CRAN Package Check Results for Package pcalg

Last updated on 2019-08-17 22:46:33 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.6-2 94.70 363.48 458.18 OK
r-devel-linux-x86_64-debian-gcc 2.6-2 84.19 282.96 367.15 OK
r-devel-linux-x86_64-fedora-gcc 2.6-2 495.01 ERROR
r-devel-windows-ix86+x86_64 2.6-2 248.00 631.00 879.00 NOTE
r-patched-linux-x86_64 2.6-2 90.62 359.93 450.55 OK
r-patched-solaris-x86 2.6-2 676.90 NOTE
r-release-linux-x86_64 2.6-2 88.55 360.18 448.73 OK
r-release-windows-ix86+x86_64 2.6-2 245.00 796.00 1041.00 NOTE
r-release-osx-x86_64 2.6-2 ERROR
r-oldrel-windows-ix86+x86_64 2.6-2 248.00 753.00 1001.00 NOTE
r-oldrel-osx-x86_64 2.6-2 NOTE

Check Details

Version: 2.6-2
Check: examples
Result: ERROR
    Running examples in ‘pcalg-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: adjustment
    > ### Title: Compute adjustment sets for covariate adjustment.
    > ### Aliases: adjustment
    > ### Keywords: models graphs
    >
    > ### ** Examples
    >
    > ## Example 4.1 in Perkovic et. al (2015), Example 2 in Perkovic et. al (2017)
    > mFig1 <- matrix(c(0,1,1,0,0,0, 1,0,1,1,1,0, 0,0,0,0,0,1,
    + 0,1,1,0,1,1, 0,1,0,1,0,1, 0,0,0,0,0,0), 6,6)
    > type <- "cpdag"
    > x <- 3; y <- 6
    > ## plot(as(t(mFig1), "graphNEL"))
    >
    > ## all
    > adjustment(amat = mFig1, amat.type = type, x = x, y = y, set.type = "all")
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffcd2ac6d30
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7feb0459888a]
     /lib64/libnode.so.64(+0x92ccd1) [0x7feb03b20cd1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7feb04594387]
     /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) [0x7feb04275843]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7feb0439a8d2]
     [0x250ae06dc0d8]
    
     *** caught illegal operation ***
    address 0x7feb0395f38d, 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 = mFig1, amat.type = type, x = x, y = y, set.type = "all")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.6-2
Check: tests
Result: ERROR
     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/11s]
     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: 0x7ffc1dfd9400
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f103a49288a]
     /lib64/libnode.so.64(+0x92ccd1) [0x7f1039a1acd1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f103a48e387]
     /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) [0x7f103a16f843]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f103a2948d2]
     [0x259c2fcdc0d8]
    
     *** caught illegal operation ***
     address 0x7f103985938d, 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: 0x7ffdc345b9a0
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fe6d7ca988a]
     /lib64/libnode.so.64(+0x92ccd1) [0x7fe6d7231cd1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fe6d7ca5387]
     /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) [0x7fe6d7986843]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fe6d7aab8d2]
     [0x38606eedc0d8]
    
     *** caught illegal operation ***
     address 0x7fe6d707038d, 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 ...
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 2.6-2
Check: installed package size
Result: NOTE
     installed size is 7.7Mb
     sub-directories of 1Mb or more:
     data 2.1Mb
     doc 1.2Mb
     libs 2.3Mb
Flavors: r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-windows-ix86+x86_64, r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 2.6-2
Check: package dependencies
Result: ERROR
    Packages required but not available: 'graph', 'RBGL'
    
    Package suggested but not available for checking: ‘Rgraphviz’
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-release-osx-x86_64