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###
### Running command:
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###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data GBScleanR
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* checking for file ‘GBScleanR/DESCRIPTION’ ... OK
* preparing ‘GBScleanR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘BasicUsageOfGBScleanR.rmd’ using rmarkdown

 *** caught bus error ***
address 0x11, cause 'invalid alignment'

Traceback:
 1: run_viterbi(p_ref = param_list$reads$p_ref, p_alt = param_list$reads$p_alt,     ref = param_list$reads$ref, alt = param_list$reads$alt, eseq_in = param_list$error_rate,     bias = param_list$bias, mismap = param_list$mismap, trans_prob = trans_prob,     init_prob = init_prob, nonzero_prob = nonzero_prob, n_pgeno = param_list$pat$n_p_pat,     n_hap = param_list$pat$n_hap_pat, n_offspring = param_list$n_samples,     n_founder = param_list$n_parents, n_marker = param_list$n_mar,     n_nonzero_prob = n_nonzero_prob, het = param_list$het_parent,     pedigree = pedigree - 1, possiblehap = possiblehap - 1, possiblegeno = param_list$pat$possiblegeno -         1, p_geno_fix = param_list$p_geno_fix - 1, ploidy = param_list$n_ploidy)
 2: .getBestSeq(param_list = param_list, outprob = outprob)
 3: .runCycle(param_list = param_list, outprob = FALSE, outgeno = FALSE)
 4: .cleanEachChr(object = object, chr_i = chr_i, node = node, error_rate = error_rate,     recomb_rate = recomb_rate, call_threshold = call_threshold,     het_parent = het_parent, optim = optim, iter = iter, parentless = parentless,     dummy_reads = dummy_reads, pat = pat)
 5: .local(object, node, recomb_rate, error_rate, call_threshold,     het_parent, optim, iter, n_threads, dummy_reads, ...)
 6: estGeno(gds, node = "filt", iter = 4)
 7: estGeno(gds, node = "filt", iter = 4)
 8: eval(expr, envir)
 9: eval(expr, envir)
10: withVisible(eval(expr, envir))
11: withCallingHandlers(code, message = function (cnd) {    watcher$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 = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...