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### Running command:
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###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data FRASER
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* checking for file ‘FRASER/DESCRIPTION’ ... OK
* preparing ‘FRASER’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘FRASER.Rnw’ using knitr

 *** caught segfault ***
address 0xfffffffffffe2770, cause 'memory not mapped'

Traceback:
 1: .Call2("C_h5mread", filepath, name, starts, counts, noreduce,     as.vector, as.integer, as.sparse, method, use.H5Dread_chunk,     PACKAGE = "h5mread")
 2: h5mread(filepath, name, starts = index, as.vector = FALSE, as.integer = as.integer,     as.sparse = as.sparse)
 3: .h5mread2(x@filepath, x@name, index, as.integer = as_int)
 4: FUN(X[[i]], ...)
 5: FUN(X[[i]], ...)
 6: lapply(x@seeds, extract_array, index)
 7: lapply(x@seeds, extract_array, index)
 8: extract_array(x@seed, index)
 9: extract_array(x@seed, index)
10: extract_array(x@seed, index)
11: extract_array(x@seed, index)
12: .nextMethod(x = x, index = index)
13: callNextMethod()
14: extract_array(x, index)
15: extract_array(x, index)
16: .from_Array_to_array(x, ...)
17: as.array.Array(x)
18: as.array(x)
19: drop(as.array(x))
20: .from_Array_to_matrix(x, ...)
21: as.matrix.Array(counts[, samples(fds)])
22: as.matrix(counts[, samples(fds)])
23: saveAsHDF5(fds, aName, as.matrix(counts[, samples(fds)]))
24: mergeCounts(countList, fds = fds, assumeEqual = TRUE, spliceSiteCoords = spliceSiteCoords)
25: getNonSplitReadCountsForAllSamples(fds = fds, splitCountRanges = splitCountRanges,     NcpuPerSample = NcpuPerSample, minAnchor = minAnchor, recount = recount,     BPPARAM = BPPARAM, outDir = file.path(countDir, "nonSplitCounts"),     ...)
26: countRNAData(fds)
27: eval(expr, envir)
28: eval(expr, envir)
29: withVisible(eval(expr, envir))
30: withCallingHandlers(code, error = function (e) rlang::entrace(e), 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)})
31: eval(call)
32: eval(call)
33: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
34: doWithOneRestart(return(expr), restart)
35: withOneRestart(expr, restarts[[1L]])
36: withRestartList(expr, restarts[-nr])
37: doWithOneRestart(return(expr), restart)
38: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
39: withRestartList(expr, restarts)
40: withRestarts(with_handlers({    for (expr in tle$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)
41: evaluate::evaluate(...)
42: 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$render, options))
43: in_dir(input_dir(), expr)
44: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
45: eng_r(options)
46: block_exec(params)
47: call_block(x)
48: process_group(group)
49: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    })
50: with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global()))
51: xfun:::handle_error(with_options(withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) {        if (progress && is.function(pb$interrupt))             pb$interrupt()        if (is_R_CMD_build() || is_R_CMD_check())             error <<- format(e)    }), list(rlang_trace_top_env = knit_global())), 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)
52: process_file(text, output)
53: (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",     file)) knit2pandoc else knit)(file, encoding = encoding,     quiet = quiet, envir = globalenv(), ...)
54: engine$weave(file, quiet = quiet, encoding = enc)
55: doTryCatch(return(expr), name, parentenv, handler)
56: tryCatchOne(expr, names, parentenv, handlers[[1L]])
57: tryCatchList(expr, classes, parentenv, handlers)
58: tryCatch({    engine$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)))})
59: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault (core dumped)