R Under development (unstable) (2026-07-17 r90265 ucrt) -- "Unsuffered Consequences"
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> # Regression test for audit item 11: bootstrap error handling.
> #
> # Changes in R/bootnet.R (sequential and parallel bootstrap loops):
> #   - New maxErrors argument (default 10, matching the previously hard-coded
> #     retry limit per bootstrap sample).
> #   - When the retry limit is reached, the stop() message now reports which
> #     bootstrap failed and the underlying estimation error (previously an
> #     uninformative "Maximum number of errors in bootstraps reached").
> #   - One aggregate warning at the end of the run reporting the total number
> #     of bootstrap estimations that failed and were resampled.
> #
> # The success path is unchanged (no RNG consumption added); that is covered
> # by tests/test-backcompat.R.
> 
> library(bootnet)
Loading required package: ggplot2
This is bootnet 1.9.1
For questions and issues, please see github.com/SachaEpskamp/bootnet.
> 
> set.seed(1)
> data <- matrix(rnorm(50 * 4), ncol = 4)
> colnames(data) <- paste0("V", 1:4)
> 
> # Custom estimator factory: fails deterministically on a given set of calls
> # via a closure counter (sequential path only; closures do not carry state
> # across parallel workers). Returns a simple correlation matrix as the
> # weights matrix, which is all bootnet needs from a custom 'fun'.
> makeFlaky <- function(failCalls) {
+     count <- 0
+     function(data) {
+         count <<- count + 1
+         if (count %in% failCalls) stop("flaky failure for testing")
+         cor(data)
+     }
+ }
> 
> ## (a) Sequential: retries happen and succeed, and the aggregate warning
> ## reports the exact number of failures.
> #
> # Call accounting: bootnet(data, fun = ...) first estimates the sample
> # network (call 1), so the failures must start at call 2 to land in the
> # bootstrap phase. Calls 2:4 fail (3 retries within bootstrap 1), call 5
> # succeeds, bootstraps 2 and 3 succeed (calls 6, 7).
> set.seed(123)
> warns <- character(0)
> boot <- withCallingHandlers(
+     bootnet(data, fun = makeFlaky(2:4), nBoots = 3, verbose = FALSE,
+             maxErrors = 10),
+     warning = function(w) {
+         warns <<- c(warns, conditionMessage(w))
+         invokeRestart("muffleWarning")
+     }
+ )
Note: bootnet will store only the following statistics:  edge, strength, outStrength, inStrength
> stopifnot(inherits(boot, "bootnet"))
> stopifnot(length(boot$boots) == 3)
> stopifnot(any(grepl("3 bootstrap estimation(s) failed and were resampled.",
+                     warns, fixed = TRUE)))
> 
> ## (b) Sequential: exceeding maxErrors stops with an informative error that
> ## includes the underlying estimation error message.
> #
> # Call 1 (sample estimation) succeeds; every bootstrap call fails. With
> # maxErrors = 2 the first bootstrap gives up after 3 failed attempts.
> set.seed(123)
> err <- tryCatch(
+     bootnet(data, fun = makeFlaky(2:1000), nBoots = 3, verbose = FALSE,
+             maxErrors = 2),
+     error = function(e) conditionMessage(e)
+ )
Note: bootnet will store only the following statistics:  edge, strength, outStrength, inStrength
> stopifnot(is.character(err))
> stopifnot(grepl("Maximum number of retries", err, fixed = TRUE))
> stopifnot(grepl("flaky failure for testing", err, fixed = TRUE))
> 
> ## (c) Parallel: a healthy run still completes, bootResults keep their
> ## previous structure (list of bootnetResult objects, not wrapped lists),
> ## and no retry warning is emitted.
> set.seed(42)
> net <- estimateNetwork(data, default = "pcor", verbose = FALSE)
> warnsPar <- character(0)
> bootPar <- withCallingHandlers(
+     bootnet(net, nBoots = 4, nCores = 2, default = "pcor", verbose = FALSE),
+     warning = function(w) {
+         warnsPar <<- c(warnsPar, conditionMessage(w))
+         invokeRestart("muffleWarning")
+     }
+ )
Note: bootnet will store only the following statistics:  edge, strength, outStrength, inStrength
> stopifnot(inherits(bootPar, "bootnet"))
> stopifnot(length(bootPar$boots) == 4)
> stopifnot(all(sapply(bootPar$boots, inherits, "bootnetResult")))
> stopifnot(!any(grepl("failed and were resampled", warnsPar)))
> 
> cat("item11-error-handling: OK\n")
item11-error-handling: OK
> 
> proc.time()
   user  system elapsed 
   4.54    0.95   11.10