Problem with version 5.0 of the package

[EmanueleAsciutto]

Hello everyone!
I'm posting this just to share awareness for other fellow users of rfishbase package.
I had to reinstall RStudio in my PC (OS Windows 11, Version 24H2) and, somehow, the rfishbase version 5.0.0 is giving me some problems. It does not matter what line of code I try to run, the console always returns this error message:

df <- length_weight("Coris julis")

Error in `duckdb_result()`:
! rapi_execute: Failed to run query
Error: HTTP Error: Failed to download extension "httpfs" at URL "http://nightly-extensions.duckdb.org/v1.1.3/windows_amd64_rtools/httpfs.duckdb_extension.gz" (HTTP 403)
Extension "httpfs" is an existing extension.
Run `rlang::last_trace()` to see where the error occurred.

Here some session info:

> sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default


locale:
[1] LC_COLLATE=Italian_Italy.utf8  LC_CTYPE=Italian_Italy.utf8   
[3] LC_MONETARY=Italian_Italy.utf8 LC_NUMERIC=C                  
[5] 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] rfishbase_4.1.2 lubridate_1.9.4 forcats_1.0.0   stringr_1.5.1   dplyr_1.1.4    
 [6] purrr_1.0.2     readr_2.1.5     tidyr_1.3.1     tibble_3.2.1    ggplot2_3.5.1  
[11] tidyverse_2.0.0

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.9    gtable_0.3.6      crayon_1.5.3      compiler_4.4.2    tidyselect_1.2.1 
 [6] progress_1.2.3    scales_1.3.0      fastmap_1.2.0     R6_2.5.1          generics_0.1.3   
[11] curl_6.0.1        openssl_2.2.2     munsell_0.5.1     DBI_1.2.3         pillar_1.9.0     
[16] tzdb_0.4.0        rlang_1.1.4       utf8_1.2.4        cachem_1.1.0      stringi_1.8.4    
[21] fs_1.6.5          memoise_2.0.1     timechange_0.3.0  cli_3.6.3         withr_3.0.2      
[26] magrittr_2.0.3    grid_4.4.2        rstudioapi_0.17.1 dbplyr_2.5.0      askpass_1.2.1    
[31] hms_1.1.3         lifecycle_1.0.4   prettyunits_1.2.0 vctrs_0.6.5       glue_1.8.0       
[36] duckdb_1.1.3-1    contentid_0.0.18  fansi_1.0.6       colorspace_2.1-1  httr_1.4.7       
[41] tools_4.4.2       pkgconfig_2.0.3  

I tried to install RTools, all the newest versions of this "duckdb" package, the ultra-latest version of rfishbase 5.0.1 and other nerdish things; however, this message always pops out.

The only way to make rfishbase work again has been to install a previous version of the package (i.e. version 4.1.2 from CRAN Archives).

It's not a problem for me to use this old version of the package, however I thought it might be useful to report this issue.

Is maybe something related to new updates conflicts?

Hoping to have been helpful!

[cboettig]

Thanks for reporting.

What version of duckdbfs are you running? (I don't see it in your namespace, but it's hard dependency of rfishbase 5.0. You've shown the sessionInfo with rfishbase 4.1.2 loaded, which doesn't give me the information I need to debug).

duckdb has been mucking around a bit with the extensions in recent versions. Can you report sessionInfo() of the setup that throws the error with the latest version of duckdbfs and rfishbase from CRAN?

Also, can you try setting:

options("duckdbfs_use_nightly" = TRUE)

and

options("duckdbfs_use_nightly" = FALSE)

and see if either of these addresses what you see?

[EmanueleAsciutto]

Hello again!
Quick update:

options("duckdbfs_use_nightly" = FALSE)

worked for me and it seems that rfishbase 5.0.0 is now running quite properly!

just for completeness:
rfishbase version 5.0.0
duckdbfs version 0.0.8

I remain available for further information, if needed.

Thank you for your help!