CRAN Package Check Results for Package ggdag

Last updated on 2020-01-27 18:49:00 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.1 10.45 150.77 161.22 OK
r-devel-linux-x86_64-debian-gcc 0.2.1 8.29 115.98 124.27 OK
r-devel-linux-x86_64-fedora-clang 0.2.1 137.60 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.1 127.08 ERROR
r-devel-windows-ix86+x86_64 0.2.1 47.00 215.00 262.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.2.1 30.00 162.00 192.00 OK
r-patched-linux-x86_64 0.2.1 OK
r-patched-solaris-x86 0.2.1 216.30 NOTE
r-release-linux-x86_64 0.2.1 8.16 132.74 140.90 OK
r-release-windows-ix86+x86_64 0.2.1 14.00 139.00 153.00 OK
r-release-osx-x86_64 0.2.1 NOTE
r-oldrel-windows-ix86+x86_64 0.2.1 9.00 132.00 141.00 OK
r-oldrel-osx-x86_64 0.2.1 NOTE

Check Details

Version: 0.2.1
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘ggforce’ ‘plyr’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.2.1
Check: examples
Result: ERROR
    Running examples in ‘ggdag-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Covariate Adjustment Sets
    > ### Title: Covariate Adjustment Sets
    > ### Aliases: 'Covariate Adjustment Sets' dag_adjustment_sets
    > ### ggdag_adjustment_set
    >
    > ### ** Examples
    >
    > dag <- dagify(y ~ x + z2 + w2 + w1,
    + x ~ z1 + w1,
    + z1 ~ w1 + v,
    + z2 ~ w2 + v,
    + w1 ~~ w2,
    + exposure = "x",
    + outcome = "y")
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffc124cacf0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f2aa03da45a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f2a9f9628b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f2aa03d5f57]
     /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) [0x7f2aa00b7413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f2aa01dc4a2]
     [0x15418a5dc0d8]
    
     *** caught illegal operation ***
    address 0x7f2a9f7a09a5, 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::dagitty(dag_txt)
    11: dagify(y ~ x + z2 + w2 + w1, x ~ z1 + w1, z1 ~ w1 + v, z2 ~ w2 + v, w1 ~ ~w2, exposure = "x", outcome = "y")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.1
Check: tests
Result: ERROR
     Running ‘spelling.R’
     Running ‘testthat.R’ [5s/14s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(ggdag)
     Loading required package: ggplot2
    
     Attaching package: 'ggdag'
    
     The following object is masked from 'package:ggplot2':
    
     expand_scale
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test_check("ggdag")
    
    
     #
     # Fatal error in , line 0
     # Failed to create ICU collator, are ICU data files missing?
     #
     #
     #
     #FailureMessage Object: 0x7ffd3b0cc9d0
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fa0b704545a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7fa0b65cd8b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fa0b7040f57]
     /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) [0x7fa0b6d22413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fa0b6e474a2]
     [0x37f51115c0d8]
    
     *** caught illegal operation ***
     address 0x7fa0b640b9a5, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphTransformer.", method, "(global.", xv, ")"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassigngraph(xv, x) .jsassign(xv, .jsp("GraphTransformer.", method, "(global.", xv, ")")) .jsassign(xv, .jsp("global.", xv, ".toString()")) r <- .jsget(xv)}, error = function(e) stop(e), finally = { .deleteJSVar(xv)})
     10: .graphTransformer(x, "dagToCpdag")
     11: dagitty::equivalenceClass(.dag$dag)
     12: eval(lhs, parent, parent)
     13: eval(lhs, parent, parent)
     14: dagitty::equivalenceClass(.dag$dag) %>% dagitty::edges(.) %>% dplyr::filter(e == "--") %>% dplyr::select(name = v, reversable = e, to = w) %>% dplyr::mutate_at(c("name", "to"), as.character) %>% dplyr::mutate(hash = hash(name, to)) %>% dplyr::select(hash, reversable)
     15: node_equivalent_class(tidy_dag)
     16: expect_function_produces_name(node_equivalent_class(tidy_dag), "reversable")
     17: eval(code, test_env)
     18: eval(code, test_env)
     19: 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)
     20: doTryCatch(return(expr), name, parentenv, handler)
     21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     23: doTryCatch(return(expr), name, parentenv, handler)
     24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     25: tryCatchList(expr, classes, parentenv, handlers)
     26: 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) { })
     27: test_code(desc, code, env = parent.frame())
     28: test_that("node functions produce correct columns", { tidy_dag <- dagify(y ~ x + z, x ~ z) %>% tidy_dagitty() expect_function_produces_name(node_ancestors(tidy_dag, "y"), "ancestor") expect_function_produces_name(node_children(tidy_dag, "z"), "children") expect_function_produces_name(node_collider(tidy_dag), "colliders") expect_function_produces_name(node_dconnected(tidy_dag, "x", "y"), c("adjusted", "d_relationship")) expect_function_produces_name(node_descendants(tidy_dag, "z"), "descendant") expect_function_produces_name(node_drelationship(tidy_dag, "x", "y"), c("adjusted", "d_relationship")) expect_function_produces_name(node_dseparated(tidy_dag, "x", "y"), c("adjusted", "d_relationship")) expect_function_produces_name(node_equivalent_class(tidy_dag), "reversable") expect_function_produces_name(node_equivalent_dags(tidy_dag), "dag") expect_function_produces_name(node_exogenous(tidy_dag), "exogenous") expect_function_produces_name(node_instrumental(tidy_dag, exposure = "x", outcome = "y"), c("adjusted", "instrumental")) expect_function_produces_name(node_parents(tidy_dag, "z"), "parent") expect_function_produces_name(node_status(tidy_dag), "status")})
     29: eval(code, test_env)
     30: eval(code, test_env)
     31: 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)
     32: doTryCatch(return(expr), name, parentenv, handler)
     33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     34: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     35: doTryCatch(return(expr), name, parentenv, handler)
     36: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     37: tryCatchList(expr, classes, parentenv, handlers)
     38: 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) { })
     39: test_code(NULL, exprs, env)
     40: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     41: force(code)
     42: doWithOneRestart(return(expr), restart)
     43: withOneRestart(expr, restarts[[1L]])
     44: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     45: 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() })
     46: FUN(X[[i]], ...)
     47: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, 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 = 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("ggdag")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘bias-structures.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:ggplot2':
    
     expand_scale
    
    The following object is masked from 'package:stats':
    
     filter
    
    --- finished re-building ‘bias-structures.Rmd’
    
    sh: line 1: 23854 Illegal instruction (core dumped) '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/Rtmp8ROzhx/working_dir/Rtmpp3YGN1/file40fa2420ff0f' 2>&1 < '/tmp/Rtmp8ROzhx/working_dir/Rtmpp3YGN1/file40fa7ca04c8a'
    --- re-building ‘intro-to-dags.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:ggplot2':
    
     expand_scale
    
    The following object is masked from 'package:stats':
    
     filter
    
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffddc144370
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f806af5745a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f806a4df8b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f806af52f57]
     /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) [0x7f806ac34413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f806ad594a2]
     [0x191d03bdc0d8]
    
     *** caught illegal operation ***
    address 0x7f806a31d9a5, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
    10: dagitty::dagitty(dag_txt)
    11: dagify(y ~ ~x)
    12: eval(lhs, parent, parent)
    13: eval(lhs, parent, parent)
    14: dagify(y ~ ~x) %>% ggdag()
    15: eval(expr, envir, enclos)
    16: eval(expr, envir, enclos)
    17: withVisible(eval(expr, envir, enclos))
    18: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    19: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    21: evaluate_call(expr, parsed$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)
    22: evaluate::evaluate(...)
    23: 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$render, options))
    24: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    25: block_exec(params)
    26: call_block(x)
    27: process_group.block(group)
    28: process_group(group)
    29: 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$get("infile"), ") ") })
    30: process_file(text, output)
    31: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    32: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
    33: vweave_rmarkdown(...)
    34: engine$weave(file, quiet = quiet, encoding = enc)
    35: doTryCatch(return(expr), name, parentenv, handler)
    36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    37: tryCatchList(expr, classes, parentenv, handlers)
    38: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    39: tools:::.buildOneVignette("intro-to-dags.Rmd", "/data/gannet/ripley/R/packages/tests-clang/ggdag.Rcheck/vign_test/ggdag", TRUE, FALSE, "intro-to-dags", "UTF-8", "/tmp/Rtmp8ROzhx/working_dir/Rtmpp3YGN1/file40fa63873594.rds")
    An irrecoverable exception occurred. R is aborting now ...
    sh: line 1: 25764 Illegal instruction (core dumped) '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/Rtmp8ROzhx/working_dir/Rtmpp3YGN1/file40fa34bada55' 2>&1 < '/tmp/Rtmp8ROzhx/working_dir/Rtmpp3YGN1/file40fa2286f425'
    --- re-building ‘intro-to-ggdag.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:ggplot2':
    
     expand_scale
    
    The following object is masked from 'package:stats':
    
     filter
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffce99ba640
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f92aa80045a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f92a9d888b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f92aa7fbf57]
     /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) [0x7f92aa4dd413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f92aa6024a2]
     [0x916ae35c0d8]
    
     *** caught illegal operation ***
    address 0x7f92a9bc69a5, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
    10: dagitty::dagitty(dag_txt)
    11: dagify(y ~ x + z, x ~ ~z)
    12: eval(lhs, parent, parent)
    13: eval(lhs, parent, parent)
    14: dagify(y ~ x + z, x ~ ~z) %>% node_canonical() %>% ggplot(aes(x = x, y = y, xend = xend, yend = yend))
    15: eval(expr, envir, enclos)
    16: eval(expr, envir, enclos)
    17: withVisible(eval(expr, envir, enclos))
    18: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    19: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    21: evaluate_call(expr, parsed$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)
    22: evaluate::evaluate(...)
    23: 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$render, options))
    24: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    25: block_exec(params)
    26: call_block(x)
    27: process_group.block(group)
    28: process_group(group)
    29: 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$get("infile"), ") ") })
    30: process_file(text, output)
    31: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    32: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
    33: vweave_rmarkdown(...)
    34: engine$weave(file, quiet = quiet, encoding = enc)
    35: doTryCatch(return(expr), name, parentenv, handler)
    36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    37: tryCatchList(expr, classes, parentenv, handlers)
    38: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    39: tools:::.buildOneVignette("intro-to-ggdag.Rmd", "/data/gannet/ripley/R/packages/tests-clang/ggdag.Rcheck/vign_test/ggdag", TRUE, FALSE, "intro-to-ggdag", "UTF-8", "/tmp/Rtmp8ROzhx/working_dir/Rtmpp3YGN1/file40faa56fc6.rds")
    An irrecoverable exception occurred. R is aborting now ...
    SUMMARY: processing the following files failed:
     ‘intro-to-dags.Rmd’ ‘intro-to-ggdag.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 0.2.1
Check: examples
Result: ERROR
    Running examples in ‘ggdag-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: Covariate Adjustment Sets
    > ### Title: Covariate Adjustment Sets
    > ### Aliases: 'Covariate Adjustment Sets' dag_adjustment_sets
    > ### ggdag_adjustment_set
    >
    > ### ** Examples
    >
    > dag <- dagify(y ~ x + z2 + w2 + w1,
    + x ~ z1 + w1,
    + z1 ~ w1 + v,
    + z2 ~ w2 + v,
    + w1 ~~ w2,
    + exposure = "x",
    + outcome = "y")
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffe8325edc0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f728184345a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f7280dcb8b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f728183ef57]
     /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) [0x7f7281520413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f72816454a2]
     [0x366f9acdc0d8]
    
     *** caught illegal operation ***
    address 0x7f7280c099a5, 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::dagitty(dag_txt)
    11: dagify(y ~ x + z2 + w2 + w1, x ~ z1 + w1, z1 ~ w1 + v, z2 ~ w2 + v, w1 ~ ~w2, exposure = "x", outcome = "y")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.1
Check: tests
Result: ERROR
     Running ‘spelling.R’
     Running ‘testthat.R’
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(ggdag)
     Loading required package: ggplot2
    
     Attaching package: 'ggdag'
    
     The following object is masked from 'package:ggplot2':
    
     expand_scale
    
     The following object is masked from 'package:stats':
    
     filter
    
     >
     > test_check("ggdag")
    
    
     #
     # Fatal error in , line 0
     # Failed to create ICU collator, are ICU data files missing?
     #
     #
     #
     #FailureMessage Object: 0x7ffd9f00e950
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f98f98bd45a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f98f8e458b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f98f98b8f57]
     /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) [0x7f98f959a413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f98f96bf4a2]
     [0x2744dfcdc0d8]
    
     *** caught illegal operation ***
     address 0x7f98f8c839a5, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphTransformer.", method, "(global.", xv, ")"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassigngraph(xv, x) .jsassign(xv, .jsp("GraphTransformer.", method, "(global.", xv, ")")) .jsassign(xv, .jsp("global.", xv, ".toString()")) r <- .jsget(xv)}, error = function(e) stop(e), finally = { .deleteJSVar(xv)})
     10: .graphTransformer(x, "dagToCpdag")
     11: dagitty::equivalenceClass(.dag$dag)
     12: eval(lhs, parent, parent)
     13: eval(lhs, parent, parent)
     14: dagitty::equivalenceClass(.dag$dag) %>% dagitty::edges(.) %>% dplyr::filter(e == "--") %>% dplyr::select(name = v, reversable = e, to = w) %>% dplyr::mutate_at(c("name", "to"), as.character) %>% dplyr::mutate(hash = hash(name, to)) %>% dplyr::select(hash, reversable)
     15: node_equivalent_class(tidy_dag)
     16: expect_function_produces_name(node_equivalent_class(tidy_dag), "reversable")
     17: eval(code, test_env)
     18: eval(code, test_env)
     19: 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)
     20: doTryCatch(return(expr), name, parentenv, handler)
     21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     23: doTryCatch(return(expr), name, parentenv, handler)
     24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     25: tryCatchList(expr, classes, parentenv, handlers)
     26: 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) { })
     27: test_code(desc, code, env = parent.frame())
     28: test_that("node functions produce correct columns", { tidy_dag <- dagify(y ~ x + z, x ~ z) %>% tidy_dagitty() expect_function_produces_name(node_ancestors(tidy_dag, "y"), "ancestor") expect_function_produces_name(node_children(tidy_dag, "z"), "children") expect_function_produces_name(node_collider(tidy_dag), "colliders") expect_function_produces_name(node_dconnected(tidy_dag, "x", "y"), c("adjusted", "d_relationship")) expect_function_produces_name(node_descendants(tidy_dag, "z"), "descendant") expect_function_produces_name(node_drelationship(tidy_dag, "x", "y"), c("adjusted", "d_relationship")) expect_function_produces_name(node_dseparated(tidy_dag, "x", "y"), c("adjusted", "d_relationship")) expect_function_produces_name(node_equivalent_class(tidy_dag), "reversable") expect_function_produces_name(node_equivalent_dags(tidy_dag), "dag") expect_function_produces_name(node_exogenous(tidy_dag), "exogenous") expect_function_produces_name(node_instrumental(tidy_dag, exposure = "x", outcome = "y"), c("adjusted", "instrumental")) expect_function_produces_name(node_parents(tidy_dag, "z"), "parent") expect_function_produces_name(node_status(tidy_dag), "status")})
     29: eval(code, test_env)
     30: eval(code, test_env)
     31: 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)
     32: doTryCatch(return(expr), name, parentenv, handler)
     33: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     34: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     35: doTryCatch(return(expr), name, parentenv, handler)
     36: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     37: tryCatchList(expr, classes, parentenv, handlers)
     38: 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) { })
     39: test_code(NULL, exprs, env)
     40: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     41: force(code)
     42: doWithOneRestart(return(expr), restart)
     43: withOneRestart(expr, restarts[[1L]])
     44: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     45: 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() })
     46: FUN(X[[i]], ...)
     47: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, 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 = 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("ggdag")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 0.2.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
    --- re-building ‘bias-structures.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:ggplot2':
    
     expand_scale
    
    The following object is masked from 'package:stats':
    
     filter
    
    --- finished re-building ‘bias-structures.Rmd’
    
    sh: line 1: 6115 Illegal instruction (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpC8QlK5/working_dir/RtmphR6hOn/file6f8584bf48' 2>&1 < '/tmp/RtmpC8QlK5/working_dir/RtmphR6hOn/file6f839f7259a'
    --- re-building ‘intro-to-dags.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:ggplot2':
    
     expand_scale
    
    The following object is masked from 'package:stats':
    
     filter
    
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffdd41a6b90
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fd19db0845a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7fd19d0908b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fd19db03f57]
     /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) [0x7fd19d7e5413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fd19d90a4a2]
     [0xb112c55c0d8]
    
     *** caught illegal operation ***
    address 0x7fd19cece9a5, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
    10: dagitty::dagitty(dag_txt)
    11: dagify(y ~ ~x)
    12: eval(lhs, parent, parent)
    13: eval(lhs, parent, parent)
    14: dagify(y ~ ~x) %>% ggdag()
    15: eval(expr, envir, enclos)
    16: eval(expr, envir, enclos)
    17: withVisible(eval(expr, envir, enclos))
    18: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    19: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    21: evaluate_call(expr, parsed$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)
    22: evaluate::evaluate(...)
    23: 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$render, options))
    24: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    25: block_exec(params)
    26: call_block(x)
    27: process_group.block(group)
    28: process_group(group)
    29: 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$get("infile"), ") ") })
    30: process_file(text, output)
    31: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    32: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
    33: vweave_rmarkdown(...)
    34: engine$weave(file, quiet = quiet, encoding = enc)
    35: doTryCatch(return(expr), name, parentenv, handler)
    36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    37: tryCatchList(expr, classes, parentenv, handlers)
    38: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    39: tools:::.buildOneVignette("intro-to-dags.Rmd", "/data/gannet/ripley/R/packages/tests-devel/ggdag.Rcheck/vign_test/ggdag", TRUE, FALSE, "intro-to-dags", "UTF-8", "/tmp/RtmpC8QlK5/working_dir/RtmphR6hOn/file6f83ec85532.rds")
    An irrecoverable exception occurred. R is aborting now ...
    sh: line 1: 6882 Illegal instruction (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpC8QlK5/working_dir/RtmphR6hOn/file6f879280337' 2>&1 < '/tmp/RtmpC8QlK5/working_dir/RtmphR6hOn/file6f8796d9871'
    --- re-building ‘intro-to-ggdag.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:ggplot2':
    
     expand_scale
    
    The following object is masked from 'package:stats':
    
     filter
    
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    
    
    #
    # Fatal error in , line 0
    # Failed to create ICU collator, are ICU data files missing?
    #
    #
    #
    #FailureMessage Object: 0x7ffd4bd36a60
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f737aab445a]
     /lib64/libnode.so.64(+0x92e8b1) [0x7f737a03c8b1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f737aaaff57]
     /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) [0x7f737a791413]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f737a8b64a2]
     [0x20914cd5c0d8]
    
     *** caught illegal operation ***
    address 0x7f7379e7a9a5, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
    10: dagitty::dagitty(dag_txt)
    11: dagify(y ~ x + z, x ~ ~z)
    12: eval(lhs, parent, parent)
    13: eval(lhs, parent, parent)
    14: dagify(y ~ x + z, x ~ ~z) %>% node_canonical() %>% ggplot(aes(x = x, y = y, xend = xend, yend = yend))
    15: eval(expr, envir, enclos)
    16: eval(expr, envir, enclos)
    17: withVisible(eval(expr, envir, enclos))
    18: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
    19: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
    20: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    21: evaluate_call(expr, parsed$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)
    22: evaluate::evaluate(...)
    23: 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$render, options))
    24: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    25: block_exec(params)
    26: call_block(x)
    27: process_group.block(group)
    28: process_group(group)
    29: 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$get("infile"), ") ") })
    30: process_file(text, output)
    31: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
    32: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
    33: vweave_rmarkdown(...)
    34: engine$weave(file, quiet = quiet, encoding = enc)
    35: doTryCatch(return(expr), name, parentenv, handler)
    36: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    37: tryCatchList(expr, classes, parentenv, handlers)
    38: 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) }}, error = function(e) { OK <<- FALSE message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    39: tools:::.buildOneVignette("intro-to-ggdag.Rmd", "/data/gannet/ripley/R/packages/tests-devel/ggdag.Rcheck/vign_test/ggdag", TRUE, FALSE, "intro-to-ggdag", "UTF-8", "/tmp/RtmpC8QlK5/working_dir/RtmphR6hOn/file6f82f50d268.rds")
    An irrecoverable exception occurred. R is aborting now ...
    SUMMARY: processing the following files failed:
     ‘intro-to-dags.Rmd’ ‘intro-to-ggdag.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc