Check the ukbflow operating environment

Runs a four-block health check covering the dx CLI, dxpy (Python), RAP authentication, and R package dependencies. Designed to be the first function a new user runs after installation.

Usage

ops_setup(
  check_dx = TRUE,
  check_auth = TRUE,
  check_deps = TRUE,
  verbose = TRUE
)

Arguments

check_dx

(logical) Check dx CLI installation (dxpy is implied by dx).

check_auth

(logical) Check RAP login status.

check_deps

(logical) Check R package dependencies.

verbose

(logical) Print the formatted report. Set to FALSE for programmatic use (results are still returned invisibly).

Value

An invisible named list with elements dx, dxpy, auth, deps, and summary. Each element reflects the result of its respective check block and can be inspected programmatically.

Details

The function is read-only: it never modifies system state, installs packages, or authenticates. Auth failures are reported as warnings, not errors, because the check itself does not require a live RAP connection.

Examples

ops_setup(check_dx = FALSE, check_auth = FALSE)
#> ── ukbflow environment check ───────────────────────────────────────────────────
#> ℹ ukbflow 0.3.3 | R 4.5.3 | 2026-04-07
#> ── 3. R packages ───────────────────────────────────────────────────────────────
#> ✔ cli  3.6.5  [core]
#> ✔ data.table  1.18.2.1  [core]
#> ✔ processx  3.8.7  [core]
#> ✔ rlang  1.2.0  [core]
#> ✔ tools  4.5.3  [core]
#> ✔ curl  7.0.0  [extract / fetch]
#> ✔ jsonlite  2.0.0  [extract / fetch]
#> ✔ survival  3.8.6  [assoc_coxph]
#> ✔ dplyr  1.2.1  [assoc / derive]
#> ✔ tidyselect  1.2.1  [assoc / derive]
#> ✔ forestploter  1.1.3  [plot_forest]
#> ✔ broom  1.0.12  [plot_tableone]
#> ✔ gt  1.3.0  [plot_tableone]
#> ✔ gtsummary  2.5.0  [plot_tableone]
#> ✔ pROC  1.19.0.1  [assoc (optional)]
#> ✔ knitr  1.51  [vignettes]
#> ✔ rmarkdown  2.31  [vignettes]
#> ────────────────────────────────────────────────────────────────────────────────
#> ✔ 17 passed

result <- ops_setup(check_dx = FALSE, check_auth = FALSE, verbose = FALSE)
result$summary$fail == 0
#> [1] TRUE