* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck’
* using R Under development (unstable) (2024-04-24 r86484)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
    GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘baRulho/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘baRulho’ version ‘2.1.0’
* 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 ‘baRulho’ can be installed ... [14s/14s] 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 ... 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 whether startup messages can be suppressed ... 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 ... [29s/29s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [48s/40s] ERROR
Running examples in ‘baRulho-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_blur_ratio
> ### Title: Plot blur ratio
> ### Aliases: plot_blur_ratio
> 
> ### ** Examples
> 
> {
+   # load example data
+   data("test_sounds_est")
+ 
+   # add reference to X
+   X <- set_reference_sounds(X = test_sounds_est)
+ 
+   # create plots
+   plot_blur_ratio(X = X, dest.path = tempdir())
+ }
Error in plot_blur_ratio(X = X, dest.path = tempdir()) : 
 1 argument check(s) failed:
 * Argument 'dest.path': Directory
 * '/tmp/RtmpxA21IX/working_dir/RtmpS0qFO9' does not exist.
Calls: plot_blur_ratio -> .report_assertions
Execution halted
* checking examples with --run-donttest ... [46s/40s] ERROR
Running examples in ‘baRulho-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_blur_ratio
> ### Title: Plot blur ratio
> ### Aliases: plot_blur_ratio
> 
> ### ** Examples
> 
> {
+   # load example data
+   data("test_sounds_est")
+ 
+   # add reference to X
+   X <- set_reference_sounds(X = test_sounds_est)
+ 
+   # create plots
+   plot_blur_ratio(X = X, dest.path = tempdir())
+ }
Error in plot_blur_ratio(X = X, dest.path = tempdir()) : 
 1 argument check(s) failed:
 * Argument 'dest.path': Directory
 * '/tmp/RtmpxA21IX/working_dir/RtmpsL9aHM' does not exist.
Calls: plot_blur_ratio -> .report_assertions
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ...Warning: elapsed-time limit of 45 minutes reached for sub-process
 [0m/45m] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘align_test_sounds.Rmd’ using rmarkdown
** Processing: /data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho/vignettes/align_test_sounds_files/figure-html/unnamed-chunk-1-1.png
560x280 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 11609 bytes
Input file size = 11699 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8836
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 8836

Output IDAT size = 8836 bytes (2773 bytes decrease)
Output file size = 8914 bytes (2785 bytes = 23.81% decrease)

** Processing: /data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho/vignettes/align_test_sounds_files/figure-html/unnamed-chunk-2-1.png
560x280 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 21248 bytes
Input file size = 21350 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14684
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 14684

Output IDAT size = 14684 bytes (6564 bytes decrease)
Output file size = 14762 bytes (6588 bytes = 30.86% decrease)

** Processing: /data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho/vignettes/align_test_sounds_files/figure-html/master sound file-1.png
560x280 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4874 bytes
Input file size = 5726 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4060
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4060

Output IDAT size = 4060 bytes (814 bytes decrease)
Output file size = 4138 bytes (1588 bytes = 27.73% decrease)

** Processing: /data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho/vignettes/align_test_sounds_files/figure-html/spectro master 1-1.png
560x280 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 17177 bytes
Input file size = 17279 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11340
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 11340

Output IDAT size = 11340 bytes (5837 bytes decrease)
Output file size = 11418 bytes (5861 bytes = 33.92% decrease)

** Processing: /data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho/vignettes/align_test_sounds_files/figure-html/unnamed-chunk-5-1.png
560x280 pixels, 8 bits/pixel, 254 colors in palette
Reducing image to 8 bits/pixel, grayscale
Input IDAT size = 4874 bytes
Input file size = 5726 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4060
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 4060

Output IDAT size = 4060 bytes (814 bytes decrease)
Output file size = 4138 bytes (1588 bytes = 27.73% decrease)

** Processing: /data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho/vignettes/align_test_sounds_files/figure-html/spectro master 2-1.png
560x280 pixels, 3x8 bits/pixel, RGB
Input IDAT size = 45124 bytes
Input file size = 45262 bytes

Trying:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26269
  zc = 9  zm = 8  zs = 1  f = 0
  zc = 1  zm = 8  zs = 2  f = 0
  zc = 9  zm = 8  zs = 3  f = 0
  zc = 9  zm = 8  zs = 0  f = 5
  zc = 9  zm = 8  zs = 1  f = 5
  zc = 1  zm = 8  zs = 2  f = 5
  zc = 9  zm = 8  zs = 3  f = 5
                               
Selecting parameters:
  zc = 9  zm = 8  zs = 0  f = 0		IDAT size = 26269

Output IDAT size = 26269 bytes (18855 bytes decrease)
Output file size = 26347 bytes (18915 bytes = 41.79% decrease)


Execution halted
--- re-building ‘quantify_degradation.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x7ff8ba400640, cause 'memory not mapped'

Traceback:
 1: solve.default(M)
 2: solve(M)
 3: which(test)
 4: .ifelse(x <= 0.0031308, 12.92 * x, 1.055 * x %^% (1/2.4) - 0.055)
 5: ungamma(xyz %*% solve(M))
 6: to$fromXYZ(xyz, to.ref.white)
 7: convertColor(cbind(palette[[1L]](x), palette[[2L]](x), palette[[3L]](x),     if (alpha) palette[[4L]](x)), from = "Lab", to = "sRGB")
 8: pmin(rgb, 1)
 9: pmax(pmin(rgb, 1), 0)
10: roundcolor(convertColor(cbind(palette[[1L]](x), palette[[2L]](x),     palette[[3L]](x), if (alpha) palette[[4L]](x)), from = "Lab",     to = "sRGB"))
11: fn_cols(seq(begin, end, length.out = n))
12: color.palette(length(levels) - 1)
13: .filled.contour(as.double(x), as.double(y), z, as.double(levels),     col = col)
14: filled_contour_wrblr_int(x = X, y = Y, z = Z, bg.col = colbg,     levels = collevels, nlevels = 20, plot.title = title(main = main,         xlab = tlab, ylab = flab), color.palette = palette, axisX = FALSE,     axisY = axisY, col.lab = collab, colaxis = colaxis, add = add)
15: warbleR:::spectro_wrblr_int2(wave = wave, palette = palette,     axisX = FALSE, axisY = FALSE, grid = FALSE, collevels = collevels,     flim = fl, wl = wl, ovlp = ovlp, ...)
16: FUN(X[[i]], ...)
17: lapply(X = S, FUN = FUN, ...)
18: doTryCatch(return(expr), name, parentenv, handler)
19: tryCatchOne(expr, names, parentenv, handlers[[1L]])
20: tryCatchList(expr, classes, parentenv, handlers)
21: 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, nlines = 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))})
22: try(lapply(X = S, FUN = FUN, ...), silent = TRUE)
23: sendMaster(try(lapply(X = S, FUN = FUN, ...), silent = TRUE))
24: FUN(X[[i]], ...)
25: lapply(seq_len(cores), inner.do)
26: parallel::mclapply(X[Split[[i]]], FUN, ..., mc.cores = as.integer(cl))
27: warbleR:::pblapply_wrblr_int(X = sort(unique(soundid_X$page)),     pbar = pb, cl = cl, FUN = .plot_degrad, X, soundid_X, flim,     path, dest.path, img_width, img_heigth, res, page_layout,     nrow, ncol, envelope, spectrum, distances, wl, spc_fill,     bg_sp_env, bg_titles, ovlp, collevels, env.smooth, palette,     ...)
28: plot_degradation(test_sounds_est, dest.path = tempdir())
29: eval(expr, envir, enclos)
30: eval(expr, envir, enclos)
31: eval_with_user_handlers(expr, envir, enclos, user_handlers)
32: withVisible(eval_with_user_handlers(expr, envir, enclos, user_handlers))
33: withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)
34: handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler))
35: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval_with_user_handlers(expr,     envir, enclos, user_handlers)), warning = wHandler, error = eHandler,     message = mHandler)))
36: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,     debug = debug, last = i == length(out), use_try = stop_on_error !=         2L, keep_warning = keep_warning, keep_message = keep_message,     log_echo = log_echo, log_warning = log_warning, output_handler = output_handler,     include_timing = include_timing)
37: evaluate::evaluate(...)
38: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
39: in_dir(input_dir(), expr)
40: 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$render, options)))
41: eng_r(options)
42: block_exec(params)
43: call_block(x)
44: process_group(group)
45: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
46: withCallingHandlers(expr, error = function(e) {    loc = if (is.function(fun))         trimws(fun(label))    else ""    if (loc != "")         loc = sprintf(" at lines %s", loc)    message(one_string(handler(e, loc)))})
47: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(e, loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
48: process_file(text, output)
49: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
50: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
51: vweave_rmarkdown(...)
52: engine$weave(file, quiet = quiet, encoding = enc)
53: doTryCatch(return(expr), name, parentenv, handler)
54: tryCatchOne(expr, names, parentenv, handlers[[1L]])
55: tryCatchList(expr, classes, parentenv, handlers)
56: 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)))})
57: tools:::.buildOneVignette("quantify_degradation.Rmd", "/data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/vign_test/baRulho",     TRUE, FALSE, "quantify_degradation", "UTF-8", "/tmp/RtmpxA21IX/working_dir/RtmpOrv1Wh/file1f3c1f799cd36d.rds")
An irrecoverable exception occurred. R is aborting now ...

* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 3 ERRORs
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/baRulho.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 48:37.52, 132.77 + 78.57