CRAN Package Check Results for Package dagitty

Last updated on 2019-09-18 05:46:56 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2-2 5.28 58.09 63.37 OK
r-devel-linux-x86_64-debian-gcc 0.2-2 4.99 45.13 50.12 OK
r-devel-linux-x86_64-fedora-clang 0.2-2 49.29 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2-2 48.88 ERROR
r-devel-windows-ix86+x86_64 0.2-2 15.00 64.00 79.00 OK
r-patched-linux-x86_64 0.2-2 5.37 57.37 62.74 OK
r-patched-solaris-x86 0.2-2 75.00 OK
r-release-linux-x86_64 0.2-2 5.46 57.89 63.35 OK
r-release-windows-ix86+x86_64 0.2-2 12.00 57.00 69.00 OK
r-release-osx-x86_64 0.2-2 OK
r-oldrel-windows-ix86+x86_64 0.2-2 10.00 60.00 70.00 OK
r-oldrel-osx-x86_64 0.2-2 OK

Check Details

Version: 0.2-2
Check: examples
Result: ERROR
    Running examples in ‘dagitty-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: AncestralRelations
    > ### Title: Ancestral Relations
    > ### Aliases: AncestralRelations adjacentNodes ancestors children
    > ### descendants markovBlanket neighbours parents spouses
    >
    > ### ** Examples
    >
    > g <- dagitty("graph{ a <-> x -> b ; c -- x <- d }")
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffdc65f6fd0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f4987ea945a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f49874318b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f4987ea4f57]
     /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) [0x7f4987b86413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f4987cab4a2]
     [0x2c83e35c0d8]
    
     *** caught illegal operation ***
    address 0x7f498726f9a5, 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("graph{ a <-> x -> b ; c -- x <- d }")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2-2
Check: tests
Result: ERROR
     Running ‘testthat.R’
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dagitty)
     >
     > test_check("dagitty")
    
    
     #
     # Fatal error in , line 0
     # Failed to create ICU collator, are ICU data files missing?
     #
     #
     #
     #FailureMessage Object: 0x7ffd2b524400
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f07ff87a45a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f07fee028b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f07ff875f57]
     /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) [0x7f07ff557413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f07ff67c4a2]
     [0x96e9d8dc0d8]
    
     *** caught illegal operation ***
     address 0x7f07fec409a5, 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(x)
     10: as.dagitty.character(x)
     11: as.dagitty(x)
     12: backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }")
     13: is(value, "JS_EVAL")
     14: .jsassign(xv, as.character(x))
     15: .jsassigngraph(xv, x)
     16: tryCatchList(expr, classes, parentenv, handlers)
     17: tryCatch({ .jsassigngraph(xv, x) for (w in v) { .jsassign(vv, as.character(w)) .jsassign(vv, .jsp("global.", xv, ".getVertex(global.", vv, ")")) .jsassign(vv, .jsp("global.", xv, ".", type, "Of([global.", vv, "])")) r <- union(r, .jsget(paste0("_.pluck(global.", vv, ",'id')"))) }}, finally = { .deleteJSVar(xv) .deleteJSVar(vv)})
     18: .kins(x, v, "children")
     19: children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")
     20: eval_bare(get_expr(quo), get_env(quo))
     21: quasi_label(enquo(object), label, arg = "object")
     22: expect_equal(length(children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")), 0)
     23: eval(code, test_env)
     24: eval(code, test_env)
     25: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     26: doTryCatch(return(expr), name, parentenv, handler)
     27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     29: doTryCatch(return(expr), name, parentenv, handler)
     30: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     31: tryCatchList(expr, classes, parentenv, handlers)
     32: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     33: test_code(desc, code, env = parent.frame())
     34: test_that("CGs", { expect_equal(length(children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")), 0)})
     35: eval(code, test_env)
     36: eval(code, test_env)
     37: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     38: doTryCatch(return(expr), name, parentenv, handler)
     39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     40: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     41: doTryCatch(return(expr), name, parentenv, handler)
     42: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     43: tryCatchList(expr, classes, parentenv, handlers)
     44: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     45: test_code(NULL, exprs, env)
     46: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     47: force(code)
     48: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
     49: FUN(X[[i]], ...)
     50: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     51: force(code)
     52: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     53: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     54: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     55: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     56: test_check("dagitty")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2-2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘dagitty4semusers.Rmd’ using rmarkdown
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffd4b5e2470
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fde4d53c45a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7fde4cac48b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fde4d537f57]
     /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) [0x7fde4d219413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fde4d33e4a2]
     [0x6bafb75c0d8]
    
     *** caught illegal operation ***
    address 0x7fde4c9029a5, cause 'illegal operand'
    
    Traceback:
     1: context_eval(join(src), private$context)
     2: get_str_output(context_eval(join(src), private$context))
     3: ct$eval(paste("global.", name, "=", value))
     4: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
     9: dagitty("dag {\n\tW1 -> Z1 -> X -> Y\n\tZ1 <- V -> Z2\n\tW2 -> Z2 -> Y\n\tX <-> W1 <-> W2 <-> Y\n}")
    10: eval(expr, envir, enclos)
    11: eval(expr, envir, enclos)
    12: withVisible(eval(expr, envir, enclos))
    13: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    14: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    17: evaluate::evaluate(...)
    18: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    19: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
    27: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    28: vweave_rmarkdown(...)
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    34: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/dagitty.Rcheck/vign_test/dagitty", ser_elibs = "/tmp/Rtmp3lsDvM/file450b415bf18d.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2-2
Check: examples
Result: ERROR
    Running examples in ‘dagitty-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: AncestralRelations
    > ### Title: Ancestral Relations
    > ### Aliases: AncestralRelations adjacentNodes ancestors children
    > ### descendants markovBlanket neighbours parents spouses
    >
    > ### ** Examples
    >
    > g <- dagitty("graph{ a <-> x -> b ; c -- x <- d }")
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffc3a75b7f0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f35b3efe45a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f35b34868b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f35b3ef9f57]
     /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) [0x7f35b3bdb413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f35b3d004a2]
     [0x1c7a6445c0d8]
    
     *** caught illegal operation ***
    address 0x7f35b32c49a5, 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("graph{ a <-> x -> b ; c -- x <- d }")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2-2
Check: tests
Result: ERROR
     Running ‘testthat.R’
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(dagitty)
     >
     > test_check("dagitty")
    
    
     #
     # Fatal error in , line 0
     # Failed to create ICU collator, are ICU data files missing?
     #
     #
     #
     #FailureMessage Object: 0x7ffe13917ab0
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fbee739945a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7fbee69218b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fbee7394f57]
     /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) [0x7fbee7076413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fbee719b4a2]
     [0x4606f35c0d8]
    
     *** caught illegal operation ***
     address 0x7fbee675f9a5, 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(x)
     10: as.dagitty.character(x)
     11: as.dagitty(x)
     12: backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }")
     13: is(value, "JS_EVAL")
     14: .jsassign(xv, as.character(x))
     15: .jsassigngraph(xv, x)
     16: tryCatchList(expr, classes, parentenv, handlers)
     17: tryCatch({ .jsassigngraph(xv, x) for (w in v) { .jsassign(vv, as.character(w)) .jsassign(vv, .jsp("global.", xv, ".getVertex(global.", vv, ")")) .jsassign(vv, .jsp("global.", xv, ".", type, "Of([global.", vv, "])")) r <- union(r, .jsget(paste0("_.pluck(global.", vv, ",'id')"))) }}, finally = { .deleteJSVar(xv) .deleteJSVar(vv)})
     18: .kins(x, v, "children")
     19: children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")
     20: eval_bare(get_expr(quo), get_env(quo))
     21: quasi_label(enquo(object), label, arg = "object")
     22: expect_equal(length(children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")), 0)
     23: eval(code, test_env)
     24: eval(code, test_env)
     25: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     26: doTryCatch(return(expr), name, parentenv, handler)
     27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     28: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     29: doTryCatch(return(expr), name, parentenv, handler)
     30: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     31: tryCatchList(expr, classes, parentenv, handlers)
     32: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     33: test_code(desc, code, env = parent.frame())
     34: test_that("CGs", { expect_equal(length(children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")), 0)})
     35: eval(code, test_env)
     36: eval(code, test_env)
     37: withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     38: doTryCatch(return(expr), name, parentenv, handler)
     39: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     40: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     41: doTryCatch(return(expr), name, parentenv, handler)
     42: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     43: tryCatchList(expr, classes, parentenv, handlers)
     44: tryCatch(withCallingHandlers({ eval(code, test_env) if (!handled && !is.null(test)) { skip_empty() }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) { })
     45: test_code(NULL, exprs, env)
     46: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     47: force(code)
     48: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { reporter$start_file(basename(path)) lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) reporter$.end_context() reporter$end_file() })
     49: FUN(X[[i]], ...)
     50: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     51: force(code)
     52: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     53: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     54: test_dir(path = test_path, reporter = reporter, env = env, filter = filter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     55: test_package_dir(package = package, test_path = test_path, filter = filter, reporter = reporter, ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     56: test_check("dagitty")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2-2
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘dagitty4semusers.Rmd’ using rmarkdown
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffe5645bdd0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fee6016845a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7fee5f6f08b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fee60163f57]
     /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) [0x7fee5fe45413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fee5ff6a4a2]
     [0x365f9b8dc0d8]
    
     *** caught illegal operation ***
    address 0x7fee5f52e9a5, cause 'illegal operand'
    
    Traceback:
     1: context_eval(join(src), private$context)
     2: get_str_output(context_eval(join(src), private$context))
     3: ct$eval(paste("global.", name, "=", value))
     4: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     7: tryCatchList(expr, classes, parentenv, handlers)
     8: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
     9: dagitty("dag {\n\tW1 -> Z1 -> X -> Y\n\tZ1 <- V -> Z2\n\tW2 -> Z2 -> Y\n\tX <-> W1 <-> W2 <-> Y\n}")
    10: eval(expr, envir, enclos)
    11: eval(expr, envir, enclos)
    12: withVisible(eval(expr, envir, enclos))
    13: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    14: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    15: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    16: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    17: evaluate::evaluate(...)
    18: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    19: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    20: block_exec(params)
    21: call_block(x)
    22: process_group.block(group)
    23: process_group(group)
    24: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    25: process_file(text, output)
    26: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, encoding = encoding)
    27: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    28: vweave_rmarkdown(...)
    29: engine$weave(file, quiet = quiet, encoding = enc)
    30: doTryCatch(return(expr), name, parentenv, handler)
    31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    32: tryCatchList(expr, classes, parentenv, handlers)
    33: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    34: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/dagitty.Rcheck/vign_test/dagitty", ser_elibs = "/tmp/RtmpiaZG2A/file71e06879224a.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc