* using log directory ‘/Users/ripley/R/packages/tests-devel/eudract.Rcheck’
* using R Under development (unstable) (2025-12-21 r89215)
* using platform: aarch64-apple-darwin25.2.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.3.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.2
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘eudract/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘eudract’ version ‘1.0.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘eudract’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 36128 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Users/ripley/R/R-devel/bin/R' --vanilla > 'eudract-Ex.Rout' 2>&1 < 'eudract-Ex.R'
 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)
'/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmph6pvj1/working_dir/RtmpJ875tG/file8d207aa783d4.xml' is created or modified

> eudract_convert(input=simple,
+                 output=eudract)
'/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmph6pvj1/working_dir/RtmpJ875tG/file8d20bc01235.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)
'/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmph6pvj1/working_dir/RtmpJ875tG/file8d206eeb5b99.xml' is created or modified


 *** caught segfault ***
address 0x13e200a7aa659e4d, 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 ...
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’/Users/ripley/R/R-devel/bin/BATCH: line 60: 36380 Segmentation fault: 11  ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eudract)
  > 
  > test_check("eudract")
  
   *** caught segfault ***
  address 0x528fe516fbe4dae2, 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 ...
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [9s/12s] ERROR
Error(s) in re-building vignettes:
sh: line 1: 38136 Segmentation fault: 11  '/Users/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmph6pvj1/working_dir/Rtmp2fCxYy/file8f1320dddba8' 2>&1 < '/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmph6pvj1/working_dir/Rtmp2fCxYy/file8f1345800373'
--- re-building ‘eudract.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x2d4614574db10655, 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", "/Users/ripley/R/packages/tests-devel/eudract.Rcheck/vign_test/eudract",     TRUE, FALSE, "eudract", "UTF-8", "/var/folders/pk/n4bndnt1287ctrd_ftthnnnr0000gp/T//Rtmph6pvj1/working_dir/Rtmp2fCxYy/file8f134c59e169.rds")
An irrecoverable exception occurred. R is aborting now ...
--- re-building ‘standard_reporting.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘standard_reporting.Rmd’

SUMMARY: processing the following file failed:
  ‘eudract.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* checking HTML version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 3 ERRORs
See
  ‘/Users/ripley/R/packages/tests-devel/eudract.Rcheck/00check.log’
for details.

       39.08 real        28.34 user         7.19 sys