Check echoverse setup

Diagnose the installation status of all echoverse packages, system dependencies, external tools, and Python/conda environments. Prints an actionable report with platform-specific fix commands.

Usage

check_echoverse_setup(
  echoverse_pkgs = c("echolocatoR", "echodata", "echotabix", "echoannot", "echoconda",
    "echoLD", "echoplot", "echofinemap", "catalogueR", "downloadR", "echogithub",
    "devoptera", "echodeps", "echoAI", "echoverseTemplate"),
  key_deps = c("data.table", "BiocManager", "reticulate", "susieR", "coloc",
    "MungeSumstats", "VariantAnnotation", "rtracklayer", "GenomicRanges", "ggbio",
    "basilisk", "Rsamtools"),
  verbose = TRUE
)

Arguments

echoverse_pkgs

Character vector of echoverse package names to check.

key_deps

Character vector of key non-echoverse dependency package names to check.

verbose

Print detailed results. Default TRUE.

Value

A list (invisibly) with elements:

packages

data.frame of echoverse package status

system

list of system dependency checks

tools

list of external tool checks

python

list of Python/conda checks

pass

logical, TRUE if all critical checks pass

Examples

if (FALSE) { # \dontrun{
## Full diagnostic report
results <- check_echoverse_setup()

## Quick check with a subset of packages
results <- check_echoverse_setup(
    echoverse_pkgs = c("echodata"),
    key_deps = c("data.table"),
    verbose = FALSE
)
} # }