_1.8.0       dbplyr_2.5.0    
[13] tibble_3.2.1     fastmap_1.2.0    lifecycle_1.0.4  memoise_2.0.1    duckdb_1.1.3-1   stringr_1.5.1   
[19] compiler_4.4.2   blob_1.2.4       fs_1.6.5         pkgconfig_2.0.3  R6_2.5.1         utf8_1.2.4      
[25] tidyselect_1.2.1 pillar_1.10.1    curl_6.1.0       magrittr_2.0.3   withr_3.0.2      tools_4.4.2     
[31] cachem_1.1.0