'R_user_dir' is not an exported object from 'namespace:tools'

[amirmazmi]

Getting the below error trying to use duckdb.

Installation step:
install.packages("duckdb")
which then compiles duckdb

try to run as per below

> con <- duckdb::dbConnect(duckdb())
Error: 'R_user_dir' is not an exported object from 'namespace:tools'

For this version of R (3.6.3 ), R_user_dir is in backports. Not sure what namespace::tools is.

Tried running

> duckdb()
Error: 'R_user_dir' is not an exported object from 'namespace:tools'

which is most likely the source calling R_user_dir()

If no workaround exists, any chance a previous version of duckdb would work with R 3.6.3? Current work centred around this version for now.

sessionInfo()

R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] LC_CTYPE=en_SG.UTF-8 LC_NUMERIC=C LC_TIME=en_SG.UTF-8 LC_COLLATE=en_SG.UTF-8
[5] LC_MONETARY=en_SG.UTF-8 LC_MESSAGES=en_SG.UTF-8 LC_PAPER=en_SG.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_SG.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] duckdb_1.1.0 DBI_1.1.1 pacman_0.5.1

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3

[krlmlr]

Thanks. It seems that duckdb requires R 4.0.0 in this case. Happy to review a PR that works around, though.

The {tools} package is one of R's base packages.

tools::R_user_dir
#> function (package, which = c("data", "config", "cache")) 
#> {
#>     stopifnot(is.character(package), length(package) == 1L)
#>     which <- match.arg(which)
#>     home <- normalizePath("~")
#>     path <- switch(which, data = {
#>         if (nzchar(p <- Sys.getenv("R_USER_DATA_DIR"))) p else if (nzchar(p <- Sys.getenv("XDG_DATA_HOME"))) p else if (.Platform$OS.type == 
#>             "windows") file.path(Sys.getenv("APPDATA"), "R", 
#>             "data") else if (Sys.info()["sysname"] == "Darwin") file.path(home, 
#>             "Library", "Application Support", "org.R-project.R") else file.path(home, 
#>             ".local", "share")
#>     }, config = {
#>         if (nzchar(p <- Sys.getenv("R_USER_CONFIG_DIR"))) p else if (nzchar(p <- Sys.getenv("XDG_CONFIG_HOME"))) p else if (.Platform$OS.type == 
#>             "windows") file.path(Sys.getenv("APPDATA"), "R", 
#>             "config") else if (Sys.info()["sysname"] == "Darwin") file.path(home, 
#>             "Library", "Preferences", "org.R-project.R") else file.path(home, 
#>             ".config")
#>     }, cache = {
#>         if (nzchar(p <- Sys.getenv("R_USER_CACHE_DIR"))) p else if (nzchar(p <- Sys.getenv("XDG_CACHE_HOME"))) p else if (.Platform$OS.type == 
#>             "windows") file.path(Sys.getenv("LOCALAPPDATA"), 
#>             "R", "cache") else if (Sys.info()["sysname"] == "Darwin") file.path(home, 
#>             "Library", "Caches", "org.R-project.R") else file.path(home, 
#>             ".cache")
#>     })
#>     file.path(path, "R", package)
#> }
#> <bytecode: 0x11047dda8>
#> <environment: namespace:tools>

^{Created on 2024-10-28 with reprex v2.1.1}

[krlmlr]

Looks like you can work around in R < 4.0.0 with something like:

dbConnect(
  duckdb(config(extension_directory = ..., secret_directory = ...))
)

With that, the R_user_dir() function isn't called. Not bumping the required R version for now, but certainly could use better behavior or a true fix.

[amirmazmi]

Thanks for this!

Working example

con <-duckdb::dbConnect( 
       duckdb( config = list( extension_directory = getwd(), secret_directory = getwd()))
)

Can be closed as a workaround has been found.