CRAN Package Check Results for Package InformativeCensoring

Last updated on 2019-12-21 10:47:47 CET.

Check Details

Version: 0.3.4
Check: tests
Result: ERROR
     Running 'testthat.R' [233s/248s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library("InformativeCensoring")
     Loading required package: survival
    
     Attaching package: 'InformativeCensoring'
    
     The following object is masked from 'package:survival':
    
     cox.zph
    
     >
     > test_check("InformativeCensoring")
     -- 1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25) -------------
     "matrix" not equal to class(imputed.data.sets$impute.time).
     Lengths differ: 1 is not 2
    
     -- 2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26) -------------
     "matrix" not equal to class(imputed.data.sets$impute.event).
     Lengths differ: 1 is not 2
    
     -- 3. Failure: GammaStatSet (@test-gammaStat.R#115) ---------------------------
     "matrix" not equal to class(ans$statistics$estimates).
     Lengths differ: 1 is not 2
    
     -- 4. Failure: GammaStatSet (@test-gammaStat.R#116) ---------------------------
     "matrix" not equal to class(ans$statistics$vars).
     Lengths differ: 1 is not 2
    
     -- 5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140) -------------
     "matrix" not equal to class(ans$statistics$estimates).
     Lengths differ: 1 is not 2
    
     -- 6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141) -------------
     "matrix" not equal to class(ans$statistics$vars).
     Lengths differ: 1 is not 2
    
     -- 7. Failure: summary_1_covar (@test-gammaStat.R#171) ------------------------
     "matrix" not equal to class(ans).
     Lengths differ: 1 is not 2
    
     -- 8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32) ---------------
     "matrix" not equal to class(ans$impute.time).
     Lengths differ: 1 is not 2
    
     -- 9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33) ---------------
     "matrix" not equal to class(ans$impute.event).
     Lengths differ: 1 is not 2
    
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     InformativeCensoring
     --- call from context ---
     .Testsurvdiff(object, formula, rho = 0, method = "logrank", ...)
     --- call from argument ---
     if (class(model$obs) == "matrix") sum(model$obs[2, ] - model$exp[2,
     ]) else (model$obs[2] - model$exp[2])
     --- R stacktrace ---
     where 1: .Testsurvdiff(object, formula, rho = 0, method = "logrank", ...)
     where 2: switch(method, logrank = .Testlogrank, Wilcoxon = .Testwilcoxon,
     Cox = .Testcox, exponential = .TestExponential, weibull = .TestWeibull,
     function(object, formula, ...) {
     stop("Unknown test type")
     })(object, formula, ...)
     where 3: .imputeStat.internal(object, method, formula, ...)
     where 4: ImputeStat.ScoreImputedData(scoreData, method = "logrank", formula = ~my.arm +
     strata(Z1))
     where 5 at testthat/test-scoreStat.R#167: ImputeStat(scoreData, method = "logrank", formula = ~my.arm +
     strata(Z1))
     where 6: eval(code, test_env)
     where 7: eval(code, test_env)
     where 8: 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 9: doTryCatch(return(expr), name, parentenv, handler)
     where 10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 11: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 12: doTryCatch(return(expr), name, parentenv, handler)
     where 13: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 14: tryCatchList(expr, classes, parentenv, handlers)
     where 15: 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 16: test_code(desc, code, env = parent.frame())
     where 17 at testthat/test-scoreStat.R#165: test_that("Logrank_Wilcoxon_usersupplied_formula", {
     scoreData <- mockImputed()
     a <- ImputeStat(scoreData, method = "logrank", formula = ~my.arm +
     strata(Z1))
     expect_equal(a$statistic, sum(a$model$obs[2, ] - a$model$exp[2,
     ])/sqrt(a$model$var[2, 2]))
     scoreData <- mockImputed()
     a <- ImputeStat(scoreData, method = "logrank", formula = ~my.arm +
     strata(Z1, Z3))
     a2 <- ImputeStat(scoreData, method = "logrank", formula = ~my.arm +
     strata(Z3) + strata(Z1))
     expect_equal(as.vector(a), as.vector(a2))
     })
     where 18: eval(code, test_env)
     where 19: eval(code, test_env)
     where 20: 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 21: doTryCatch(return(expr), name, parentenv, handler)
     where 22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 23: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 24: doTryCatch(return(expr), name, parentenv, handler)
     where 25: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 26: tryCatchList(expr, classes, parentenv, handlers)
     where 27: 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 28: test_code(NULL, exprs, env)
     where 29: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 30: force(code)
     where 31: doWithOneRestart(return(expr), restart)
     where 32: withOneRestart(expr, restarts[[1L]])
     where 33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 34: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
     {
     reporter$start_file(basename(path))
     lister$start_file(basename(path))
     source_file(path, new.env(parent = env), chdir = TRUE,
     wrap = wrap)
     reporter$.end_context()
     reporter$end_file()
     })
     where 35: FUN(X[[i]], ...)
     where 36: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 37: force(code)
     where 38: doWithOneRestart(return(expr), restart)
     where 39: withOneRestart(expr, restarts[[1L]])
     where 40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 41: with_reporter(reporter = current_reporter, results <- lapply(paths,
     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
     load_helpers = FALSE, wrap = wrap))
     where 42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 43: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
     wrap = wrap)
     where 44: test_package_dir(package = package, test_path = test_path, filter = filter,
     reporter = reporter, ..., stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 45: test_check("InformativeCensoring")
    
     --- value of length: 2 type: logical ---
     [1] TRUE FALSE
     --- function from context ---
     function (object, formula, rho, method, ...)
     {
     model <- survdiff(formula = formula, data = object$data,
     rho = rho, ...)
     list(model = model, method = paste(method, "(estimator for O-E)"),
     estimate = if (class(model$obs) == "matrix") sum(model$obs[2,
     ] - model$exp[2, ]) else (model$obs[2] - model$exp[2]),
     var = model$var[2, 2])
     }
     <bytecode: 0xbf87668>
     <environment: namespace:InformativeCensoring>
     --- function search by body ---
     Function .Testsurvdiff in namespace InformativeCensoring has this body.
     ----------- END OF FAILURE REPORT --------------
     -- 10. Error: Logrank_Wilcoxon_usersupplied_formula (@test-scoreStat.R#167) ---
     the condition has length > 1
     Backtrace:
     1. InformativeCensoring::ImputeStat(...)
     2. InformativeCensoring:::ImputeStat.ScoreImputedData(...)
     3. InformativeCensoring:::.imputeStat.internal(...)
     4. switch(method, logrank = .Testlogrank, Wilcoxon = .Testwilcoxon, ...
     5. InformativeCensoring:::.Testsurvdiff(...)
    
     == testthat results ===========================================================
     [ OK: 490 | SKIPPED: 0 | WARNINGS: 19 | FAILED: 10 ]
     1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25)
     2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26)
     3. Failure: GammaStatSet (@test-gammaStat.R#115)
     4. Failure: GammaStatSet (@test-gammaStat.R#116)
     5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140)
     6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141)
     7. Failure: summary_1_covar (@test-gammaStat.R#171)
     8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32)
     9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33)
     10. Error: Logrank_Wilcoxon_usersupplied_formula (@test-scoreStat.R#167)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.4
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building 'gamma_imputation_Jackson_2014.Rnw' using knitr
    Loading required package: survival
    
    Attaching package: 'InformativeCensoring'
    
    The following object is masked from 'package:survival':
    
     cox.zph
    
    --- finished re-building 'gamma_imputation_Jackson_2014.Rnw'
    
    --- re-building 'risk_score_imputation_Hsu_2009.Rnw' using knitr
    
    Attaching package: 'InformativeCensoring'
    
    The following object is masked from 'package:survival':
    
     cox.zph
    
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    InformativeCensoring
     --- call from context ---
    .Testsurvdiff(object, formula, rho = 0, method = "logrank", ...)
     --- call from argument ---
    if (class(model$obs) == "matrix") sum(model$obs[2, ] - model$exp[2,
     ]) else (model$obs[2] - model$exp[2])
     --- R stacktrace ---
    where 1: .Testsurvdiff(object, formula, rho = 0, method = "logrank", ...)
    where 2: switch(method, logrank = .Testlogrank, Wilcoxon = .Testwilcoxon,
     Cox = .Testcox, exponential = .TestExponential, weibull = .TestWeibull,
     function(object, formula, ...) {
     stop("Unknown test type")
     })(object, formula, ...)
    where 3: .imputeStat.internal(object, method, formula, ...)
    where 4: ImputeStat.ScoreImputedData(ExtractSingle(object, x), method = method,
     formula = formula, ...)
    where 5: ImputeStat(ExtractSingle(object, x), method = method, formula = formula,
     ...)
    where 6: FUN(X[[i]], ...)
    where 7: lapply(seq_len(object$m), extract_stat, method, formula)
    where 8: .internalImputeStatset(object, method, formula, ..., parallel = parallel,
     ncpus = ncpus, cl = cl)
    where 9: ImputeStat.ScoreImputedSet(imputed.data.sets, method = "logrank",
     formula = ~arm + strata(Z1, Z3))
    where 10: ImputeStat(imputed.data.sets, method = "logrank", formula = ~arm +
     strata(Z1, Z3))
    where 11: eval(expr, envir, enclos)
    where 12: eval(expr, envir, enclos)
    where 13: withVisible(eval(expr, envir, enclos))
    where 14: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
     error = eHandler, message = mHandler)
    where 15: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
     enclos)), warning = wHandler, error = eHandler, message = mHandler))
    where 16: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
     envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
    where 17: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
     debug = debug, last = i == length(out), use_try = stop_on_error !=
     2L, keep_warning = keep_warning, keep_message = keep_message,
     output_handler = output_handler, include_timing = include_timing)
    where 18: evaluate::evaluate(...)
    where 19: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
     keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
     options$include) 0L else 2L, output_handler = knit_handlers(options$render,
     options))
    where 20: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
     keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
     stop_on_error = if (options$error && options$include) 0L else 2L,
     output_handler = knit_handlers(options$render, options)))
    where 21: block_exec(params)
    where 22: call_block(x)
    where 23: process_group.block(group)
    where 24: process_group(group)
    where 25: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
     error = function(e) {
     setwd(wd)
     cat(res, sep = "\n", file = output %n% "")
     message("Quitting from lines ", paste(current_lines(i),
     collapse = "-"), " (", knit_concord$get("infile"),
     ") ")
     })
    where 26: process_file(text, output)
    where 27: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",
     file)) knit2pandoc else knit)(file, encoding = encoding,
     quiet = quiet, envir = globalenv(), ...)
    where 28: engine$weave(file, quiet = quiet, encoding = enc)
    where 29: doTryCatch(return(expr), name, parentenv, handler)
    where 30: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 31: tryCatchList(expr, classes, parentenv, handlers)
    where 32: tryCatch({
     engine$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)))
    })
    where 33: tools:::.buildOneVignette("risk_score_imputation_Hsu_2009.Rnw",
     "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/InformativeCensoring.Rcheck/vign_test/InformativeCensoring",
     TRUE, FALSE, "risk_score_imputation_Hsu_2009", "", "/tmp/RtmpvLctEm/file41c33e986289.rds")
    
     --- value of length: 2 type: logical ---
    [1] TRUE FALSE
     --- function from context ---
    function (object, formula, rho, method, ...)
    {
     model <- survdiff(formula = formula, data = object$data,
     rho = rho, ...)
     list(model = model, method = paste(method, "(estimator for O-E)"),
     estimate = if (class(model$obs) == "matrix") sum(model$obs[2,
     ] - model$exp[2, ]) else (model$obs[2] - model$exp[2]),
     var = model$var[2, 2])
    }
    <bytecode: 0xababd48>
    <environment: namespace:InformativeCensoring>
     --- function search by body ---
    Function .Testsurvdiff in namespace InformativeCensoring has this body.
     ----------- END OF FAILURE REPORT --------------
    Quitting from lines 185-190 (risk_score_imputation_Hsu_2009.Rnw)
    Error: processing vignette 'risk_score_imputation_Hsu_2009.Rnw' failed with diagnostics:
    the condition has length > 1
    --- failed re-building 'risk_score_imputation_Hsu_2009.Rnw'
    
    SUMMARY: processing the following file failed:
     'risk_score_imputation_Hsu_2009.Rnw'
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.3.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [168s/239s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library("InformativeCensoring")
     Loading required package: survival
    
     Attaching package: 'InformativeCensoring'
    
     The following object is masked from 'package:survival':
    
     cox.zph
    
     >
     > test_check("InformativeCensoring")
     ── 1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25) ─────────────
     "matrix" not equal to class(imputed.data.sets$impute.time).
     Lengths differ: 1 is not 2
    
     ── 2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26) ─────────────
     "matrix" not equal to class(imputed.data.sets$impute.event).
     Lengths differ: 1 is not 2
    
     ── 3. Failure: GammaStatSet (@test-gammaStat.R#115) ───────────────────────────
     "matrix" not equal to class(ans$statistics$estimates).
     Lengths differ: 1 is not 2
    
     ── 4. Failure: GammaStatSet (@test-gammaStat.R#116) ───────────────────────────
     "matrix" not equal to class(ans$statistics$vars).
     Lengths differ: 1 is not 2
    
     ── 5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140) ─────────────
     "matrix" not equal to class(ans$statistics$estimates).
     Lengths differ: 1 is not 2
    
     ── 6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141) ─────────────
     "matrix" not equal to class(ans$statistics$vars).
     Lengths differ: 1 is not 2
    
     ── 7. Failure: summary_1_covar (@test-gammaStat.R#171) ────────────────────────
     "matrix" not equal to class(ans).
     Lengths differ: 1 is not 2
    
     ── 8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32) ───────────────
     "matrix" not equal to class(ans$impute.time).
     Lengths differ: 1 is not 2
    
     ── 9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33) ───────────────
     "matrix" not equal to class(ans$impute.event).
     Lengths differ: 1 is not 2
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 492 | SKIPPED: 0 | WARNINGS: 22 | FAILED: 9 ]
     1. Failure: GammaImputeSet_object (@test-gammaImputedata.R#25)
     2. Failure: GammaImputeSet_object (@test-gammaImputedata.R#26)
     3. Failure: GammaStatSet (@test-gammaStat.R#115)
     4. Failure: GammaStatSet (@test-gammaStat.R#116)
     5. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#140)
     6. Failure: GammaStatSet_multiplecovar (@test-gammaStat.R#141)
     7. Failure: summary_1_covar (@test-gammaStat.R#171)
     8. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#32)
     9. Failure: ScoreImputeSet_extract (@test-scoreExtract.R#33)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc