CRAN Package Check Results for Package ggdag

Last updated on 2020-04-05 23:47:26 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.2.2 12.73 173.84 186.57 OK
r-devel-linux-x86_64-debian-gcc 0.2.2 0.65 2.82 3.47 ERROR
r-devel-linux-x86_64-fedora-clang 0.2.2 129.81 ERROR
r-devel-linux-x86_64-fedora-gcc 0.2.2 132.71 ERROR
r-devel-windows-ix86+x86_64 0.2.2 18.00 168.00 186.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.2.2 16.00 168.00 184.00 OK
r-patched-linux-x86_64 0.2.2 9.75 165.80 175.55 OK
r-patched-solaris-x86 0.2.2 283.90 OK
r-release-linux-x86_64 0.2.2 9.51 163.80 173.31 OK
r-release-windows-ix86+x86_64 0.2.2 23.00 278.00 301.00 OK
r-release-osx-x86_64 0.2.2 OK
r-oldrel-windows-ix86+x86_64 0.2.2 13.00 185.00 198.00 OK
r-oldrel-osx-x86_64 0.2.2 OK

Check Details

Version: 0.2.2
Check: whether package can be installed
Result: ERROR
    Installation failed.
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.2.2
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: 0x7ffcedb35eb0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fcea734361a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7fcea68cb2a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fcea733f117]
     /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) [0x7fcea701f693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fcea7144632]
     [0x2fc298f5c0d8]
    
     *** caught illegal operation ***
    address 0x7fcea6708b7d, 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: 0.2.2
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:stats':
    
     filter
    
     >
     > test_check("ggdag")
    
    
     #
     # Fatal error in , line 0
     # Failed to create ICU collator, are ICU data files missing?
     #
     #
     #
     #FailureMessage Object: 0x7ffe39612990
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fd37b38d61a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7fd37a9152a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fd37b389117]
     /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) [0x7fd37b069693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fd37b18e632]
     [0x2dd2a80dc0d8]
    
     *** caught illegal operation ***
     address 0x7fd37a752b7d, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
     10: dagitty::dagitty(dag_txt)
     11: dagify(y ~ x + z2 + w2 + w1, x ~ z1 + w1, z1 ~ w1 + v, z2 ~ w2 + v, w1 ~ ~w2, exposure = "x", outcome = "y")
     12: eval(exprs, env)
     13: eval(exprs, env)
     14: FUN(X[[i]], ...)
     15: lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
     16: source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
     17: source_test_helpers(path, env)
     18: 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)
     19: 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)
     20: test_check("ggdag")
     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 ‘bias-structures.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:stats':
    
     filter
    
    --- finished re-building ‘bias-structures.Rmd’
    
    sh: line 1: 44815 Illegal instruction (core dumped) R_LIBS=/tmp/RtmpEbWZwW/RLIBS_5cf91172826e R_ENVIRON_USER='' R_LIBS_USER='' R_LIBS_SITE='no_such_dir' '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/RtmpEbWZwW/working_dir/Rtmp9VKnJw/filea0f24ec9bdb3' 2>&1 < '/tmp/RtmpEbWZwW/working_dir/Rtmp9VKnJw/filea0f26dd1e962'
    --- re-building ‘intro-to-dags.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    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: 0x7ffe78c24e90
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f901740e61a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7f90169962a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f901740a117]
     /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) [0x7f90170ea693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f901720f632]
     [0x2ab6728dc0d8]
    
     *** caught illegal operation ***
    address 0x7f90167d3b7d, 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/RtmpEbWZwW/working_dir/Rtmp9VKnJw/filea0f2aff10ad.rds")
    An irrecoverable exception occurred. R is aborting now ...
    sh: line 1: 45784 Illegal instruction (core dumped) R_LIBS=/tmp/RtmpEbWZwW/RLIBS_5cf91172826e R_ENVIRON_USER='' R_LIBS_USER='' R_LIBS_SITE='no_such_dir' '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/RtmpEbWZwW/working_dir/Rtmp9VKnJw/filea0f210947cdc' 2>&1 < '/tmp/RtmpEbWZwW/working_dir/Rtmp9VKnJw/filea0f22c09011c'
    --- re-building ‘intro-to-ggdag.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    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: 0x7ffd25c123f0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fe6d7b1961a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7fe6d70a12a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fe6d7b15117]
     /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) [0x7fe6d77f5693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fe6d791a632]
     [0x1a7486edc0d8]
    
     *** caught illegal operation ***
    address 0x7fe6d6edeb7d, 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/RtmpEbWZwW/working_dir/Rtmp9VKnJw/filea0f243c4d2e3.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: 0.2.2
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: 0x7ffcaf052750
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fa33083c61a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7fa32fdc42a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fa330838117]
     /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) [0x7fa330518693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fa33063d632]
     [0x329b40d5c0d8]
    
     *** caught illegal operation ***
    address 0x7fa32fc01b7d, 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: 0.2.2
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:stats':
    
     filter
    
     >
     > test_check("ggdag")
    
    
     #
     # Fatal error in , line 0
     # Failed to create ICU collator, are ICU data files missing?
     #
     #
     #
     #FailureMessage Object: 0x7fff0bd03430
     ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fdd748c361a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7fdd73e4b2a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fdd748bf117]
     /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) [0x7fdd7459f693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fdd746c4632]
     [0x344deeedc0d8]
    
     *** caught illegal operation ***
     address 0x7fdd73c88b7d, 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$eval(paste("global.", name, "=", value))
     5: .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()"))
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ .jsassign(xv, as.character(x)) .jsassign(xv, .jsp("GraphParser.parseGuess(global.", xv, ").toString()")) r <- structure(.jsget(xv), class = "dagitty")}, error = function(e) { stop(e)}, finally = { .deleteJSVar(xv)})
     10: dagitty::dagitty(dag_txt)
     11: dagify(y ~ x + z2 + w2 + w1, x ~ z1 + w1, z1 ~ w1 + v, z2 ~ w2 + v, w1 ~ ~w2, exposure = "x", outcome = "y")
     12: eval(exprs, env)
     13: eval(exprs, env)
     14: FUN(X[[i]], ...)
     15: lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
     16: source_dir(path, "^helper.*\\.[rR]$", env = env, wrap = FALSE)
     17: source_test_helpers(path, env)
     18: 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)
     19: 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)
     20: test_check("ggdag")
     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 ‘bias-structures.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    The following object is masked from 'package:stats':
    
     filter
    
    --- finished re-building ‘bias-structures.Rmd’
    
    sh: line 1: 7570 Illegal instruction (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpSEHp1j/working_dir/RtmpPwc8Wm/filebf23afdbc5f' 2>&1 < '/tmp/RtmpSEHp1j/working_dir/RtmpPwc8Wm/filebf23312ca113'
    --- re-building ‘intro-to-dags.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    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: 0x7ffc0c394eb0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7f0791af461a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7f079107c2a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7f0791af0117]
     /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) [0x7f07917d0693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7f07918f5632]
     [0x32efe4dc0d8]
    
     *** caught illegal operation ***
    address 0x7f0790eb9b7d, 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/RtmpSEHp1j/working_dir/RtmpPwc8Wm/filebf23ccde235.rds")
    An irrecoverable exception occurred. R is aborting now ...
    sh: line 1: 9199 Illegal instruction (core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpSEHp1j/working_dir/RtmpPwc8Wm/filebf236b404c11' 2>&1 < '/tmp/RtmpSEHp1j/working_dir/RtmpPwc8Wm/filebf239c0d9a8'
    --- re-building ‘intro-to-ggdag.Rmd’ using rmarkdown
    Loading required package: ggplot2
    
    Attaching package: 'ggdag'
    
    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: 0x7ffe128ed1a0
    ==== C stack trace ===============================
    
     /lib64/libnode.so.64(v8::base::debug::StackTrace::StackTrace()+0x1a) [0x7fed2ffca61a]
     /lib64/libnode.so.64(+0x92f2a1) [0x7fed2f5522a1]
     /lib64/libnode.so.64(V8_Fatal(char const*, int, char const*, ...)+0x177) [0x7fed2ffc6117]
     /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) [0x7fed2fca6693]
     /lib64/libnode.so.64(v8::internal::Runtime_CreateCollator(int, v8::internal::Object**, v8::internal::Isolate*)+0x192) [0x7fed2fdcb632]
     [0x3492e32dc0d8]
    
     *** caught illegal operation ***
    address 0x7fed2f38fb7d, 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/RtmpSEHp1j/working_dir/RtmpPwc8Wm/filebf235d4167e2.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