The version 5 does not support old mac anymore.

[kbubio]

I updated Rfishbase to version 5.0.0, but every time I tried to execute it, I ran into an issue with the DuckDB package related to the httpfs extension. It turns out that the latest version of DuckDB with httpfs support only works on macOS versions 13.0 or higher. Unfortunately, I’m still using macOS 11.0 (Big Sur).

After two days of attempting and failing to downgrade httpfs and struggling with compatibility issues, I’ve had to roll back to the previous version of Rfishbase (4.1.2), which works perfectly fine for now.

I’m sharing this here to raise awareness for those of us still on older Macs.

[cboettig]

apologies, I think this is a temporary issue with duckdb extensions --

Can you try:

remotes::install_github("cboettig/duckdbfs")

then restart R and try again?

And thanks for opening an issue to report this!

[jjacquemont]

Have been running into the same issue (also using macOS 11.0). Tried to run remotes::install_github("cboettig/duckdbfs") but that did not fix the issue.

[cboettig]

@jjacquemont I know this is frustrating but it really helps if you can give details from the error message. I don't think this is a mac issue, and we've seen several different things that can go wrong for users between version 4 and 5.

Please provide the error log you see, along with the contents of sessionInfo() after creating the error and I'll take a look?

[jjacquemont]

Thanks for reaching out! I ended up updating my OS to v15 and that fixed the issue.

[kbubio]

I did the remote but nothing works !

after running species() I 've got

Error in duckdb_result():
! rapi_execute: Failed to run query
Error: IO Error: Extension "/Users/kbubio/Library/Application Support/org.R-project.R/R/duckdb/extensions/v1.1.3/osx_amd64/httpfs.duckdb_extension" could not be loaded: dlopen(/Users/kbubio/Library/Application Support/org.R-project.R/R/duckdb/extensions/v1.1.3/osx_amd64/httpfs.duckdb_extension, 6): Symbol not found: __ZNKSt3__115basic_stringbufIcNS_11char_traitsIcEENS_9allocatorIcEEE3strEv
Referenced from: /Users/kbubio/Library/Application Support/org.R-project.R/R/duckdb/extensions/v1.1.3/osx_amd64/httpfs.duckdb_extension (which was built for Mac OS X 13.3)
Expected in: /usr/lib/libc++.1.dylib
Run rlang::last_trace() to see where the error occurred.

sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-apple-darwin20
Running under: macOS Big Sur 11.7.10

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London
tzcode source: internal

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

other attached packages:
[1] tidyr_1.3.1 rfishbase_5.0.1

loaded via a namespace (and not attached):
[1] R6_2.5.1 tidyselect_1.2.1 magrittr_2.0.3 remotes_2.5.0 glue_1.8.0 stringr_1.5.1 tibble_3.2.1
[8] pkgconfig_2.0.3 duckdbfs_0.0.9 dplyr_1.1.4 generics_0.1.3 lifecycle_1.0.4 cli_3.6.3 DBI_1.2.3
[15] vctrs_0.6.5 renv_1.0.11 compiler_4.4.2 httr_1.4.7 purrr_1.0.2 tools_4.4.2 curl_6.1.0
[22] pillar_1.10.1 duckdb_1.1.3-1 fs_1.6.5 jsonlite_1.8.9 rlang_1.1.4 stringi_1.8.4

[kbubio]

And I am so sorry to say that now my mac is old and can't update anymore, any help?

[cboettig]

this seems to be the case with duckdb extension for older macs stuck on OS X 11. still investigating, I don't have a mac.

Can you test with:

duckdbfs::open_dataset("https://huggingface.co/datasets/cboettig/fishbase/resolve/main/data/fb/v24.07/parquet/species.parquet")

[cboettig]

(and apologies, it's frustrating when Apple no longer provides support for perfectly functional hardware. you could consider running linux on your old intel mac if you want to keep the hardware functional beyond Apple's support period).