Running ‘test_LINGAM.R’
  Running ‘test_addBgKnowledge.R’
  Running ‘test_adjustment.R’
  Running ‘test_ages.R’
  Running ‘test_amat2dag.R’
  Running ‘test_arges.R’
  Running ‘test_backdoor.R’ [10s/10s]
  Comparing ‘test_backdoor.Rout’ to ‘test_backdoor.Rout.save’ ... OK
  Running ‘test_bicscore.R’
  Running ‘test_causalEffect.R’
  Running ‘test_compareGraphs.R’
  Running ‘test_dag2cpdag.R’
  Running ‘test_dag2essgraph.R’
  Running ‘test_displayAmat.R’
  Running ‘test_dsep.R’
  Running ‘test_fci.R’
  Running ‘test_fciPlus.R’
  Running ‘test_gSquareBin.R’
  Running ‘test_gSquareDis.R’
  Running ‘test_gac.R’
  Running ‘test_getNextSet.R’
  Running ‘test_gies.R’
  Running ‘test_ida.R’
  Running ‘test_idaFast.R’
  Running ‘test_isValidGraph.R’
  Running ‘test_jointIda.R’
  Running ‘test_mat2targets.R’
  Running ‘test_pc.R’
  Running ‘test_pcSelect.R’
  Running ‘test_pcalg2dagitty.R’
  Running ‘test_pcorOrder.R’
  Running ‘test_pdag2allDags.R’
  Running ‘test_pdag2dag.R’
  Running ‘test_possDeAn.R’
  Running ‘test_randDAG.R’
  Comparing ‘test_randDAG.Rout’ to ‘test_randDAG.Rout.save’ ... OK
  Running ‘test_randomDAG.R’
  Running ‘test_rfci.R’
  Running ‘test_rmvDAG.R’
  Running ‘test_shd.R’
  Running ‘test_skeleton.R’
  Running ‘test_udag2pag.R’
  Running ‘test_udag2pdag.R’
  Running ‘test_wgtMatrix.R’
Running the tests in ‘tests/test_adjustment.R’ failed.
Complete output:
  > library(pcalg)
  > (doExtras <- pcalg:::doExtras())
  [1] FALSE
  > 
  > ## Minimalistic CRAN checks
  > 
  > ## Test 1 ############################
  > ## Test that "no adjustment set" and "empty adjustment set" are distinguished properly
  > x <- 1; y <- 2
  > cpdag <- matrix(c(0,1,1,0),2,2) ## 1 --- 2 => no adj set
  > dag <- matrix(c(0,1,0,0),2,2) ## 1 --> 2 => empty adj set
  > 
  > adjC <- adjustment(amat = cpdag, amat.type = "cpdag", x = 1, y = 2, set.type = "canonical")
  
  
  #
  # Fatal error in , line 0
  # Failed to create ICU collator, are ICU data files missing?
  #
  #
  #
  #FailureMessage Object: 0x7fffffed2eb0
  ==== C stack trace ===============================
  
      /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f86a6b6488a]
      /lib64/libnode.so.64(+0x92ccd1) [0x7f86a60eccd1]
      /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f86a6b60387]
      /lib64/libnode.so.64(v8::internal::Collator::InitializeCollator(v8::internal::Isolate*, v8::internal::Handle<v8::internal::JSObject>, v8::internal::Handle<v8::internal::String>, v8::internal::Handle<v8::internal::JSObject>, v8::internal::Handle<v8::internal::JSObject>)+0x473) [0x7f86a6841843]
      /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f86a69668d2]
      [0x1dd990a5c0d8]
  
   *** caught illegal operation ***
  address 0x7f86a5f2b38d, cause 'illegal operand'
  
  Traceback:
   1: context_eval(join(src), private$context)
   2: get_str_output(context_eval(join(src), private$context))
   3: ct$eval(paste("global.", name, "=", value))
   4: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
   5: doTryCatch(return(expr), name, parentenv, handler)
   6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7: tryCatchList(expr, classes, parentenv, handlers)
   8: tryCatch({    .jsassign(xv, as.character(x))    .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv,         ").toString()"))    r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) {    stop(e)}, finally = {    .deleteJSVar(xv)})
   9: dagitty(result)
  10: pcalg2dagitty(amat = amat, labels = lb, type = amat.type)
  11: adjustment(amat = cpdag, amat.type = "cpdag", x = 1, y = 2, set.type = "canonical")
  An irrecoverable exception occurred. R is aborting now ...
Running the tests in ‘tests/test_pcalg2dagitty.R’ failed.
Complete output:
  > ## Translate amat as describes in amatType to dagitty object
  > 
  > library(pcalg)
  > library(dagitty)
  
  Attaching package: 'dagitty'
  
  The following object is masked from 'package:pcalg':
  
      randomDAG
  
  > suppressWarnings(RNGversion("3.5.0"))
  > doExtras <- pcalg:::doExtras()
  > 
  > res <- rep(FALSE, 10)
  > ####################
  > ## Test DAG 1
  > ####################
  > data(gmG)
  > n <- nrow    (gmG8$x)
  > V <- colnames(gmG8$x) # labels aka node names
  > 
  > amat <- wgtMatrix(gmG8$g)
  > amat[amat != 0] <- 1
  > dagitty_dag1 <- pcalg2dagitty(amat,V,type="dag")
  > ## Use dagitty:::graphLayout instead of just graphLayout
  > ## because Rgraphviz package that R uses has a function w the same name
  > ## par(mfrow=c(1,2))
  > ## plot(gmG8$g, main = "True DAG")
  > ## plot(dagitty:::graphLayout(dagitty_dag1))
  > 
  > res[1] <- (dagitty_dag1 == "dag {\nAuthor\nBar\nCtrl\nGoal\nV5\nV6\nV7\nV8\nAuthor -> Bar\nAuthor -> V6\nAuthor -> V8\nBar -> Ctrl\nBar -> V5\nV5 -> V6\nV5 -> V8\nV6 -> V7\n}\n")
  > 
  > #############
  > ## Test DAG 2
  > #############
  > set.seed(123)
  > p <- 10
  > V <- sample(LETTERS, p)
  > g <- pcalg::randomDAG(p,prob=0.3, V = V)
  > 
  > amat <- wgtMatrix(g)
  > amat[amat != 0] <- 1
  > dagitty_dag2 <- pcalg2dagitty(amat,V,type="dag")
  > ## Use dagitty:::graphLayout instead of just graphLayout
  > ## because Rgraphviz package that R uses has a function w the same name
  > ## par(mfrow=c(1,2))
  > ## plot(g, main = "True DAG")
  > ## plot(dagitty:::graphLayout(dagitty_dag2))
  > 
  > res[2] <- (dagitty_dag2 == "dag {\nA\nH\nJ\nK\nQ\nT\nU\nW\nX\nZ\nA -> Q\nH -> A\nH -> K\nH -> Q\nH -> T\nH -> Z\nJ -> W\nT -> A\nT -> Q\nT -> X\nU -> Q\nU -> W\nU -> X\nW -> K\n}\n")
  > 
  > ###############
  > ## Test CPDAG 1
  > ###############
  > data(gmG)
  > n <- nrow(gmG8$ x)
  > V <- colnames(gmG8$ x) # labels aka node names
  > 
  > ## estimate CPDAG
  > pc.fit <- pc(suffStat = list(C = cor(gmG8$x), n = n),
  +              indepTest = gaussCItest, ## indep.test: partial correlations
  +              alpha=0.01, labels = V, verbose = FALSE)
  > amat <- as(pc.fit, "amat")
  > dagitty_cpdag1 <- pcalg2dagitty(amat,V,type="cpdag")
  
  
  #
  # Fatal error in , line 0
  # Failed to create ICU collator, are ICU data files missing?
  #
  #
  #
  #FailureMessage Object: 0x7ffe43d20800
  ==== C stack trace ===============================
  
      /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f249d38188a]
      /lib64/libnode.so.64(+0x92ccd1) [0x7f249c909cd1]
      /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f249d37d387]
      /lib64/libnode.so.64(v8::internal::Collator::InitializeCollator(v8::internal::Isolate*, v8::internal::Handle<v8::internal::JSObject>, v8::internal::Handle<v8::internal::String>, v8::internal::Handle<v8::internal::JSObject>, v8::internal::Handle<v8::internal::JSObject>)+0x473) [0x7f249d05e843]
      /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f249d1838d2]
      [0xde665dc0d8]
  
   *** caught illegal operation ***
  address 0x7f249c74838d, cause 'illegal operand'
  
  Traceback:
   1: context_eval(join(src), private$context)
   2: get_str_output(context_eval(join(src), private$context))
   3: ct$eval(paste("global.", name, "=", value))
   4: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
   5: doTryCatch(return(expr), name, parentenv, handler)
   6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
   7: tryCatchList(expr, classes, parentenv, handlers)
   8: tryCatch({    .jsassign(xv, as.character(x))    .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv,         ").toString()"))    r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) {    stop(e)}, finally = {    .deleteJSVar(xv)})
   9: dagitty(result)
  10: pcalg2dagitty(amat, V, type = "cpdag")
  An irrecoverable exception occurred. R is aborting now ...