Garbage-collect VCFArrow temp directories

Triggers R's garbage collector (three full passes to handle the finalizer -> pending-queue -> unlink chain), then flushes any directories whose reference count has already reached zero.

Usage

vcf_gc(force = FALSE, verbose = TRUE)

Arguments

force

Logical. If TRUE, also force-deregister and delete directories for objects that are still nominally live in the registry. Use this when you have called rm() on all VCFArrow objects but the temp directories have not been cleaned up (common in RStudio, which can hold display references that delay GC).

verbose

Logical. Print a status message.

Value

Invisibly returns NULL; called for its side effect of deleting temporary directories.

Typical workflow

  rm(vcf1, vcf2, vcf3)
  vcf_gc()              # usually sufficient
  vcf_gc(force = TRUE)  # if directories remain after rm()

Examples

f <- system.file("extdata", "vaillantii_discosnp_sub.vcf.gz",
                 package = "VCFArrow")
vcf <- read_vcf(f)
#> ℹ VCF is being read in chunks of 50000 variants
#> ✔ VCF successfully read into a VCFArrow object
rm(vcf)
vcf_gc()
#> VCFArrow: 2 temp directories are still live (VCFArrow objects not yet GC'd):
#>   /tmp/RtmpSpcr9J/arrow_vcf_1ff85b135cd3
#>   /tmp/RtmpSpcr9J/arrow_vcf_1ff8794bfce
#>   → rm() all VCFArrow objects, then call vcf_gc() again.
#>   → Or call vcf_gc(force = TRUE) to delete regardless.