R Under development (unstable) (2024-09-06 r87103 ucrt) -- "Unsuffered Consequences"
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> library(pcalg)
> suppressWarnings(RNGversion("3.5.0"))
> .libPaths()
[1] "D:/temp/Rtmp8cLpRq/RLIBS_76c4389f364"
[2] "D:/RCompile/recent/R/library"        
> ## acyclic graphs
> 
> nreps <- 30
> p <- 8
> n <- 1000
> 
> for(u2pd in c("rand", "retry", "relaxed")) {
+     cat("\n u2pd =", u2pd, "\n ------------\n")
+     cyc.res <- logical(nreps)
+     for (i in 1:nreps) {
+         set.seed(i)
+         myDAG <- randomDAG(p, prob = 0.2)
+         d.mat <- rmvDAG(n, myDAG, errDist = "normal")
+         res <- suppressWarnings(pcAlgo(d.mat, alpha = 0.05, directed=TRUE, u2pd = u2pd))
+         ##                      ------ directed;  u2pd = "rand" --> udag2pdag()
+         res.A <- wgtMatrix(res@graph)
+         res.A[res.A!=0] <- 1
+         undir.A <- res.A + t(res.A)
+         undir.A[undir.A==1] <- 0
+         undir.A[undir.A==2] <- 1
+         res.dir <- res.A - undir.A
+         cyc.res[i] <- ggm::isAcyclic(res.dir)
+     }
+     if (!all(cyc.res)) stop("Test of pcAlgo(*, directed): Cyclic part in PDAG!")
+ } ## for(u2pd ...)

 u2pd = rand 
 ------------

 u2pd = retry 
 ------------

 u2pd = relaxed 
 ------------
> cat('Time elapsed: ', (.pt <- proc.time()),"\n")
Time elapsed:  2.51 0.18 2.71 NA NA 
> 
> ## find collider correctly
> set.seed(123)
> myDAG <- randomDAG(3, prob = 0.5)
> library(Matrix)
> as(myDAG,"sparseMatrix")
3 x 3 sparse Matrix of class "dgCMatrix"
  1 2         3
1 . . 0.4680792
2 . . 0.9464206
3 . . .        
> d.mat <- rmvDAG(n, myDAG, errDist = "normal")
> res <- pcAlgo(d.mat, alpha = 0.05, corMethod = "standard",directed=TRUE)
Warning message:
In pcAlgo(d.mat, alpha = 0.05, corMethod = "standard", directed = TRUE) :
  pcAlgo() is deprecated and only kept for backward compatibility.
 Please use skeleton, pc, or fci instead

> gEst <- wgtMatrix(res@graph)
> gTrue <- rbind(0,0, c(1,1,0))
> if(!all(gEst==gTrue)) stop("Test of udag2pdag: Problem finding a collider!")
> 
> cat('Time elapsed: ', proc.time() - .pt,'\n') # "stats"
Time elapsed:  0.7 0.03 0.74 NA NA 
> 
> 
> proc.time()
   user  system elapsed 
   3.21    0.21    3.45