rfishbase length-weight function doesn't work anymore

[EmanueleAsciutto]

Hello everyone! I'm kinda new in RStudio and I'm currently using rfishbase as support to reconstruct fishes length-weight relationships. I've recently updated R to version 4.2.2 and reinstalled rfishbase (version 4.0.0). Sadly, when I search for some data, as you can see in the code, rfishbase stops working as it did before the updates I've done. What I'm doing is just calling for the package and search the species I'm looking for, but it seems like RStudio just can't create anymore the dataset with the retrieved information. It stalls while working and if I hit the "stop" button sometimes it gives me the error I pasted below, then I have to restart RStudio because it crashes. I have no idea what can be the issue and how to fix it! Thanks a lot in advance :)

PS: I tried to install the rfisbase package bot with "remotes::install_github("ropensci/rfishbase")" and "install.packages("rfishbase")", same problem as described above.

My session info: R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

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

My code:

library(rfishbase)
length_weight("Dicentrarchus labrax")

#2: Error in curl::curl_fetch_memory(file, handle): Timeout was reached: [hash-archive.org] Connection timed out after 10003 milliseconds

[cboettig]

Thanks for the report, we'll check this out.

[cboettig]

hmm, can't reproduce this. Can you confirm the version of contentid is 0.0.15? Can you try and reproduce this error again?

[EmanueleAsciutto]

hmm, can't reproduce this. Can you confirm the version of contentid is 0.0.15? Can you try and reproduce this error again?

Hello, yes I confirm contentid is 0.0.15 as you can see in the SessionInfo summary below (4th column, 2nd row). I've tried to delete and reinstall the package again allowing R to do the suggested uploads, but still all the process stalls after calling for the length-weight function, returning the same error as reported in my first message. Can I provide some more helpful information somehow? If yes, could you please explain in an easy way how to do so? I'm sorry but I'm really new in RStudio universe! Thanks a lot for your interest.

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

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    

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

other attached packages:
[1] rfishbase_4.0.0

loaded via a namespace (and not attached):
 [1] pillar_1.8.1      compiler_4.2.2    dbplyr_2.2.1      prettyunits_1.1.1
 [5] tools_4.2.2       progress_1.2.2    bit_4.0.5         **_contentid_0.0.15_** 
 [9] jsonlite_1.8.3    memoise_2.0.1     lifecycle_1.0.3   tibble_3.1.8     
[13] pkgconfig_2.0.3   rlang_1.0.6       DBI_1.1.3         cli_3.4.1        
[17] rstudioapi_0.14   parallel_4.2.2    curl_4.3.3        fastmap_1.1.0    
[21] withr_2.5.0       duckdb_0.6.0      dplyr_1.0.10      httr_1.4.4       
[25] stringr_1.4.1     generics_0.1.3    fs_1.5.2          vctrs_0.5.1      
[29] askpass_1.1       hms_1.1.2         bit64_4.0.5       tidyselect_1.2.0 
[33] glue_1.6.2        R6_2.5.1          fansi_1.0.3       vroom_1.6.0      
[37] purrr_0.3.5       readr_2.1.3       tzdb_0.3.0        magrittr_2.0.3   
[41] ellipsis_0.3.2    assertthat_0.2.1  archive_1.1.5     utf8_1.2.2       
[45] stringi_1.7.8     openssl_2.0.4     cachem_1.0.6      crayon_1.5.2

[gustavdelius]

I had the same problem. There is something wrong with the version of the contentid package on CRAN. You need to install it from Github with

remotes::install_github("cboettig/contentid")

Restart RStudio after that to make sure it loads the new version.

[cboettig]

Thanks @gustavdelius for confirming. We'll see if we can get a new contentid onto CRAN ASAP

[cboettig]

contentid 0.0.16 is now on CRAN

[cboettig]

please feel free to re-open or comment if this does not resolve the issue.