Last updated on 2026-01-16 17:50:35 CET.
| Package | ERROR | OK |
|---|---|---|
| eudract | 4 | 9 |
| mreg | 13 | |
| rpsftm | 13 |
Current CRAN status: ERROR: 4, OK: 9
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘eudract-Ex.R’ failed
The error most likely occurred in:
> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ### ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
>
> ### ** Examples
>
> safety_statistics <- safety_summary(safety,
+ exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'/Volumes/Temp/tmp/Rtmp9Q2HKe/file164381f8c1627.xml' is created or modified
> eudract_convert(input=simple,
+ output=eudract)
'/Volumes/Temp/tmp/Rtmp9Q2HKe/file1643826026a9f.xml' is created or modified
Please email cuh.cctu@nhs.net to tell us if you have successfully uploaded a study to EudraCT.
This is to allow us to measure the impact of this tool.
> clintrials_gov_convert(input=simple,
+ original=system.file("extdata", "1234.xml", package ="eudract"),
+ output=ct)
'/Volumes/Temp/tmp/Rtmp9Q2HKe/file1643868a60037.xml' is created or modified
*** caught segfault ***
address 0xb0962bb6048, cause 'invalid permissions'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-macos-arm64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(eudract)
>
> test_check("eudract")
*** caught segfault ***
address 0x7b47ef48e048, cause 'invalid permissions'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml"))
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
14: test_code(code, parent.frame())
15: test_that("convert to ClinicalTrials.Gov", { clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml")) new <- read_xml(file.path(path, "table_ct.xml")) ref <- read_xml(file.path(reference_path, "table_ct.xml")) expect_equal(new, ref) if (Sys.getenv("ct_user") == "" | Sys.getenv("ct_pass") == "") { skip("Need to have the userid/password as environment variables") } output <- clintrials_gov_upload(input = file.path(path, "simple.xml"), backup = file.path(path, "bak_study_file.xml"), output = file.path(path, "study_file.xml"), orgname = "AddenbrookesH", username = Sys.getenv("ct_user"), password = Sys.getenv("ct_pass"), studyid = "1234", url = "https://prstest.clinicaltrials.gov/") expect_equal(names(output), c("download", "upload"))})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
26: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
27: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("eudract")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-macos-arm64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
sh: line 1: 97119 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmp7AlTCb/file16c8d622a2f7f' 2>&1 < '/Volumes/Temp/tmp/Rtmp7AlTCb/file16c8d3f946d32'
--- re-building ‘eudract.Rmd’ using rmarkdown
*** caught segfault ***
address 0xd5477b882048, cause 'invalid permissions'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct_upload_file)
4: eval(expr, envir)
5: eval(expr, envir)
6: withVisible(eval(expr, envir))
7: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
8: eval(call)
9: eval(call)
10: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestartList(expr, restarts[-nr])
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
16: withRestartList(expr, restarts)
17: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
18: evaluate::evaluate(...)
19: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
20: in_dir(input_dir(), expr)
21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
22: eng_r(options)
23: block_exec(params)
24: call_block(x)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
27: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
28: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools:::.buildOneVignette("eudract.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.5/eudract.Rcheck/vign_test/eudract", TRUE, FALSE, "eudract", "UTF-8", "/Volumes/Temp/tmp/Rtmp7AlTCb/file16c8d2df5c44b.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘standard_reporting.Rmd’ using rmarkdown
2026-01-17 01:03:21.611 R[97654:752747] XType: Using static font registry.
--- finished re-building ‘standard_reporting.Rmd’
SUMMARY: processing the following file failed:
‘eudract.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-arm64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘eudract-Ex.R’ failed
The error most likely occurred in:
> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ### ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
>
> ### ** Examples
>
> safety_statistics <- safety_summary(safety,
+ exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'/Volumes/Temp/tmp/RtmpObxWVh/file2f0a6c9f6643.xml' is created or modified
> eudract_convert(input=simple,
+ output=eudract)
'/Volumes/Temp/tmp/RtmpObxWVh/file2f0a54f2f06b.xml' is created or modified
Please email cuh.cctu@nhs.net to tell us if you have successfully uploaded a study to EudraCT.
This is to allow us to measure the impact of this tool.
> clintrials_gov_convert(input=simple,
+ original=system.file("extdata", "1234.xml", package ="eudract"),
+ output=ct)
'/Volumes/Temp/tmp/RtmpObxWVh/file2f0a19862c5f.xml' is created or modified
*** caught segfault ***
address 0x799fdb948728, cause 'memory not mapped'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(eudract)
>
> test_check("eudract")
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml"))
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
14: test_code(code, parent.frame())
15: test_that("convert to ClinicalTrials.Gov", { clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml")) new <- read_xml(file.path(path, "table_ct.xml")) ref <- read_xml(file.path(reference_path, "table_ct.xml")) expect_equal(new, ref) if (Sys.getenv("ct_user") == "" | Sys.getenv("ct_pass") == "") { skip("Need to have the userid/password as environment variables") } output <- clintrials_gov_upload(input = file.path(path, "simple.xml"), backup = file.path(path, "bak_study_file.xml"), output = file.path(path, "study_file.xml"), orgname = "AddenbrookesH", username = Sys.getenv("ct_user"), password = Sys.getenv("ct_pass"), studyid = "1234", url = "https://prstest.clinicaltrials.gov/") expect_equal(names(output), c("download", "upload"))})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
26: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
27: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("eudract")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
sh: line 1: 15633 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpSxwLzD/file3115220615e8' 2>&1 < '/Volumes/Temp/tmp/RtmpSxwLzD/file31153d8843cb'
--- re-building ‘eudract.Rmd’ using rmarkdown
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: xml_validate.xml_document(output_xml, schema_output)
2: xml2::xml_validate(output_xml, schema_output)
3: eudract_convert(input = simple, output = eudract_upload_file)
4: eval(expr, envir)
5: eval(expr, envir)
6: withVisible(eval(expr, envir))
7: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
8: eval(call)
9: eval(call)
10: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestartList(expr, restarts[-nr])
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
16: withRestartList(expr, restarts)
17: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
18: evaluate::evaluate(...)
19: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
20: in_dir(input_dir(), expr)
21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
22: eng_r(options)
23: block_exec(params)
24: call_block(x)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
27: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
28: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools:::.buildOneVignette("eudract.Rmd", "/Volumes/Builds/packages/big-sur-x86_64/results/4.5/eudract.Rcheck/vign_test/eudract", TRUE, FALSE, "eudract", "UTF-8", "/Volumes/Temp/tmp/RtmpSxwLzD/file31155a1cf0d0.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘standard_reporting.Rmd’ using rmarkdown
--- finished re-building ‘standard_reporting.Rmd’
SUMMARY: processing the following file failed:
‘eudract.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-release-macos-x86_64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘eudract-Ex.R’ failed
The error most likely occurred in:
> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ### ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
>
> ### ** Examples
>
> safety_statistics <- safety_summary(safety,
+ exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'/Volumes/Temp/tmp/RtmphKb1Kx/file342e7d8ddf27.xml' is created or modified
> eudract_convert(input=simple,
+ output=eudract)
'/Volumes/Temp/tmp/RtmphKb1Kx/file342e6d35b9d6.xml' is created or modified
Please email cuh.cctu@nhs.net to tell us if you have successfully uploaded a study to EudraCT.
This is to allow us to measure the impact of this tool.
> clintrials_gov_convert(input=simple,
+ original=system.file("extdata", "1234.xml", package ="eudract"),
+ output=ct)
'/Volumes/Temp/tmp/RtmphKb1Kx/file342e623bc89d.xml' is created or modified
*** caught segfault ***
address 0x100fe3d6e048, cause 'invalid permissions'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(eudract)
>
> test_check("eudract")
*** caught segfault ***
address 0xc85d62464fc8, cause 'invalid permissions'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml"))
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
14: test_code(code, parent.frame())
15: test_that("convert to ClinicalTrials.Gov", { clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml")) new <- read_xml(file.path(path, "table_ct.xml")) ref <- read_xml(file.path(reference_path, "table_ct.xml")) expect_equal(new, ref) if (Sys.getenv("ct_user") == "" | Sys.getenv("ct_pass") == "") { skip("Need to have the userid/password as environment variables") } output <- clintrials_gov_upload(input = file.path(path, "simple.xml"), backup = file.path(path, "bak_study_file.xml"), output = file.path(path, "study_file.xml"), orgname = "AddenbrookesH", username = Sys.getenv("ct_user"), password = Sys.getenv("ct_pass"), studyid = "1234", url = "https://prstest.clinicaltrials.gov/") expect_equal(names(output), c("download", "upload"))})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
26: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
27: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("eudract")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
sh: line 1: 20534 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/Rtmpon4RLd/file3f6f5462f4d6' 2>&1 < '/Volumes/Temp/tmp/Rtmpon4RLd/file3f6f2cb838e2'
--- re-building ‘eudract.Rmd’ using rmarkdown
*** caught segfault ***
address 0x3e3c12959a48, cause 'invalid permissions'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct_upload_file)
4: eval(expr, envir)
5: eval(expr, envir)
6: withVisible(eval(expr, envir))
7: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
8: eval(call)
9: eval(call)
10: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestartList(expr, restarts[-nr])
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
16: withRestartList(expr, restarts)
17: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
18: evaluate::evaluate(...)
19: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
20: in_dir(input_dir(), expr)
21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
22: eng_r(options)
23: block_exec(params)
24: call_block(x)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
27: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
28: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools:::.buildOneVignette("eudract.Rmd", "/Volumes/Builds/packages/big-sur-arm64/results/4.4/eudract.Rcheck/vign_test/eudract", TRUE, FALSE, "eudract", "UTF-8", "/Volumes/Temp/tmp/Rtmpon4RLd/file3f6f5346e8e0.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘standard_reporting.Rmd’ using rmarkdown
2026-01-17 00:51:38.747 R[21229:335635] XType: Using static font registry.
--- finished re-building ‘standard_reporting.Rmd’
SUMMARY: processing the following file failed:
‘eudract.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-arm64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘eudract-Ex.R’ failed
The error most likely occurred in:
> ### Name: clintrials_gov_convert
> ### Title: applies a conversion using xslt from a simple xml file to a
> ### ClinicalTrials.gov compatible file, and checks against the schema
> ### Aliases: clintrials_gov_convert
>
> ### ** Examples
>
> safety_statistics <- safety_summary(safety,
+ exposed=c("Experimental"=60,"Control"=67))
> simple <- tempfile(fileext = ".xml")
> eudract <- tempfile(fileext = ".xml")
> ct <- tempfile(fileext = ".xml")
> simple_safety_xml(safety_statistics, simple)
'/Volumes/Temp/tmp/Rtmp1QvaQc/file151a6385d6205.xml' is created or modified
> eudract_convert(input=simple,
+ output=eudract)
'/Volumes/Temp/tmp/Rtmp1QvaQc/file151a67ace532b.xml' is created or modified
Please email cuh.cctu@nhs.net to tell us if you have successfully uploaded a study to EudraCT.
This is to allow us to measure the impact of this tool.
> clintrials_gov_convert(input=simple,
+ original=system.file("extdata", "1234.xml", package ="eudract"),
+ output=ct)
'/Volumes/Temp/tmp/Rtmp1QvaQc/file151a67fb66b09.xml' is created or modified
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct)
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-macos-x86_64
Version: 1.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(eudract)
>
> test_check("eudract")
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml"))
4: eval(code, test_env)
5: eval(code, test_env)
6: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
7: doTryCatch(return(expr), name, parentenv, handler)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
9: tryCatchList(expr, classes, parentenv, handlers)
10: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
14: test_code(code, parent.frame())
15: test_that("convert to ClinicalTrials.Gov", { clintrials_gov_convert(input = file.path(path, "simple.xml"), original = file.path(original_path, "1234.xml"), output = file.path(path, "table_ct.xml")) new <- read_xml(file.path(path, "table_ct.xml")) ref <- read_xml(file.path(reference_path, "table_ct.xml")) expect_equal(new, ref) if (Sys.getenv("ct_user") == "" | Sys.getenv("ct_pass") == "") { skip("Need to have the userid/password as environment variables") } output <- clintrials_gov_upload(input = file.path(path, "simple.xml"), backup = file.path(path, "bak_study_file.xml"), output = file.path(path, "study_file.xml"), orgname = "AddenbrookesH", username = Sys.getenv("ct_user"), password = Sys.getenv("ct_pass"), studyid = "1234", url = "https://prstest.clinicaltrials.gov/") expect_equal(names(output), c("download", "upload"))})
16: eval(code, test_env)
17: eval(code, test_env)
18: withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt)
19: doTryCatch(return(expr), name, parentenv, handler)
20: tryCatchOne(expr, names, parentenv, handlers[[1L]])
21: tryCatchList(expr, classes, parentenv, handlers)
22: tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal)
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(expr, restarts[[1L]])
25: withRestarts(tryCatch(withCallingHandlers({ eval(code, test_env) new_expectations <- the$test_expectations > starting_expectations if (snapshot_skipped) { skip("On CRAN") } else if (!new_expectations && skip_on_empty) { skip_empty() }}, expectation = handle_expectation, packageNotFoundError = function(e) { if (on_cran()) { skip(paste0("{", e$package, "} is not installed.")) }}, snapshot_on_cran = function(cnd) { snapshot_skipped <<- TRUE invokeRestart("muffle_cran_snapshot")}, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error, interrupt = handle_interrupt), error = handle_fatal), end_test = function() { })
26: test_code(code = exprs, env = env, reporter = get_reporter() %||% StopReporter$new())
27: source_file(path, env = env(env), desc = desc, shuffle = shuffle, error_call = error_call)
28: FUN(X[[i]], ...)
29: lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call)
30: doTryCatch(return(expr), name, parentenv, handler)
31: tryCatchOne(expr, names, parentenv, handlers[[1L]])
32: tryCatchList(expr, classes, parentenv, handlers)
33: tryCatch(code, testthat_abort_reporter = function(cnd) { cat(conditionMessage(cnd), "\n") NULL})
34: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, desc = desc, shuffle = shuffle, error_call = error_call))
35: test_files_serial(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, desc = desc, load_package = load_package, shuffle = shuffle, error_call = error_call)
36: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, load_package = load_package, parallel = parallel, shuffle = shuffle)
37: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
38: test_check("eudract")
An irrecoverable exception occurred. R is aborting now ...
Flavor: r-oldrel-macos-x86_64
Version: 1.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
sh: line 1: 87243 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmpsZK8yI/file153c112e8308a' 2>&1 < '/Volumes/Temp/tmp/RtmpsZK8yI/file153c149cabdb8'
--- re-building ‘eudract.Rmd’ using rmarkdown
*** caught segfault ***
address 0x0, cause 'unknown'
Traceback:
1: xml_validate.xml_document(safety, schema_results)
2: xml2::xml_validate(safety, schema_results)
3: clintrials_gov_convert(input = simple, original = system.file("extdata", "1234.xml", package = "eudract"), output = ct_upload_file)
4: eval(expr, envir)
5: eval(expr, envir)
6: withVisible(eval(expr, envir))
7: withCallingHandlers(code, error = function (e) rlang::entrace(e), message = function (cnd) { watcher$capture_plot_and_output() if (on_message$capture) { watcher$push(cnd) } if (on_message$silence) { invokeRestart("muffleMessage") }}, warning = function (cnd) { if (getOption("warn") >= 2 || getOption("warn") < 0) { return() } watcher$capture_plot_and_output() if (on_warning$capture) { cnd <- sanitize_call(cnd) watcher$push(cnd) } if (on_warning$silence) { invokeRestart("muffleWarning") }}, error = function (cnd) { watcher$capture_plot_and_output() cnd <- sanitize_call(cnd) watcher$push(cnd) switch(on_error, continue = invokeRestart("eval_continue"), stop = invokeRestart("eval_stop"), error = NULL)})
8: eval(call)
9: eval(call)
10: with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers)
11: doWithOneRestart(return(expr), restart)
12: withOneRestart(expr, restarts[[1L]])
13: withRestartList(expr, restarts[-nr])
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
16: withRestartList(expr, restarts)
17: withRestarts(with_handlers({ for (expr in tle$exprs) { ev <- withVisible(eval(expr, envir)) watcher$capture_plot_and_output() watcher$print_value(ev$value, ev$visible, envir) } TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
18: evaluate::evaluate(...)
19: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options))
20: in_dir(input_dir(), expr)
21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$warning)) TRUE else options$warning, keep_message = if (is.numeric(options$message)) TRUE else options$message, stop_on_error = if (is.numeric(options$error)) options$error else { if (options$error && options$include) 0L else 2L }, output_handler = knit_handlers(options$render, options)))
22: eng_r(options)
23: block_exec(params)
24: call_block(x)
25: process_group(group)
26: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) })
27: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global()))
28: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { if (progress && is.function(pb$interrupt)) pb$interrupt() if (is_R_CMD_build() || is_R_CMD_check()) error <<- format(e) }), list(rlang_trace_top_env = knit_global())), function(loc) { setwd(wd) write_utf8(res, output %n% stdout()) paste0("\nQuitting from ", loc, if (!is.null(error)) paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
29: process_file(text, output)
30: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
31: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), output_dir = getwd(), ...)
32: vweave_rmarkdown(...)
33: engine$weave(file, quiet = quiet, encoding = enc)
34: doTryCatch(return(expr), name, parentenv, handler)
35: tryCatchOne(expr, names, parentenv, handlers[[1L]])
36: tryCatchList(expr, classes, parentenv, handlers)
37: tryCatch({ engine$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)))})
38: tools:::.buildOneVignette("eudract.Rmd", "/Volumes/Builds/packages/big-sur-x86_64/results/4.4/eudract.Rcheck/vign_test/eudract", TRUE, FALSE, "eudract", "UTF-8", "/Volumes/Temp/tmp/RtmpsZK8yI/file153c14dd5da32.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘standard_reporting.Rmd’ using rmarkdown
--- finished re-building ‘standard_reporting.Rmd’
SUMMARY: processing the following file failed:
‘eudract.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-oldrel-macos-x86_64
Current CRAN status: OK: 13
Current CRAN status: OK: 13