rduckhts_connect: Create a DuckDB connection with bundled DuckHTS loaded

In Rduckhts: 'DuckDB' High Throughput Sequencing File Formats Reader Extension

Create a DuckDB connection with bundled DuckHTS loaded

Description

Creates a DuckDB connection that explicitly permits loading the package-built DuckHTS extension, disables automatic installation and loading of unrelated known DuckDB extensions, and loads the bundled DuckHTS extension.

Usage

rduckhts_connect(
  dbdir = ":memory:",
  read_only = FALSE,
  bigint = "numeric",
  config = list(),
  extension_path = NULL
)

Arguments

dbdir	Path to a DuckDB database, or ":memory:" for an in-memory database.
read_only	Logical; open a file-backed database read-only.
bigint	How DuckDB 64-bit integers are returned; passed to duckdb::duckdb().
config	Named list of additional DuckDB configuration settings.
extension_path	Optional path to a DuckHTS .duckdb_extension file. If NULL, uses the extension bundled with Rduckhts.

Details

Current versions of the duckdb R package can disable extension loading on Linux builds that use a C++ standard library other than libstdc++. DuckHTS is compiled locally with the same package toolchain, so this helper explicitly enables extension loading for this package-owned connection. Package-owned connections use per-session DuckDB extension/secret storage by default when the installed duckdb version supports that setting.

DuckDB reuses a live database instance when the same file-backed dbdir is opened again, ignoring new driver and configuration settings. This helper rejects such reuse rather than silently weakening its connection policy. Use rduckhts_load() on the existing connection if it already permits unsigned, driver-level extension loading, or close the existing database instance before calling this helper.

The settings allow_unsigned_extensions, autoinstall_known_extensions, and autoload_known_extensions are controlled by this helper and override entries with those names in config. Other named DuckDB settings are passed through unchanged.

Value

A DuckDB connection with DuckHTS loaded. File-backed connections also have connection-local TEMP macros installed without modifying the database catalog.

Examples

con <- rduckhts_connect()
DBI::dbGetQuery(con, "SELECT duckhts_htslib_version() AS version")
DBI::dbDisconnect(con, shutdown = TRUE)

Rduckhts documentation built on Oct. 25, 2026, 1:08 a.m.