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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data infercnv
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* checking for file ‘infercnv/DESCRIPTION’ ... OK
* preparing ‘infercnv’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘inferCNV.Rmd’ using rmarkdown
Calculating gene variances
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Calculating feature variances of standardized and clipped values
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**************************************************|

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 *** caught segfault ***
address 0x19, cause 'memory not mapped'

Traceback:
 1: parallelDist(t(tumor_expr_data[, which(partition == i), drop = FALSE]),     threads = infercnv.env$GLOBAL_NUM_THREADS)
 2: hclust(parallelDist(t(tumor_expr_data[, which(partition == i),     drop = FALSE]), threads = infercnv.env$GLOBAL_NUM_THREADS),     method = hclust_method)
 3: as.phylo(hclust(parallelDist(t(tumor_expr_data[, which(partition ==     i), drop = FALSE]), threads = infercnv.env$GLOBAL_NUM_THREADS),     method = hclust_method))
 4: .single_tumor_leiden_subclustering(tumor_group = tumor_group,     tumor_group_idx = tumor_group_idx, tumor_expr_data = tumor_expr_data,     k_nn = k_nn, leiden_resolution = leiden_resolution, leiden_method = leiden_method,     leiden_function = leiden_function, hclust_method = hclust_method)
 5: define_signif_tumor_subclusters(infercnv_obj = infercnv_obj,     p_val = tumor_subcluster_pval, k_nn = k_nn, leiden_resolution = leiden_resolution,     leiden_method = leiden_method, leiden_function = leiden_function,     leiden_method_per_chr = leiden_method_per_chr, leiden_function_per_chr = leiden_function_per_chr,     leiden_resolution_per_chr = leiden_resolution_per_chr, hclust_method = hclust_method,     cluster_by_groups = cluster_by_groups, partition_method = tumor_subcluster_partition_method,     per_chr_hmm_subclusters = per_chr_hmm_subclusters, z_score_filter = z_score_filter)
 6: infercnv::run(infercnv_obj, cutoff = 1, out_dir = out_dir, cluster_by_groups = TRUE,     plot_steps = FALSE, denoise = TRUE, HMM = FALSE, no_prelim_plot = TRUE,     png_res = 60)
 7: eval(expr, envir)
 8: eval(expr, envir)
 9: withVisible(eval(expr, envir))
10: withCallingHandlers(code, message = function (cnd) {    watcher$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$push(cnd)    switch(on_error, continue = invokeRestart("eval_continue"),         stop = invokeRestart("eval_stop"), error = NULL)})
11: eval(call)
12: eval(call)
13: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
14: doWithOneRestart(return(expr), restart)
15: withOneRestart(expr, restarts[[1L]])
16: withRestartList(expr, restarts[-nr])
17: doWithOneRestart(return(expr), restart)
18: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
19: withRestartList(expr, restarts)
20: withRestarts(with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers), eval_continue = function() TRUE, eval_stop = function() FALSE)
21: evaluate::evaluate(...)
22: evaluate(code, envir = env, new_device = FALSE, keep_warning = if (is.numeric(options$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))
23: in_dir(input_dir(), expr)
24: 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$render, options)))
25: eng_r(options)
26: block_exec(params)
27: call_block(x)
28: process_group(group)
29: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
30: xfun:::handle_error(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e)),     function(loc) {        setwd(wd)        write_utf8(res, output %n% stdout())        paste0("\nQuitting from lines ", loc)    }, if (labels[i] != "") sprintf(" [%s]", labels[i]), get_loc)
31: process_file(text, output)
32: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
33: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
34: vweave_rmarkdown(...)
35: engine$weave(file, quiet = quiet, encoding = enc)
36: doTryCatch(return(expr), name, parentenv, handler)
37: tryCatchOne(expr, names, parentenv, handlers[[1L]])
38: tryCatchList(expr, classes, parentenv, handlers)
39: 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)))})
40: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...