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 |
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