Package: MetaComp
Check: examples
New result: ERROR
  Running examples in ‘MetaComp-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: plot_edge_assignment
  > ### Title: Generates a single column ggplot for a taxonomic assignment
  > ###   table and also outputs a PDF.
  > ### Aliases: plot_edge_assignment
  > 
  > ### ** Examples
  > 
  > pa_fpath <- system.file("extdata", "HMP_even//allReads-pangia.list.txt", package="MetaComp")
  > pangia_assignment = load_edge_assignment(pa_fpath, type = "pangia")
  > 
  > plot_edge_assignment(pangia_assignment, "phylum", "Pangia", "HMP Even",
  +                                                      file.path(tempdir(), "assignment.pdf"))
  Warning in Cairo(width, height, file, "pdf", pointsize = pointsize, bg = bg,  :
    Unsupported PDF version requested, ignoring, only 1.4 or 1.5 is supported by cairographics
  
   *** caught segfault ***
  address (nil), cause 'memory not mapped'
  
  Traceback:
   1: grid.newpage()
   2: print.ggplot(p)
   3: print(p)
   4: plot_edge_assignment(pangia_assignment, "phylum", "Pangia", "HMP Even",     file.path(tempdir(), "assignment.pdf"))
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault

Package: MetaComp
Check: tests
New result: ERROR
    Running ‘testthat.R’ [2s/2s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > library(testthat)
    > library(MetaComp)
    > 
    > test_check("MetaComp")
    [1] "gottcha"
    [1] "kraken"
    
     *** caught segfault ***
    address (nil), cause 'memory not mapped'
    
    Traceback:
     1: grid.newpage()
     2: print.ggplot(p)
     3: print(p)
     4: withCallingHandlers(expr, warning = function(w) if (inherits(w,     classes)) tryInvokeRestart("muffleWarning"))
     5: suppressWarnings(print(p))
     6: plot_merged_assignment(assignment = merged_assignments_table,     taxonomy_level = "family", sorting_order = "abundance", row_limit = 60,     plot_title = "Test Plot #3", filename = file.path(tmp_folder,         "test_pdf3"))
     7: eval(code, test_env)
     8: eval(code, test_env)
     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)
    10: doTryCatch(return(expr), name, parentenv, handler)
    11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
    13: doTryCatch(return(expr), name, parentenv, handler)
    14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),     names[nh], parentenv, handlers[[nh]])
    15: tryCatchList(expr, classes, parentenv, handlers)
    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) {    })
    17: test_code(test = NULL, code = exprs, env = env, reporter = get_reporter() %||%     StopReporter$new())
    18: source_file(path, env = env(env), desc = desc, error_call = error_call)
    19: FUN(X[[i]], ...)
    20: lapply(test_paths, test_one_file, env = env, desc = desc, error_call = error_call)
    21: doTryCatch(return(expr), name, parentenv, handler)
    22: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    23: tryCatchList(expr, classes, parentenv, handlers)
    24: tryCatch(code, testthat_abort_reporter = function(cnd) {    cat(conditionMessage(cnd), "\n")    NULL})
    25: with_reporter(reporters$multi, lapply(test_paths, test_one_file,     env = env, desc = desc, error_call = error_call))
    26: test_files_serial(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,     desc = desc, load_package = load_package, error_call = error_call)
    27: 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,     load_package = load_package, parallel = parallel)
    28: test_dir("testthat", package = package, reporter = reporter,     ..., load_package = "installed")
    29: test_check("MetaComp")
    An irrecoverable exception occurred. R is aborting now ...
    Segmentation fault

Package: visStatistics
Check: examples
New result: ERROR
  Running examples in ‘visStatistics-Ex.R’ failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: visstat
  > ### Title: Wrapper for visstat_core allowing two different input styles
  > ### Aliases: visstat
  > 
  > ### ** Examples
  > 
  > ## Standardised usage (preferred):
  > visstat(mtcars$am, mtcars$mpg)
  > 
  > ## Backward-compatible usage (same result):
  > visstat(mtcars, "mpg", "am")
  > 
  > ## Wilcoxon rank sum test
  > grades_gender <- data.frame(
  +   Sex = as.factor(c(rep("Girl", 20), rep("Boy", 20))),
  +   Grade = c(
  +     19.3, 18.1, 15.2, 18.3, 7.9, 6.2, 19.4, 20.3, 9.3, 11.3,
  +     18.2, 17.5, 10.2, 20.1, 13.3, 17.2, 15.1, 16.2, 17.3, 16.5,
  +     5.1, 15.3, 17.1, 14.8, 15.4, 14.4, 7.5, 15.5, 6.0, 17.4,
  +     7.3, 14.3, 13.5, 8.0, 19.5, 13.4, 17.9, 17.7, 16.4, 15.6
  +   )
  + )
  > visstat(grades_gender$Sex, grades_gender$Grade)
  > 
  > ## Welch's one-way ANOVA
  > visstat(npk$block, npk$yield)
  > 
  > ## Kruskal-Wallis
  > visstat(iris$Species, iris$Petal.Width)
  > 
  > ## Simple linear regression
  > visstat(trees$Height, trees$Girth, conf.level = 0.99)
  > 
  > ## Chi-squared
  > HairEyeColorDataFrame <- counts_to_cases(as.data.frame(HairEyeColor))
  > visstat(HairEyeColorDataFrame$Eye, HairEyeColorDataFrame$Hair)
  > 
  > ## Fisher's test
  > HairEyeColorMaleFisher <- HairEyeColor[, , 1]
  > blackBrownHazelGreen <- HairEyeColorMaleFisher[1:2, 3:4]
  > blackBrownHazelGreen <- counts_to_cases(as.data.frame(blackBrownHazelGreen))
  > visstat(blackBrownHazelGreen$Eye, blackBrownHazelGreen$Hair)
  > 
  > ## Save PNG
  > visstat(blackBrownHazelGreen$Hair, blackBrownHazelGreen$Eye,
  +         graphicsoutput = "png", plotDirectory = tempdir())
  
   *** caught segfault ***
  address (nil), cause 'memory not mapped'
  
  Traceback:
   1: grid.newpage()
   2: strucplot(x, condvars = if (is.null(condvars)) NULL else length(condvars),     core = struc_mosaic(zero_size = zero_size, zero_split = zero_split,         zero_shade = zero_shade, zero_gp = zero_gp, panel = panel),     split_vertical = split_vertical, spacing = spacing, spacing_args = spacing_args,     gp = gp, expected = expected, shade = shade, main = main,     sub = sub, ...)
   3: mosaic.default(counts, shade = TRUE, legend = TRUE, pop = F)
   4: mosaic(counts, shade = TRUE, legend = TRUE, pop = F)
   5: vis_mosaic(samples, fact, name_of_sample = name_of_sample, name_of_factor = name_of_factor,     minperc = 0, numbers = numberflag)
   6: visstat_core(dataframe = dataframe, varsample = sample_name,     varfactor = factor_name, conf.level = conf.level, numbers = numbers,     minpercent = minpercent, graphicsoutput = graphicsoutput,     plotName = plotName, plotDirectory = plotDirectory)
   7: visstat(blackBrownHazelGreen$Hair, blackBrownHazelGreen$Eye,     graphicsoutput = "png", plotDirectory = tempdir())
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault

Package: visStatistics
Check: re-building of vignette outputs
New result: ERROR
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘visStatistics.Rmd’ using rmarkdown
  
   *** caught segfault ***
  address (nil), cause 'memory not mapped'
  
  Traceback:
   1: grid.newpage()
   2: strucplot(x, condvars = if (is.null(condvars)) NULL else length(condvars),     core = struc_mosaic(zero_size = zero_size, zero_split = zero_split,         zero_shade = zero_shade, zero_gp = zero_gp, panel = panel),     split_vertical = split_vertical, spacing = spacing, spacing_args = spacing_args,     gp = gp, expected = expected, shade = shade, main = main,     sub = sub, ...)
   3: mosaic.default(counts, shade = TRUE, legend = TRUE, pop = F)
   4: mosaic(counts, shade = TRUE, legend = TRUE, pop = F)
   5: vis_mosaic(samples, fact, name_of_sample = name_of_sample, name_of_factor = name_of_factor,     minperc = 0, numbers = numberflag)
   6: visstat_core(dataframe = dataframe, varsample = varsample, varfactor = varfactor,     conf.level = conf.level, numbers = numbers, minpercent = minpercent,     graphicsoutput = graphicsoutput, plotName = plotName, plotDirectory = plotDirectory)
   7: visstat(black_brown_hazel_green_male, "Hair", "Eye", graphicsoutput = "png",     plotDirectory = tempdir())
   8: eval(expr, envir)
   9: eval(expr, envir)
  10: withVisible(eval(expr, envir))
  11: withCallingHandlers(code, message = function (cnd) {    watcher$capture_plot_and_output()    if (on_message$capture) {        watcher$push(cnd)    }    if (on_message$silence) {        invokeRestart("muffleMessage")    }}, warning = function (cnd) {    if (getOption("warn") >= 2 || getOption("warn") < 0) {        return()    }    watcher$capture_plot_and_output()    if (on_warning$capture) {        cnd <- sanitize_call(cnd)        watcher$push(cnd)    }    if (on_warning$silence) {        invokeRestart("muffleWarning")    }}, error = function (cnd) {    watcher$capture_plot_and_output()    cnd <- sanitize_call(cnd)    watcher$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
  12: eval(call)
  13: eval(call)
  14: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
  15: doWithOneRestart(return(expr), restart)
  16: withOneRestart(expr, restarts[[1L]])
  17: withRestartList(expr, restarts[-nr])
  18: doWithOneRestart(return(expr), restart)
  19: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
  20: withRestartList(expr, restarts)
  21: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
  22: evaluate::evaluate(...)
  23: 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$render, options))
  24: in_dir(input_dir(), expr)
  25: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
  26: eng_r(options)
  27: block_exec(params)
  28: call_block(x)
  29: process_group(group)
  30: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (xfun::pkg_available("rlang", "1.0.0")) {            if (is_R_CMD_build() || is_R_CMD_check()) {                cnd = tryCatch(rlang::entrace(e), error = identity)                error <<- format(cnd)            }            else {                rlang::entrace(e)            }        }    })
  31: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (xfun::pkg_available("rlang", "1.0.0")) {            if (is_R_CMD_build() || is_R_CMD_check()) {                cnd = tryCatch(rlang::entrace(e), error = identity)                error <<- format(cnd)            }            else {                rlang::entrace(e)            }        }    }), function(loc) {    setwd(wd)    write_utf8(res, output %n% stdout())    paste0("\nQuitting from ", loc, if (!is.null(error))         paste0("\n", rule(), error, "\n", rule()))}, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
  32: process_file(text, output)
  33: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  34: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
  35: vweave_rmarkdown(...)
  36: engine$weave(file, quiet = quiet, encoding = enc)
  37: doTryCatch(return(expr), name, parentenv, handler)
  38: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  39: tryCatchList(expr, classes, parentenv, handlers)
  40: tryCatch({    engine$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)))})
  41: tools::buildVignettes(dir = "/home/hornik/tmp/CRAN_recheck/visStatistics.Rcheck/vign_test/visStatistics",     skip = TRUE, ser_elibs = "/home/hornik/tmp/scratch/RtmpyMFKta/file9fec269ade6a0.rds")
  An irrecoverable exception occurred. R is aborting now ...
  Segmentation fault