Check results for 'eudract'

using R version 4.5.1 (2025-06-13)
using platform: x86_64-apple-darwin20
R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 14.2.0
running under: macOS Ventura 13.3.1
using session charset: UTF-8
checking for file ‘eudract/DESCRIPTION’ ... OK
checking extension type ... Package
this is package ‘eudract’ version ‘1.1.0’
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 ... [5s/7s] OK See the install log for details.
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 ... [1s/2s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] 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 ... [4s/5s] OK
checking Rd files ... [0s/0s] 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 ... [0s/0s] OK
checking LazyData ... OK
checking data for ASCII and uncompressed saves ... OK
checking sizes of PDF files under ‘inst/doc’ ... OK
checking installed files from ‘inst/doc’ ... OK
checking files in ‘vignettes’ ... OK
checking examples ... [2s/2s] 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/Rtmp16hSVA/filefe7331762f0f.xml' is created or modified > eudract_convert(input=simple, + output=eudract) '/Volumes/Temp/tmp/Rtmp16hSVA/filefe73460b9b27.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/Rtmp16hSVA/filefe7323f7415e.xml' is created or modified *** caught segfault *** address 0x476bd74605a8, 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 ...
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [3s/3s] ERROR Running ‘testthat.R’ [3s/3s] 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 ...
checking for unstated dependencies in vignettes ... OK
checking package vignettes ... OK
checking re-building of vignette outputs ... [19s/26s] ERROR Error(s) in re-building vignettes: sh: line 1: 66306 Segmentation fault: 11 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla --no-echo > '/Volumes/Temp/tmp/RtmppKMCXH/file102435083ef63' 2>&1 < '/Volumes/Temp/tmp/RtmppKMCXH/file102435d975e1' --- 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/4.5/eudract.Rcheck/vign_test/eudract", TRUE, FALSE, "eudract", "UTF-8", "/Volumes/Temp/tmp/RtmppKMCXH/file1024335d18d0f.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
checking PDF version of manual ... [6s/8s] OK
DONE Status: 3 ERRORs
using check arguments '--no-clean-on-error '