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###
### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data HiCool
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* checking for file ‘HiCool/DESCRIPTION’ ... OK
* preparing ‘HiCool’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ...sh: line 1: 91486 Segmentation fault: 11  '/Library/Frameworks/R.framework/Resources/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.', tangle = TRUE)" > '/tmp/Rtmp6yYj8t/xshell15d3c3a43b3c' 2>&1
 ERROR
--- re-building ‘HiCool.Rmd’ using rmarkdown

 *** caught segfault ***
address 0x540, cause 'memory not mapped'

Traceback:
 1: py_initialize(config$python, config$libpython, config$pythonhome,     config$virtualenv_activate, config$version$major, config$version$minor,     interactive(), numpy_load_error)
 2: (function() {    Sys.setenv(PYTHONPATH = newpythonpath)    on.exit(Sys.setenv(PYTHONPATH = oldpythonpath), add = TRUE)    py_initialize(config$python, config$libpython, config$pythonhome,         config$virtualenv_activate, config$version$major, config$version$minor,         interactive(), numpy_load_error)})()
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch({    oldpythonpath <- Sys.getenv("PYTHONPATH")    newpythonpath <- Sys.getenv("RETICULATE_PYTHONPATH", unset = paste(config$pythonpath,         system.file("python", package = "reticulate"), sep = .Platform$path.sep))    local({        Sys.setenv(PYTHONPATH = newpythonpath)        on.exit(Sys.setenv(PYTHONPATH = oldpythonpath), add = TRUE)        py_initialize(config$python, config$libpython, config$pythonhome,             config$virtualenv_activate, config$version$major,             config$version$minor, interactive(), numpy_load_error)    })}, error = function(e) {    Sys.setenv(PATH = oldpath)    if (is.na(curr_session_env)) {        Sys.unsetenv("R_SESSION_INITIALIZED")    }    else {        Sys.setenv(R_SESSION_INITIALIZED = curr_session_env)    }    stop(e)})
 7: initialize_python()
 8: ensure_python_initialized()
 9: reticulate::py_config()
10: useBasiliskEnv(envpath, full.activation)
11: basilisk::basiliskStart(env_HiCool)
12: HiCool(r1 = HiContactsData::HiContactsData(sample = "yeast_wt",     format = "fastq_R1"), r2 = HiContactsData::HiContactsData(sample = "yeast_wt",     format = "fastq_R2"), restriction = "DpnII,HinfI", resolutions = c(4000,     8000, 16000), genome = "R64-1-1", output = "./HiCool/")
13: eval(expr, envir)
14: eval(expr, envir)
15: withVisible(eval(expr, envir))
16: 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)})
17: eval(call)
18: eval(call)
19: with_handlers({    for (expr in tle$exprs) {        ev <- withVisible(eval(expr, envir))        watcher$capture_plot_and_output()        watcher$print_value(ev$value, ev$visible, envir)    }    TRUE}, handlers)
20: doWithOneRestart(return(expr), restart)
21: withOneRestart(expr, restarts[[1L]])
22: withRestartList(expr, restarts[-nr])
23: doWithOneRestart(return(expr), restart)
24: withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
25: withRestartList(expr, restarts)
26: withRestarts(with_handlers({    for (expr in tle$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)
27: evaluate::evaluate(...)
28: 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$render, options))
29: in_dir(input_dir(), expr)
30: in_input_dir(evaluate(code, envir = env, new_device = FALSE,     keep_warning = if (is.numeric(options$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)))
31: eng_r(options)
32: block_exec(params)
33: call_block(x)
34: process_group(group)
35: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),     error = function(e) if (xfun::pkg_available("rlang", "1.0.0")) rlang::entrace(e))
36: 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)
37: process_file(text, output)
38: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
39: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),     output_dir = getwd(), ...)
40: vweave_rmarkdown(...)
41: engine$weave(file, quiet = quiet, encoding = enc)
42: doTryCatch(return(expr), name, parentenv, handler)
43: tryCatchOne(expr, names, parentenv, handlers[[1L]])
44: tryCatchList(expr, classes, parentenv, handlers)
45: tryCatch({    engine$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)))})
46: tools::buildVignettes(dir = ".", tangle = TRUE)
An irrecoverable exception occurred. R is aborting now ...