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Added package-unrestricted results with BIOC 3.8
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outputs_38_all/AgreementInterval.Rcheck/tests/testthat.Rout.fail
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| R Under development (unstable) (2018-10-04 r75396) -- "Unsuffered Consequences" | ||
| Copyright (C) 2018 The R Foundation for Statistical Computing | ||
| Platform: x86_64-pc-linux-gnu (64-bit) | ||
|
|
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| R is free software and comes with ABSOLUTELY NO WARRANTY. | ||
| You are welcome to redistribute it under certain conditions. | ||
| Type 'license()' or 'licence()' for distribution details. | ||
|
|
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| R is a collaborative project with many contributors. | ||
| Type 'contributors()' for more information and | ||
| 'citation()' on how to cite R or R packages in publications. | ||
|
|
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| Type 'demo()' for some demos, 'help()' for on-line help, or | ||
| 'help.start()' for an HTML browser interface to help. | ||
| Type 'q()' to quit R. | ||
|
|
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| > library(testthat) | ||
| > library(AgreementInterval) | ||
| Loading required package: psych | ||
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| Attaching package: 'psych' | ||
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| The following object is masked from 'package:testthat': | ||
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| describe | ||
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| > | ||
| > test_check("AgreementInterval") | ||
| a and b agree with each other at discordance rate of 0.05 with tolerance probability of 0.23 from sample size n= 5 . | ||
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| Tomography and Urography agree with each other at discordance rate of 0.05 with tolerance probability of 0.49 from sample size n= 52 . | ||
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| Urography and Tomography agree with each other at discordance rate of 0.05 with tolerance probability of 0.49 from sample size n= 52 . | ||
| Given clinical relevant limit, Urography and Tomography agree with each other at discordance rate of 0.124 with tolerance probability of 0.64 from the same sample size n= 52 . | ||
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| Tomography and Urography agree with each other at discordance rate of 0.05 with tolerance probability of 0.49 from sample size n= 52 . | ||
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| ----------- FAILURE REPORT -------------- | ||
| --- srcref --- | ||
| at /var/scratch2/tomas/tmp/Rtmpg5ULm3/R.INSTALL68a27fd9fdf0/AgreementInterval/R/tolProb.R#25: | ||
| --- package (from environment) --- | ||
| AgreementInterval | ||
| --- call from context --- | ||
| tolProb(n = 3, k = c(2, 3)) | ||
| --- call from argument --- | ||
| if (!is.numeric(n) | length(n) != 1 | !is.numeric(k) | length(k) != | ||
| 1 | n < k) stop("Please enter n and k as a integer with n>=k") | ||
| --- R stacktrace --- | ||
| where 1 at /var/scratch2/tomas/tmp/RtmpzMuy2s/R.INSTALL6094aa1b0d0/rlang/R/eval.R#103: tolProb(n = 3, k = c(2, 3)) | ||
| where 2 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/expectation.R#99: eval_bare(get_expr(quo), get_env(quo)) | ||
| where 3: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 4: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | ||
| where 5: tryCatchList(expr, classes, parentenv, handlers) | ||
| where 6 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/capture-condition.R#36: tryCatch({ | ||
| code | ||
| NULL | ||
| }, error = function(e) e) | ||
| where 7 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/expectation.R#99: capture(act$val <- eval_bare(get_expr(quo), get_env(quo))) | ||
| where 8 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/expect-output.R#120: quasi_capture(enquo(object), capture_error, label = label) | ||
| where 9 at testthat/test-tolProb.R#10: expect_error(tolProb(n = 3, k = c(2, 3))) | ||
| where 10: eval(code, test_env) | ||
| where 11 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#152: eval(code, test_env) | ||
| where 12 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#149: 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 13: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 14: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | ||
| where 15: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) | ||
| where 16: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 17: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), | ||
| names[nh], parentenv, handlers[[nh]]) | ||
| where 18: tryCatchList(expr, classes, parentenv, handlers) | ||
| where 19 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#149: 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 20 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#31: test_code(desc, code, env = parent.frame()) | ||
| where 21 at testthat/test-tolProb.R#7: test_that("tolProb errors correctly", { | ||
| expect_error(tolProb(n = 3, k = "a")) | ||
| expect_error(tolProb(n = 3, k = 4)) | ||
| expect_error(tolProb(n = 3, k = c(2, 3))) | ||
| expect_error(tolProb(n = c(3, 4), 2)) | ||
| }) | ||
| where 22: eval(code, test_env) | ||
| where 23 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#152: eval(code, test_env) | ||
| where 24 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#149: 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 25: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 26: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | ||
| where 27: tryCatchList(expr, names[-nh], parentenv, handlers[-nh]) | ||
| where 28: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 29: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), | ||
| names[nh], parentenv, handlers[[nh]]) | ||
| where 30: tryCatchList(expr, classes, parentenv, handlers) | ||
| where 31 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-that.R#149: 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 32 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/source.R#42: test_code(NULL, exprs, env) | ||
| where 33 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-files.R#131: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) | ||
| where 34 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/reporter-zzz.R#53: force(code) | ||
| where 35 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-files.R#125: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, | ||
| { | ||
| lister$start_file(basename(path)) | ||
| source_file(path, new.env(parent = env), chdir = TRUE, | ||
| wrap = wrap) | ||
| end_context() | ||
| }) | ||
| where 36: FUN(X[[i]], ...) | ||
| where 37 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-files.R#25: lapply(paths, test_file, env = env, reporter = current_reporter, | ||
| start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap) | ||
| where 38 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/reporter-zzz.R#53: force(code) | ||
| where 39 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-files.R#25: 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 40 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-directory.R#86: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, | ||
| stop_on_warning = stop_on_warning, wrap = wrap) | ||
| where 41 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-directory.R#190: 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 42 at /var/scratch2/tomas/tmp/RtmpbDGq4U/R.INSTALL26fb6717adb2/testthat/R/test-directory.R#171: 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 43: test_check("AgreementInterval") | ||
|
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| --- value of length: 2 type: logical --- | ||
| [1] TRUE TRUE | ||
| --- function from context --- | ||
| function(n, k, alpha=0.05){ | ||
| if (!is.numeric(n) | length(n)!=1 | | ||
| !is.numeric(k) | length(k)!=1 | n<k) | ||
| stop("Please enter n and k as a integer with n>=k") | ||
| i=0:k | ||
| x1=choose(n, i) | ||
| x2=(1-alpha)^(n-i) | ||
| x3=alpha^i | ||
| x0=sum(x1*x2*x3) | ||
| beta=1-x0 | ||
| return(beta) | ||
| } | ||
| <bytecode: 0x36bf7d0> | ||
| <environment: namespace:AgreementInterval> | ||
| --- function search by body --- | ||
| Function tolProb in namespace AgreementInterval has this body. | ||
| ----------- END OF FAILURE REPORT -------------- | ||
| Fatal error: the condition has length > 1 |
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outputs_38_all/ArgumentCheck.Rcheck/build_vignettes.log
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,125 @@ | ||
| ----------- FAILURE REPORT -------------- | ||
| --- srcref --- | ||
| at <text>#7: | ||
| --- package (from environment) --- | ||
| package:ArgumentCheck | ||
| --- call from context --- | ||
| cylinder.volume(height = c(-3, 3), radius = -4) | ||
| --- call from argument --- | ||
| if (height < 0) ArgumentCheck::addError(msg = "'height' must be >= 0", | ||
| argcheck = Check) | ||
| --- R stacktrace --- | ||
| where 1: cylinder.volume(height = c(-3, 3), radius = -4) | ||
| where 2: eval(expr, envir, enclos) | ||
| where 3 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#189: eval(expr, envir, enclos) | ||
| where 4 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#189: withVisible(eval(expr, envir, enclos)) | ||
| where 5 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#189: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, | ||
| error = eHandler, message = mHandler) | ||
| where 6: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 7: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | ||
| where 8: tryCatchList(expr, classes, parentenv, handlers) | ||
| where 9: tryCatch(expr, error = function(e) { | ||
| call <- conditionCall(e) | ||
| if (!is.null(call)) { | ||
| if (identical(call[[1L]], quote(doTryCatch))) | ||
| call <- sys.call(-4L) | ||
| dcall <- deparse(call)[1L] | ||
| prefix <- paste("Error in", dcall, ": ") | ||
| LONG <- 75L | ||
| sm <- strsplit(conditionMessage(e), "\n")[[1L]] | ||
| w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w") | ||
| if (is.na(w)) | ||
| w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L], | ||
| type = "b") | ||
| if (w > LONG) | ||
| prefix <- paste0(prefix, "\n ") | ||
| } | ||
| else prefix <- "Error : " | ||
| msg <- paste0(prefix, conditionMessage(e), "\n") | ||
| .Internal(seterrmessage(msg[1L])) | ||
| if (!silent && isTRUE(getOption("show.error.messages"))) { | ||
| cat(msg, file = outFile) | ||
| .Internal(printDeferredWarnings()) | ||
| } | ||
| invisible(structure(msg, class = "try-error", condition = e)) | ||
| }) | ||
| where 10 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#166: try(f, silent = TRUE) | ||
| where 11 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#189: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, | ||
| enclos)), warning = wHandler, error = eHandler, message = mHandler)) | ||
| where 12 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#189: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, | ||
| envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))) | ||
| where 13 at /var/scratch2/tomas/tmp/RtmpZGXXbh/R.INSTALL11c011f1a149/evaluate/R/eval.r#73: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, | ||
| debug = debug, last = i == length(out), use_try = stop_on_error != | ||
| 2L, keep_warning = keep_warning, keep_message = keep_message, | ||
| output_handler = output_handler, include_timing = include_timing) | ||
| where 14 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/hooks.R#17: evaluate::evaluate(...) | ||
| where 15 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/block.R#170: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$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 16 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/block.R#170: 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$render, options))) | ||
| where 17 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/block.R#91: block_exec(params) | ||
| where 18 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/block.R#6: call_block(x) | ||
| where 19 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/block.R#3: process_group.block(group) | ||
| where 20 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/output.R#314: process_group(group) | ||
| where 21 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/output.R#314: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), | ||
| error = function(e) { | ||
| setwd(wd) | ||
| cat(res, sep = "\n", file = output %n% "") | ||
| message("Quitting from lines ", paste(current_lines(i), | ||
| collapse = "-"), " (", knit_concord$get("infile"), | ||
| ") ") | ||
| }) | ||
| where 22 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/output.R#258: process_file(text, output) | ||
| where 23 at /var/scratch2/tomas/tmp/Rtmpewp0dw/R.INSTALL922570d793a8/rmarkdown/R/render.R#501: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet, | ||
| encoding = encoding) | ||
| where 24 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/utils-vignettes.R#40: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv()) | ||
| where 25 at /var/scratch2/tomas/tmp/Rtmp2EOpgb/R.INSTALL70d861d842ef/knitr/R/utils-vignettes.R#92: vweave_rmarkdown(...) | ||
| where 26 at ../../../../R/src/library/tools/R/Vignettes.R#520: engine$weave(file, quiet = quiet, encoding = enc) | ||
| where 27: doTryCatch(return(expr), name, parentenv, handler) | ||
| where 28: tryCatchOne(expr, names, parentenv, handlers[[1L]]) | ||
| where 29: tryCatchList(expr, classes, parentenv, handlers) | ||
| where 30 at ../../../../R/src/library/tools/R/Vignettes.R#518: tryCatch({ | ||
| engine$weave(file, quiet = quiet, encoding = enc) | ||
| setwd(startdir) | ||
| find_vignette_product(name, by = "weave", engine = engine) | ||
| }, error = function(e) { | ||
| stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s", | ||
| file, conditionMessage(e)), domain = NA, call. = FALSE) | ||
| }) | ||
| where 31: buildVignettes(dir = "/var/scratch2/tomas/test/mine/R-75396/check/ArgumentCheck.Rcheck/vign_test/ArgumentCheck") | ||
|
|
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| --- value of length: 2 type: logical --- | ||
| [1] TRUE FALSE | ||
| --- function from context --- | ||
| function(height, radius) | ||
| { | ||
| #* Establish a new 'ArgCheck' object | ||
| Check <- ArgumentCheck::newArgCheck() | ||
|
|
||
| #* Add an error if height < 0 | ||
| if (height < 0) | ||
| ArgumentCheck::addError( | ||
| msg = "'height' must be >= 0", | ||
| argcheck = Check | ||
| ) | ||
|
|
||
| #* Add an error if radius < 0 | ||
| if (radius < 0) | ||
| ArgumentCheck::addError( | ||
| msg = "'radius' must be >= 0", | ||
| argcheck = Check | ||
| ) | ||
|
|
||
| #* Return errors and warnings (if any) | ||
| ArgumentCheck::finishArgCheck(Check) | ||
|
|
||
| pi * radius^2 * height | ||
| } | ||
| <bytecode: 0x6bea9b0> | ||
| --- function search by body --- | ||
| ----------- END OF FAILURE REPORT -------------- | ||
| Fatal error: the condition has length > 1 |
Oops, something went wrong.