Install log for 'ragnar'

* installing *source* package ‘ragnar’ ...
** this is package ‘ragnar’ version ‘0.3.0’
** package ‘ragnar’ successfully unpacked and MD5 sums checked
** using staged installation
Downloading uv...Done!
Downloading cpython-3.12.13-linux-x86_64-gnu (download) (32.6MiB)
 Downloaded cpython-3.12.13-linux-x86_64-gnu (download)
Downloading cryptography (4.5MiB)
Downloading pandas (10.5MiB)
Downloading lxml (5.0MiB)
Downloading numpy (15.9MiB)
Downloading pypdfium2 (3.5MiB)
Downloading onnxruntime (18.3MiB)
Downloading speechrecognition (31.3MiB)
Downloading pillow (6.6MiB)
Downloading pdfminer-six (6.3MiB)
Downloading youtube-transcript-api (2.1MiB)
Downloading magika (14.7MiB)
 Downloaded youtube-transcript-api
 Downloaded pypdfium2
 Downloaded cryptography
 Downloaded lxml
 Downloaded pdfminer-six
 Downloaded pillow
 Downloaded pandas
 Downloaded magika
 Downloaded numpy
 Downloaded speechrecognition
 Downloaded onnxruntime
Installed 48 packages in 198ms
python:         /data/gannet/ripley/.cache/R/reticulate/uv/cache/archive-v0/3iZAlJ8EpDORCOrQ/bin/python
libpython:      /data/gannet/ripley/.cache/R/reticulate/uv/python/cpython-3.12.13-linux-x86_64-gnu/lib/libpython3.12.so
pythonhome:     /data/gannet/ripley/.cache/R/reticulate/uv/cache/archive-v0/3iZAlJ8EpDORCOrQ:/data/gannet/ripley/.cache/R/reticulate/uv/cache/archive-v0/3iZAlJ8EpDORCOrQ
virtualenv:     /data/gannet/ripley/.cache/R/reticulate/uv/cache/archive-v0/3iZAlJ8EpDORCOrQ/bin/activate_this.py
version:        3.12.13 (main, Jul 18 2026, 17:02:19) [Clang 22.1.3 ]
numpy:          /data/gannet/ripley/.cache/R/reticulate/uv/cache/archive-v0/3iZAlJ8EpDORCOrQ/lib/python3.12/site-packages/numpy
numpy_version:  2.5.1

NOTE: Python version was forced by py_require()
Module(markitdown)
duckdb is storing downloaded extensions and secrets under ~/.duckdb:
ℹ /data/gannet/ripley/.duckdb
This persists across sessions and is shared with the DuckDB CLI and other clients.
ℹ Run duckdb(shared_home = FALSE) to use a temporary directory instead.
ℹ See ?duckdb_storage for details and alternatives.
duckdb was built with libc++ (not libstdc++) on Linux, so DuckDB extensions are disabled:
• Loading a prebuilt (libstdc++) extension could crash R (https://github.com/duckdb/duckdb-r/issues/1107).
• INSTALL/LOAD of an extension will error, and automatic extension loading is off.
ℹ Pass duckdb(allow_extensions = FALSE) to accept this and silence this message.
ℹ Pass duckdb(allow_extensions = TRUE) to attempt loading anyway (may crash R).
ℹ See ?duckdb for details.
Error in `dbSendQuery()`:
! DuckDB extension loading (INSTALL / LOAD) is disabled for this driver.
ℹ Recreate the driver with duckdb(allow_extensions = TRUE) to enable it (this may crash R on a Linux build not compiled with libstdc++; see https://github.com/duckdb/duckdb-r/issues/1107).
ℹ See ?duckdb for details.
ℹ Context: load_extension
Backtrace:
     ▆
  1. ├─DBI::dbExecute(con, "INSTALL fts; INSTALL vss;")
  2. ├─DBI::dbExecute(con, "INSTALL fts; INSTALL vss;")
  3. │ ├─DBI::dbSendStatement(conn, statement, ...)
  4. │ └─DBI::dbSendStatement(conn, statement, ...)
  5. │   ├─DBI::dbSendQuery(conn, statement, ...)
  6. │   └─duckdb::dbSendQuery(conn, statement, ...)
  7. │     └─duckdb (local) .local(conn, statement, ...)
  8. │       └─duckdb:::rethrow_rapi_prepare(conn@conn_ref, statement, env)
  9. │         ├─rlang::try_fetch(...)
 10. │         │ ├─base::tryCatch(...)
 11. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14. │         │ └─base::withCallingHandlers(...)
 15. │         └─duckdb:::rapi_prepare(conn, query, env)
 16. ├─duckdb (local) `<fn>`("load_extension", "")
 17. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)
 18. │   └─rlang:::signal_abort(cnd, .file)
 19. │     └─base::signalCondition(cnd)
 20. └─rlang (local) `<fn>`(`<dckdb_rr>`)
 21.   └─handlers[[1L]](cnd)
 22.     └─duckdb:::rethrow_error_from_rapi(e, call)
 23.       └─rlang::abort(msg, call = call)
Execution halted
NULL
** libs
using C compiler: ‘clang version 22.1.8 (https://github.com/llvm/llvm-project ca7933e47d3a3451d81e72ac174dcb5aa28b59d1)’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ragnar/src'
clang-22 -std=gnu23 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG   -isystem /usr/local/clang22/include -I/usr/local/clang/include    -fpic  -O3 -Wall -pedantic -Wp,-D_FORTIFY_SOURCE=3  -c chunk.c -o chunk.o
clang-22 -std=gnu23 -shared -L/usr/local/clang/lib64 -L/usr/local/clang22/lib -L/usr/local/clang22/lib/x86_64-unknown-linux-gnu -L/usr/local/lib64 -o ragnar.so chunk.o
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ragnar/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/ragnar/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/ragnar/src'
installing to /data/gannet/ripley/R/packages/tests-clang/ragnar.Rcheck/00LOCK-ragnar/00new/ragnar/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ragnar)