Last updated on 2020-02-20 05:48:19 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.2-2 | 7.27 | 63.82 | 71.09 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.2-2 | 5.26 | 49.32 | 54.58 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.2-2 | 58.16 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.2-2 | 55.87 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.2-2 | 11.00 | 63.00 | 74.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.2-2 | 17.00 | 92.00 | 109.00 | OK | |
| r-patched-linux-x86_64 | 0.2-2 | 4.95 | 58.32 | 63.27 | OK | |
| r-patched-solaris-x86 | 0.2-2 | 77.90 | OK | |||
| r-release-linux-x86_64 | 0.2-2 | 5.02 | 58.53 | 63.55 | OK | |
| r-release-windows-ix86+x86_64 | 0.2-2 | 10.00 | 59.00 | 69.00 | OK | |
| r-release-osx-x86_64 | 0.2-2 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.2-2 | 6.00 | 65.00 | 71.00 | OK | |
| r-oldrel-osx-x86_64 | 0.2-2 | OK |
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: 0x7ffed3b7d5b0
==== C stack trace ===============================
/lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7feeee57145a]
/lib64/libnode.so.64(+0x92e8b1) [0x7feeedaf98b1]
/lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7feeee56cf57]
/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) [0x7feeee24e413]
/lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7feeee3734a2]
[0x26584385c0d8]
*** caught illegal operation ***
address 0x7feeed9379a5, cause 'illegal operand'
Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = serialize)
4: ct$eval(paste("global.", name, "=", value))
5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
10: dagitty("graph{ a <-> x -> b ; c -- x <- d }")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2-2
Check: tests
Result: ERROR
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(dagitty)
>
> test_check("dagitty")
#
# Fatal error in , line 0
# Failed to create ICU collator, are ICU data files missing?
#
#
#
#FailureMessage Object: 0x7fffc772e0a0
==== C stack trace ===============================
/lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f470b6f045a]
/lib64/libnode.so.64(+0x92e8b1) [0x7f470ac788b1]
/lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f470b6ebf57]
/lib64/libnode.so.64(v8::internal::Collator::InitializeCollator(v8::internal::Isolate*, v8::internal::Handle<v8::internal::JSObject>, v8::internal::Handle<v8::internal::String>, v8::internal::Handle<v8::internal::JSObject>, v8::internal::Handle<v8::internal::JSObject>)+0x473) [0x7f470b3cd413]
/lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f470b4f24a2]
[0x14d91b7dc0d8]
*** caught illegal operation ***
address 0x7f470aab69a5, cause 'illegal operand'
Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = serialize)
4: ct$eval(paste("global.", name, "=", value))
5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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)})
10: dagitty(x)
11: as.dagitty.character(x)
12: as.dagitty(x)
13: backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }")
14: is(value, "JS_EVAL")
15: .jsassign(xv, as.character(x))
16: .jsassigngraph(xv, x)
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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)})
19: .kins(x, v, "children")
20: children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")
21: eval_bare(expr, quo_get_env(quo))
22: quasi_label(enquo(object), label, arg = "object")
23: expect_equal(length(children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")), 0)
24: eval(code, test_env)
25: eval(code, test_env)
26: 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)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: 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) { })
34: test_code(desc, code, env = parent.frame())
35: 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)})
36: eval(code, test_env)
37: eval(code, test_env)
38: 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)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: 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) { })
46: test_code(NULL, exprs, env)
47: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
48: force(code)
49: doWithOneRestart(return(expr), restart)
50: withOneRestart(expr, restarts[[1L]])
51: withRestarts(testthat_abort_reporter = function() NULL, force(code))
52: 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() })
53: FUN(X[[i]], ...)
54: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
55: force(code)
56: doWithOneRestart(return(expr), restart)
57: withOneRestart(expr, restarts[[1L]])
58: withRestarts(testthat_abort_reporter = function() NULL, force(code))
59: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
60: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
61: 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)
62: 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)
63: 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: 0x7fff4101fc20
==== C stack trace ===============================
/lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f1563d1e45a]
/lib64/libnode.so.64(+0x92e8b1) [0x7f15632a68b1]
/lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f1563d19f57]
/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) [0x7f15639fb413]
/lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f1563b204a2]
[0x35f885dc0d8]
*** caught illegal operation ***
address 0x7f15630e49a5, cause 'illegal operand'
Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = serialize)
4: ct$eval(paste("global.", name, "=", value))
5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
10: dagitty("dag {\n\tW1 -> Z1 -> X -> Y\n\tZ1 <- V -> Z2\n\tW2 -> Z2 -> Y\n\tX <-> W1 <-> W2 <-> Y\n}")
11: eval(expr, envir, enclos)
12: eval(expr, envir, enclos)
13: withVisible(eval(expr, envir, enclos))
14: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
15: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
16: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
17: evaluate_call(expr, parsed$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)
18: evaluate::evaluate(...)
19: 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$render, options))
20: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
21: block_exec(params)
22: call_block(x)
23: process_group.block(group)
24: process_group(group)
25: 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$get("infile"), ") ") })
26: process_file(text, output)
27: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
28: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
29: vweave_rmarkdown(...)
30: engine$weave(file, quiet = quiet, encoding = enc)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: 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)))})
35: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/dagitty.Rcheck/vign_test/dagitty", ser_elibs = "/tmp/RtmpMEp4f8/file604b34f005b5.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: 0x7ffef9db8170
==== C stack trace ===============================
/lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f6ea1a8545a]
/lib64/libnode.so.64(+0x92e8b1) [0x7f6ea100d8b1]
/lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f6ea1a80f57]
/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) [0x7f6ea1762413]
/lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f6ea18874a2]
[0xdc759c5c0d8]
*** caught illegal operation ***
address 0x7f6ea0e4b9a5, cause 'illegal operand'
Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = serialize)
4: ct$eval(paste("global.", name, "=", value))
5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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)})
10: 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: 0x7ffea6aebfa0
==== C stack trace ===============================
/lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f1dc029745a]
/lib64/libnode.so.64(+0x92e8b1) [0x7f1dbf81f8b1]
/lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f1dc0292f57]
/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) [0x7f1dbff74413]
/lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f1dc00994a2]
[0x18aba76dc0d8]
*** caught illegal operation ***
address 0x7f1dbf65d9a5, cause 'illegal operand'
Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = serialize)
4: ct$eval(paste("global.", name, "=", value))
5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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)})
10: dagitty(x)
11: as.dagitty.character(x)
12: as.dagitty(x)
13: backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }")
14: is(value, "JS_EVAL")
15: .jsassign(xv, as.character(x))
16: .jsassigngraph(xv, x)
17: tryCatchList(expr, classes, parentenv, handlers)
18: 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)})
19: .kins(x, v, "children")
20: children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")
21: eval_bare(expr, quo_get_env(quo))
22: quasi_label(enquo(object), label, arg = "object")
23: expect_equal(length(children(backDoorGraph("pdag{ {i j} -> x -> {a -- b -- c -- a } a -> z b -> y x[e] y[o] }"), "x")), 0)
24: eval(code, test_env)
25: eval(code, test_env)
26: 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)
27: doTryCatch(return(expr), name, parentenv, handler)
28: tryCatchOne(expr, names, parentenv, handlers[[1L]])
29: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: 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) { })
34: test_code(desc, code, env = parent.frame())
35: 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)})
36: eval(code, test_env)
37: eval(code, test_env)
38: 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)
39: doTryCatch(return(expr), name, parentenv, handler)
40: tryCatchOne(expr, names, parentenv, handlers[[1L]])
41: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: 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) { })
46: test_code(NULL, exprs, env)
47: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
48: force(code)
49: doWithOneRestart(return(expr), restart)
50: withOneRestart(expr, restarts[[1L]])
51: withRestarts(testthat_abort_reporter = function() NULL, force(code))
52: 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() })
53: FUN(X[[i]], ...)
54: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
55: force(code)
56: doWithOneRestart(return(expr), restart)
57: withOneRestart(expr, restarts[[1L]])
58: withRestarts(testthat_abort_reporter = function() NULL, force(code))
59: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
60: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
61: 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)
62: 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)
63: 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: 0x7ffffb44e3e0
==== C stack trace ===============================
/lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f893a1a245a]
/lib64/libnode.so.64(+0x92e8b1) [0x7f893972a8b1]
/lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f893a19df57]
/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) [0x7f8939e7f413]
/lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f8939fa44a2]
[0xfd8a70dc0d8]
*** caught illegal operation ***
address 0x7f89395689a5, cause 'illegal operand'
Traceback:
1: context_eval(join(src), private$context, serialize)
2: get_str_output(context_eval(join(src), private$context, serialize))
3: evaluate_js(src, serialize = serialize)
4: ct$eval(paste("global.", name, "=", value))
5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
6: doTryCatch(return(expr), name, parentenv, handler)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
8: tryCatchList(expr, classes, parentenv, handlers)
9: 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)})
10: dagitty("dag {\n\tW1 -> Z1 -> X -> Y\n\tZ1 <- V -> Z2\n\tW2 -> Z2 -> Y\n\tX <-> W1 <-> W2 <-> Y\n}")
11: eval(expr, envir, enclos)
12: eval(expr, envir, enclos)
13: withVisible(eval(expr, envir, enclos))
14: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
15: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
16: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
17: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
18: evaluate::evaluate(...)
19: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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: 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$render, options)))
21: block_exec(params)
22: call_block(x)
23: process_group.block(group)
24: process_group(group)
25: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
26: process_file(text, output)
27: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
28: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
29: vweave_rmarkdown(...)
30: engine$weave(file, quiet = quiet, encoding = enc)
31: doTryCatch(return(expr), name, parentenv, handler)
32: tryCatchOne(expr, names, parentenv, handlers[[1L]])
33: tryCatchList(expr, classes, parentenv, handlers)
34: tryCatch({ engine$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)))})
35: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/dagitty.Rcheck/vign_test/dagitty", ser_elibs = "/tmp/RtmpBdVG5K/file7b853206ae10.rds")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc