* using log directory ‘/data/gannet/ripley/R/packages/tests-LENGTH1/advclust.Rcheck’
* using R Under development (unstable) (2022-04-26 r82260)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘advclust/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘advclust’ version ‘0.4’
* 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 ‘advclust’ can be installed ... [12s/32s] 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 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 ... [17s/43s] OK
* 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 LazyData ... NOTE
  'LazyData' is specified without a 'data' directory
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [6s/16s] ERROR
Running examples in ‘advclust-Ex.R’ failed
The error most likely occurred in:

> ### Name: biploting
> ### Title: Biploting Fuzzy Cluster Result
> ### Aliases: biploting
> 
> ### ** Examples
> 
> fuzzy.CM(iris[,1:4],K=3,m=2,max.iteration=100,threshold=1e-5,RandomNumber=1234)->cl1

Membership initialiazed randomly
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
advclust
 --- call from context --- 
validityMethod(object)
 --- call from argument --- 
member(object) < 0 || member(object) > 1
 --- R stacktrace ---
where 1: validityMethod(object)
where 2: isTRUE(x)
where 3: anyStrings(validityMethod(object))
where 4: validObject(.Object)
where 5: initialize(value, ...)
where 6: initialize(value, ...)
where 7: new("membership", member = (member), hard.label = (hard.label))
where 8: membership(K = K, n = n, RandomNumber = RandomNumber)
where 9: fuzzy.CM(iris[, 1:4], K = 3, m = 2, max.iteration = 100, threshold = 1e-05, 
    RandomNumber = 1234)

 --- value of length: 450 type: logical ---
        [,1]  [,2]  [,3]
  [1,] FALSE FALSE FALSE
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[148,] FALSE FALSE FALSE
[149,] FALSE FALSE FALSE
[150,] FALSE FALSE FALSE
 --- function from context --- 
function (object) 
{
    if (length(hard.label(object)) != nrow(member(object))) 
        return("hard.label Mismatch\n")
    if (any(member(object) < 0 || member(object) > 1)) 
        return("Constraint of membership matrix violated\n")
    rowSum.membership <- rowSums(member(object))
    rowSum.membership <- round(rowSum.membership, 3)
    if (any(rowSum.membership != 1)) {
        return("Constraint of membership matrix violated\n")
    }
    if (any(!is.numeric(member(object)))) 
        return("Not Numeric")
    if (anyNA(object)) 
        return("Missing value on membership detected\n")
}
<bytecode: 0x58a7f70>
<environment: namespace:advclust>
 --- function search by body ---
 ----------- END OF FAILURE REPORT -------------- 
Fatal error: length > 1 in coercion to logical
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... [7s/17s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘advclust.Rmd’ using rmarkdown
 ----------- FAILURE REPORT -------------- 
 --- failure: length > 1 in coercion to logical ---
 --- srcref --- 
: 
 --- package (from environment) --- 
advclust
 --- call from context --- 
validityMethod(object)
 --- call from argument --- 
member(object) < 0 || member(object) > 1
 --- R stacktrace ---
where 1: validityMethod(object)
where 2: isTRUE(x)
where 3: anyStrings(validityMethod(object))
where 4: validObject(.Object)
where 5: initialize(value, ...)
where 6: initialize(value, ...)
where 7: new("membership", member = (member), hard.label = (hard.label))
where 8: membership(K = K, n = n, RandomNumber = RandomNumber)
where 9: fuzzy.CM(X = iris[, 1:4], K = 3, m = 2, RandomNumber = 1234)
where 10: eval(expr, envir, enclos)
where 11: eval(expr, envir, enclos)
where 12: eval_with_user_handlers(expr, envir, enclos, user_handlers)
where 13: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
where 14: withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler)
where 15: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), warning = wHandler, error = eHandler, 
    message = mHandler))
where 16: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr, 
    envir, enclos, user_handlers)), 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$message), stop_on_error = if (is.numeric(options$error)) options$error else {
        if (options$error && options$include) 
            0L
        else 2L
    }, output_handler = knit_handlers(options$render, options))
where 20: in_dir(input_dir(), expr)
where 21: in_input_dir(evaluate(code, envir = env, new_device = FALSE, 
    keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$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$render, options)))
where 22: eng_r(options)
where 23: block_exec(params)
where 24: call_block(x)
where 25: process_group.block(group)
where 26: process_group(group)
where 27: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), 
    error = function(e) {
        setwd(wd)
        cat(res, sep = "\n", file = output %n% "")
        message("Quitting from lines ", paste(current_lines(i), 
            collapse = "-"), " (", knit_concord$get("infile"), 
            ") ")
    })
where 28: process_file(text, output)
where 29: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 30: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(), 
    output_dir = getwd(), ...)
where 31: vweave_rmarkdown(...)
where 32: engine$weave(file, quiet = quiet, encoding = enc)
where 33: doTryCatch(return(expr), name, parentenv, handler)
where 34: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 35: tryCatchList(expr, classes, parentenv, handlers)
where 36: tryCatch({
    engine$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)
    }
    outputs <- c(outputs, output)
}, error = function(e) {
    thisOK <<- FALSE
    fails <<- c(fails, file)
    message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", 
        file, conditionMessage(e)))
})
where 37: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-LENGTH1/advclust.Rcheck/vign_test/advclust")

 --- value of length: 450 type: logical ---
        [,1]  [,2]  [,3]
  [1,] FALSE FALSE FALSE
  [2,] FALSE FALSE FALSE
  [3,] FALSE FALSE FALSE
  [4,] FALSE FALSE FALSE
  [5,] FALSE FALSE FALSE
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[100,] FALSE FALSE FALSE
[101,] FALSE FALSE FALSE
[102,] FALSE FALSE FALSE
[103,] FALSE FALSE FALSE
[104,] FALSE FALSE FALSE
[105,] FALSE FALSE FALSE
[106,] FALSE FALSE FALSE
[107,] FALSE FALSE FALSE
[108,] FALSE FALSE FALSE
[109,] FALSE FALSE FALSE
[110,] FALSE FALSE FALSE
[111,] FALSE FALSE FALSE
[112,] FALSE FALSE FALSE
[113,] FALSE FALSE FALSE
[114,] FALSE FALSE FALSE
[115,] FALSE FALSE FALSE
[116,] FALSE FALSE FALSE
[117,] FALSE FALSE FALSE
[118,] FALSE FALSE FALSE
[119,] FALSE FALSE FALSE
[120,] FALSE FALSE FALSE
[121,] FALSE FALSE FALSE
[122,] FALSE FALSE FALSE
[123,] FALSE FALSE FALSE
[124,] FALSE FALSE FALSE
[125,] FALSE FALSE FALSE
[126,] FALSE FALSE FALSE
[127,] FALSE FALSE FALSE
[128,] FALSE FALSE FALSE
[129,] FALSE FALSE FALSE
[130,] FALSE FALSE FALSE
[131,] FALSE FALSE FALSE
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[133,] FALSE FALSE FALSE
[134,] FALSE FALSE FALSE
[135,] FALSE FALSE FALSE
[136,] FALSE FALSE FALSE
[137,] FALSE FALSE FALSE
[138,] FALSE FALSE FALSE
[139,] FALSE FALSE FALSE
[140,] FALSE FALSE FALSE
[141,] FALSE FALSE FALSE
[142,] FALSE FALSE FALSE
[143,] FALSE FALSE FALSE
[144,] FALSE FALSE FALSE
[145,] FALSE FALSE FALSE
[146,] FALSE FALSE FALSE
[147,] FALSE FALSE FALSE
[148,] FALSE FALSE FALSE
[149,] FALSE FALSE FALSE
[150,] FALSE FALSE FALSE
 --- function from context --- 
function (object) 
{
    if (length(hard.label(object)) != nrow(member(object))) 
        return("hard.label Mismatch\n")
    if (any(member(object) < 0 || member(object) > 1)) 
        return("Constraint of membership matrix violated\n")
    rowSum.membership <- rowSums(member(object))
    rowSum.membership <- round(rowSum.membership, 3)
    if (any(rowSum.membership != 1)) {
        return("Constraint of membership matrix violated\n")
    }
    if (any(!is.numeric(member(object)))) 
        return("Not Numeric")
    if (anyNA(object)) 
        return("Missing value on membership detected\n")
}
<bytecode: 0x61118d0>
<environment: namespace:advclust>
 --- function search by 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: 2 ERRORs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-LENGTH1/advclust.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:39.25, 94.33 + 11.26