* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/james.analysis.Rcheck’
* using R Under development (unstable) (2022-04-03 r82074)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘james.analysis/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘james.analysis’ version ‘1.0.1’
* 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 ‘james.analysis’ can be installed ... OK
* checking package 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 R 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 ... NOTE
boxplot.james: no visible global function definition for ‘mtext’
getBestSolutionValues.james : <anonymous>: no visible global function
  definition for ‘tail’
isMinimizing: no visible global function definition for ‘head’
isMinimizing: no visible global function definition for ‘tail’
mergeJAMES.james: no visible global function definition for ‘glob2rx’
plotConvergence.james : <anonymous> : <anonymous>: no visible global
  function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘tail’
plotConvergence.james: no visible global function definition for ‘head’
plotConvergence.james : <anonymous>: no visible global function
  definition for ‘tail’
plotConvergence.james: no visible global function definition for
  ‘matplot’
plotConvergence.james: no visible global function definition for
  ‘mtext’
summary.james: no visible global function definition for ‘sd’
summary.james: no visible global function definition for ‘median’
summary.james: no visible global function definition for ‘IQR’
Undefined global functions or variables:
  IQR glob2rx head matplot median mtext sd tail
Consider adding
  importFrom("graphics", "matplot", "mtext")
  importFrom("stats", "IQR", "median", "sd")
  importFrom("utils", "glob2rx", "head", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(james.analysis)
  > 
  > test_check("james.analysis")
   ----------- FAILURE REPORT -------------- 
   --- failure: length > 1 in coercion to logical ---
   --- srcref --- 
  : 
   --- package (from environment) --- 
  james.analysis
   --- call from context --- 
  readJAMES(c("a", "b"))
   --- call from argument --- 
  is.null(file) || is.na(file)
   --- R stacktrace ---
  where 1: readJAMES(c("a", "b"))
  where 2: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
  where 3: withCallingHandlers({
      code
      NULL
  }, error = function(cnd) {
      if (can_entrace(cnd)) {
          cnd <- cnd_entrace(cnd)
      }
      return_from(env, cnd)
  })
  where 4: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)), 
      ...)
  where 5: quasi_capture(enquo(object), label, capture_error, entrace = TRUE)
  where 6 at testReadJAMES.R#16: expect_error(readJAMES(c("a", "b")), "non-empty string")
  where 7: eval(code, test_env)
  where 8: eval(code, test_env)
  where 9: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 10: doTryCatch(return(expr), name, parentenv, handler)
  where 11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 13: doTryCatch(return(expr), name, parentenv, handler)
  where 14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 15: tryCatchList(expr, classes, parentenv, handlers)
  where 16: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 17: test_code(desc, code, env = parent.frame(), reporter = reporter)
  where 18 at testReadJAMES.R#12: test_that("readJAMES complains on invalid arguments", {
      expect_error(readJAMES(NULL), "non-empty string")
      expect_error(readJAMES(NA), "non-empty string")
      expect_error(readJAMES(""), "non-empty string")
      expect_error(readJAMES(c("a", "b")), "non-empty string")
  })
  where 19: eval(code, test_env)
  where 20: eval(code, test_env)
  where 21: withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error)
  where 22: doTryCatch(return(expr), name, parentenv, handler)
  where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 24: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  where 25: doTryCatch(return(expr), name, parentenv, handler)
  where 26: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), 
      names[nh], parentenv, handlers[[nh]])
  where 27: tryCatchList(expr, classes, parentenv, handlers)
  where 28: tryCatch(withCallingHandlers({
      eval(code, test_env)
      if (!handled && !is.null(test)) {
          skip_empty()
      }
  }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
      message = handle_message, error = handle_error), error = handle_fatal, 
      skip = function(e) {
      })
  where 29: test_code(NULL, exprs, env)
  where 30: source_file(path, child_env(env), wrap = wrap)
  where 31: FUN(X[[i]], ...)
  where 32: lapply(test_paths, test_one_file, env = env, wrap = wrap)
  where 33: doTryCatch(return(expr), name, parentenv, handler)
  where 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  where 35: tryCatchList(expr, classes, parentenv, handlers)
  where 36: tryCatch(code, testthat_abort_reporter = function(cnd) {
      cat(conditionMessage(cnd), "\n")
      NULL
  })
  where 37: with_reporter(reporters$multi, lapply(test_paths, test_one_file, 
      env = env, wrap = wrap))
  where 38: test_files(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, 
      wrap = wrap, load_package = load_package)
  where 39: 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, 
      wrap = wrap, load_package = load_package, parallel = parallel)
  where 40: test_dir("testthat", package = package, reporter = reporter, 
      ..., load_package = "installed")
  where 41: test_check("james.analysis")
  
   --- value of length: 2 type: logical ---
  [1] FALSE FALSE
   --- function from context --- 
  function (file) 
  {
      if (is.null(file) || is.na(file) || !is.character(file) || 
          length(file) != 1 || nchar(file) == 0) {
          stop("'file' should be a non-empty string")
      }
      if (!file.exists(file)) {
          msg <- sprintf("'file' %s does not exist", file)
          stop(msg)
      }
      results <- rjson::fromJSON(file = file)
      unexpectedStructure <- function() {
          msg <- sprintf("'unexpected JSON structure in file' %s", 
              file)
          stop(msg)
      }
      if (!is.list(results) || length(results) == 0) {
          unexpectedStructure()
      }
      problem.names <- names(results)
      if (is.null(problem.names) || anyDuplicated(problem.names)) {
          unexpectedStructure()
      }
      for (n in problem.names) {
          if (is.na(n) || nchar(n) == 0) {
              unexpectedStructure()
          }
      }
      for (problem in results) {
          if (!is.list(problem) || length(problem) == 0) {
              unexpectedStructure()
          }
          search.names <- names(problem)
          if (is.null(search.names) || anyDuplicated(search.names)) {
              unexpectedStructure()
          }
          for (n in search.names) {
              if (is.na(n) || nchar(n) == 0) {
                  unexpectedStructure()
              }
          }
          for (search in problem) {
              if (!is.list(search) || length(search) == 0) {
                  unexpectedStructure()
              }
              for (run in search) {
                  if (!is.list(run) || !any(length(run) == c(2, 
                    3))) {
                    unexpectedStructure()
                  }
                  run.components <- names(run)
                  if (is.null(run.components) || anyDuplicated(run.components)) {
                    unexpectedStructure()
                  }
                  for (n in run.components) {
                    if (is.na(n) || nchar(n) == 0) {
                      unexpectedStructure()
                    }
                  }
                  if (!("times" %in% run.components) || !("values" %in% 
                    run.components) || (length(run) == 3) && !("best.solution" %in% 
                    run.components)) {
                    unexpectedStructure()
                  }
                  if (length(run$times) != length(run$values)) {
                    unexpectedStructure()
                  }
                  if (is.unsorted(run$times)) {
                    unexpectedStructure()
                  }
                  if (is.unsorted(run$values) && is.unsorted(rev(run$values))) {
                    unexpectedStructure()
                  }
              }
          }
      }
      class(results) <- c("james", class(results))
      return(results)
  }
  <bytecode: 0x496c2c8>
  <environment: namespace:james.analysis>
   --- function search by body ---
  Function readJAMES in namespace james.analysis has this body.
   ----------- END OF FAILURE REPORT -------------- 
  Fatal error: length > 1 in coercion to logical
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/james.analysis.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:07.28, 39.05 + 6.22